Contacts of the helix formed by residues 371 - 398 (chain C) in PDB entry 6VVT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 371 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL* 4.7 10.1 - - + +
51C SER* 2.5 31.1 + - - -
54C TRP* 5.2 0.2 - - - -
168C SER* 4.4 6.1 - - - -
369C LEU* 3.5 6.0 + - + +
370C ARG* 1.3 74.8 - - - +
372C VAL* 1.3 65.8 + - - +
374C GLU* 2.6 44.7 + - - +
375C LEU* 2.9 16.8 + - - +
497C VAL* 3.9 32.1 - - + -
498C ASN 5.7 0.2 - - - +
501C GLY* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 372 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL 4.1 1.7 + - - +
48C GLN* 3.1 55.4 - - - +
51C SER* 2.9 9.8 + - - -
52C PHE* 3.8 4.5 - - + +
151C MET* 3.9 10.5 - - + -
157C PHE* 4.2 7.2 - - + -
166C VAL* 3.4 35.9 - - + +
168C SER* 4.8 6.1 - - - +
371C THR* 1.3 70.5 - - - +
373C GLY* 1.3 69.6 + - - +
375C LEU* 2.9 24.7 - - - +
376C ILE* 3.1 20.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 373 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C SER* 2.2 42.2 + - - -
52C PHE* 3.9 3.8 - - - -
54C TRP* 3.6 6.3 - - - -
55C LEU* 3.0 37.5 - - - +
372C VAL* 1.3 73.7 - - - +
374C GLU* 1.3 55.1 + - - -
376C ILE* 3.4 1.0 + - - +
377C GLN 3.0 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 374 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C SER* 3.3 0.2 + - - -
54C TRP* 3.2 35.0 - - + -
370C ARG* 4.7 9.3 - - + +
371C THR* 2.6 41.9 + - - +
373C GLY* 1.3 76.2 - - - +
375C LEU* 1.3 59.2 + - - +
377C GLN* 3.0 18.2 + - - +
378C ASN* 3.1 22.2 + - - +
498C ASN 5.2 0.2 - - - +
499C PRO 3.7 11.1 - - - +
500C PHE* 2.6 35.3 - - - +
501C GLY* 4.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 375 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C VAL* 3.9 16.4 - - + -
167C VAL 4.2 2.7 - - - +
169C GLN* 3.7 14.8 - - + +
370C ARG* 3.3 46.4 - - + +
371C THR 2.9 12.7 + - - +
372C VAL* 2.9 38.8 - - - +
374C GLU* 1.3 74.3 - - - +
376C ILE* 1.3 61.7 + - + +
378C ASN* 3.9 13.0 + - - +
379C GLN* 3.6 16.6 + - - +
421C PHE* 4.2 15.4 - - + -
427C LEU* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 376 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C PHE* 5.6 2.2 - - + -
55C LEU* 3.3 28.3 - - + -
148C PHE* 4.8 11.2 - - + -
157C PHE* 5.6 2.0 - - + -
166C VAL* 5.1 0.2 - - + -
372C VAL* 3.1 32.1 + - + +
373C GLY 3.5 4.3 - - - +
374C GLU 3.1 0.6 - - - -
375C LEU* 1.3 76.6 - - + +
377C GLN* 1.3 65.0 + - - +
379C GLN* 3.1 16.2 + - + +
380C ILE* 3.2 15.0 + - + +
418C ILE* 5.7 6.0 - - + +
421C PHE* 3.1 42.0 - - + -
422C PHE* 3.6 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C TRP* 3.0 32.2 - - - -
55C LEU* 3.5 18.2 - - + -
76C GLY* 3.0 25.5 + - - -
79C GLU* 5.1 4.8 - - - +
80C VAL* 3.6 15.7 - - + +
373C GLY 3.0 5.8 + - - +
374C GLU* 3.0 8.3 + - - +
376C ILE* 1.3 77.4 - - - +
378C ASN* 1.3 61.3 + - - +
380C ILE* 2.8 27.6 + - - +
381C ARG* 2.3 48.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 378 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C ARG* 3.6 36.8 - - - +
374C GLU* 3.1 17.7 + - - +
375C LEU* 4.1 8.5 - - - +
376C ILE 3.3 0.2 - - - -
377C GLN* 1.3 78.1 - - - +
379C GLN* 1.3 60.9 + - - +
381C ARG* 3.2 42.3 + - - +
382C VAL* 3.4 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 379 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C LEU 3.6 9.5 + - - +
376C ILE* 3.1 12.8 + - + +
378C ASN* 1.3 79.1 - - - +
380C ILE* 1.3 60.1 + - + +
382C VAL* 3.5 17.7 + - - +
383C GLY 3.4 14.0 + - - -
417C ALA* 3.1 43.7 + - - +
418C ILE* 4.8 5.2 - - + +
420C GLU* 4.9 6.7 + - - +
421C PHE* 3.8 33.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 380 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LEU* 5.4 0.9 - - + -
77C LEU* 5.3 14.8 - - + -
80C VAL* 4.3 12.1 - - + -
124C LEU* 6.3 1.3 - - + -
148C PHE* 3.6 34.8 - - + -
376C ILE* 3.2 14.8 + - + +
377C GLN* 2.8 23.4 + - - +
379C GLN* 1.3 70.1 - - - +
381C ARG* 1.3 54.3 + - - +
383C GLY* 2.8 4.6 + - - +
384C LEU* 2.7 57.1 + - + +
414C VAL* 5.7 6.9 - - + +
417C ALA* 5.7 0.9 - - - -
418C ILE* 4.2 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 381 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C GLU* 5.0 6.9 + - - +
80C VAL* 4.4 18.3 - - + +
83C GLU* 2.3 39.0 + - - +
377C GLN* 2.3 51.8 + - - +
378C ASN* 3.2 26.6 + - - +
380C ILE* 1.3 76.7 - - - +
382C VAL* 1.3 58.7 + - + +
384C LEU* 3.3 5.2 + - - +
385C SER* 2.8 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 382 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C ASN 3.4 12.4 + - - +
379C GLN* 3.7 20.0 - - - +
380C ILE 3.2 0.6 - - - -
381C ARG* 1.3 77.5 - - + +
383C GLY* 1.3 62.6 + - - +
385C SER* 4.3 3.5 - - - -
386C ARG* 3.2 42.2 + - + +
417C ALA* 5.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 383 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C GLN 3.4 5.3 + - - -
380C ILE* 2.8 9.2 + - - -
382C VAL* 1.3 80.0 - - - +
384C LEU* 1.3 59.9 + - - -
386C ARG* 4.0 1.7 - - - +
387C MET* 3.0 23.4 + - - +
413C PRO* 3.9 20.9 - - - +
414C VAL* 3.3 19.1 + - - +
417C ALA* 4.2 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 384 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C VAL* 3.2 34.5 - - + +
81C LEU* 3.5 23.8 - - + -
84C LEU* 4.9 18.3 - - + +
98C PHE* 6.2 7.0 - - + -
145C MET* 4.6 10.8 - - + -
380C ILE* 2.7 31.4 + - + +
381C ARG* 3.9 3.1 - - - +
383C GLY* 1.3 70.7 - - - +
385C SER* 1.3 66.2 + - - +
387C MET* 2.9 16.2 + - + +
388C GLU* 2.9 14.4 + - - +
414C VAL* 4.2 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 385 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C GLU* 5.8 0.2 + - - -
84C LEU* 4.7 14.4 - - - +
381C ARG* 2.8 27.4 + - - +
382C VAL* 4.3 3.8 - - - -
384C LEU* 1.3 72.7 - - - +
386C ARG* 1.3 59.2 + - - +
388C GLU* 3.0 23.1 + - - +
389C ARG* 3.0 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C VAL* 3.2 33.0 + - + +
383C GLY 4.4 1.3 - - - +
385C SER* 1.3 79.4 - - - +
387C MET* 1.3 61.2 + - - +
388C GLU 3.3 0.2 - - - -
389C ARG* 3.4 13.1 + - + +
390C VAL* 3.3 25.8 + - - +
413C PRO* 4.7 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PHE* 6.5 1.1 - - + -
145C MET* 6.0 1.3 - - + -
383C GLY 3.0 15.9 + - - +
384C LEU* 2.9 15.5 + - + +
386C ARG* 1.3 77.7 - - - +
388C GLU* 1.3 60.9 + - - +
390C VAL* 3.2 7.3 + - - +
391C VAL* 3.1 28.2 + - + +
409C ILE* 6.0 4.7 - - + -
410C ASN 5.1 7.0 + - - +
411C ILE* 5.6 1.1 - - - -
413C PRO* 4.5 10.7 - - + +
414C VAL* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU* 4.9 19.5 - - + -
87C ILE* 6.3 3.4 - - + -
98C PHE* 6.4 1.8 - - + -
384C LEU 2.9 10.5 + - - +
385C SER* 3.0 10.7 + - - +
387C MET* 1.3 74.8 - - - +
389C ARG* 1.3 63.6 + - - +
391C VAL* 2.8 30.4 - - + +
392C ARG* 3.0 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C SER 3.0 12.7 + - - +
386C ARG* 3.6 17.9 - - + +
387C MET 3.2 0.4 - - - -
388C GLU* 1.3 77.1 - - - +
390C VAL* 1.3 61.2 + - + +
392C ARG* 3.8 5.9 + - - +
393C GLU* 3.7 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C ARG 3.3 13.9 + - - +
387C MET* 3.2 10.9 + - - +
388C GLU 3.2 0.4 - - - -
389C ARG* 1.3 78.3 - - + +
391C VAL* 1.3 61.0 + - + +
393C GLU* 3.3 7.0 + - - +
394C ARG* 3.0 27.8 + - + +
408C LEU 4.7 6.7 - - - +
410C ASN* 4.4 24.5 - - + +
413C PRO* 5.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ILE* 6.2 4.0 - - + -
98C PHE* 6.0 3.4 - - + -
387C MET* 3.3 13.7 - - + +
388C GLU* 2.8 37.0 - - + +
390C VAL* 1.3 73.4 - - + +
392C ARG* 1.3 66.7 + - + +
394C ARG* 3.8 2.8 - - - +
395C MET* 3.0 36.5 + - - +
408C LEU* 3.2 38.8 - - + +
409C ILE* 4.3 16.2 - - + -
410C ASN 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C GLU 3.0 15.9 + - - +
389C ARG* 4.0 7.9 - - - +
390C VAL 3.3 0.2 - - - -
391C VAL* 1.3 78.0 - - + +
393C GLU* 1.3 61.5 + - - +
395C MET* 3.2 18.3 - - - +
396C THR* 3.1 24.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C ARG 3.7 10.1 + - - +
390C VAL* 3.3 9.0 + - - +
391C VAL 3.3 0.2 - - - -
392C ARG* 1.3 79.5 - - - +
394C ARG* 1.3 65.6 + - - +
396C THR* 3.0 23.5 + - - +
397C THR* 3.3 25.6 + - - +
247F ARG* 4.5 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C VAL* 3.0 20.7 + - + +
391C VAL* 3.3 5.1 + - - +
393C GLU* 1.3 83.1 + - - +
395C MET* 1.3 57.9 + - - +
397C THR* 3.2 5.7 + - - -
398C GLN* 2.9 32.9 + - + +
407C THR 5.3 2.2 - - - +
408C LEU* 3.8 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C VAL* 3.0 27.0 + - - +
392C ARG* 3.2 20.6 - - - +
394C ARG* 1.3 77.4 - - - +
396C THR* 1.3 65.6 + - + +
398C GLN* 3.0 18.1 - - - +
400C VAL* 5.3 5.7 - - - +
408C LEU* 3.7 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C ARG 3.1 18.8 - - - +
393C GLU* 3.0 15.0 + - - -
395C MET* 1.3 82.9 - - + +
397C THR* 1.3 77.8 + - - +
398C GLN 3.6 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 397 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C GLU* 3.3 31.3 + - - +
394C ARG* 3.2 13.3 + - - -
396C THR* 1.3 86.3 + - - +
398C GLN* 1.3 60.0 + - - +
399C ASP 3.8 0.5 + - - -
247F ARG* 5.1 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 398 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ARG* 2.9 21.1 + - + +
395C MET* 3.0 18.6 - - - +
396C THR 3.6 3.8 - - - +
397C THR* 1.3 80.3 + - - +
399C ASP* 1.3 69.3 + - - +
400C VAL* 3.6 4.3 + - - +
403C ILE* 4.4 17.0 - - + -
408C LEU* 4.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il