Contacts of the helix formed by residues 361 - 375 (chain B) in PDB entry 3FVS
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 PRO 361 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ASP* 3.3 8.9 - - - +
360B GLU* 1.4 90.5 - - + +
362B TYR* 1.3 65.2 + - - +
363B ASP* 3.4 17.9 - - - +
364B ARG* 3.2 24.7 + - - +
365B ARG* 3.4 8.5 + - - +
382B SER* 3.7 13.9 - - - +
390B GLN* 4.3 29.4 - - + +
391B LYS* 5.2 3.4 - - - +
394B ASP* 4.1 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ILE* 3.7 26.9 - - + -
347B PHE 3.2 11.4 + - - -
348B LYS* 3.5 45.5 - - + -
351B MET* 2.8 45.6 + - - +
352B PRO 3.8 11.4 - - - -
354B LEU* 3.7 18.6 - - + +
360B GLU 3.4 2.0 + - - -
361B PRO* 1.3 71.1 - - - +
363B ASP* 1.3 58.4 + - - +
365B ARG* 3.0 35.5 + - - +
366B PHE* 2.7 37.1 + + + -
394B ASP* 3.8 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ILE* 4.0 11.7 - - + -
361B PRO* 3.4 9.4 - - - +
362B TYR* 1.3 74.6 - - - +
364B ARG* 1.3 71.2 + - - +
366B PHE* 3.6 0.9 - - - +
367B VAL* 2.9 34.0 + - - +
380B PRO* 3.5 8.9 - - + +
381B VAL* 3.0 7.8 + - - +
382B SER* 2.8 49.3 + - - -
393B PHE 4.2 0.5 - - - +
394B ASP 2.9 25.8 + - - +
396B TYR 3.2 18.2 - - - +
397B ILE* 4.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TYR* 2.9 41.0 + - - -
17B PRO* 4.0 3.4 - - - +
20B GLU* 4.0 18.6 + - - -
21B PHE* 4.3 7.1 - - + -
360B GLU* 3.5 22.3 + - - +
361B PRO* 3.2 30.1 + - - +
363B ASP* 1.3 88.0 + - - +
365B ARG* 1.3 62.7 + - - +
367B VAL* 3.5 2.6 + - - +
368B LYS* 3.3 29.6 + - - +
380B PRO* 3.8 24.2 - - + -
382B SER* 4.0 5.2 + - - +
383B ILE* 3.7 26.9 - - - +
390B GLN* 5.3 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LYS* 5.8 1.8 - - - +
352B PRO 3.3 22.2 + - - -
353B ASP* 4.3 1.0 - - - +
354B LEU* 3.0 43.4 + - + +
355B PRO 3.4 19.0 - - - +
356B GLY* 3.7 10.3 - - - -
357B ALA 5.0 1.3 + - - -
360B GLU* 3.1 39.9 + - - +
361B PRO 3.4 5.1 + - - +
362B TYR* 3.0 41.3 + - - +
364B ARG* 1.3 73.4 - - - +
366B PHE* 1.3 65.2 + - - +
368B LYS* 3.3 12.0 + - - +
369B TRP* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B LEU* 4.3 3.6 - - + -
344B ILE* 3.7 24.7 - - + -
347B PHE* 3.6 36.8 - + + -
351B MET* 3.9 7.6 - - + -
354B LEU* 3.5 6.9 - - - +
362B TYR* 2.7 43.5 + + + +
363B ASP 3.6 4.3 - - - +
365B ARG* 1.3 71.6 - - - +
367B VAL* 1.3 63.7 + - - +
369B TRP* 3.3 28.5 + + - +
370B MET* 2.8 39.4 + - + +
397B ILE* 3.8 28.5 - - + -
418B TRP* 4.1 11.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PHE* 6.0 4.0 - - + -
363B ASP 2.9 21.1 + - - +
364B ARG 4.0 3.8 - - - +
366B PHE* 1.3 76.7 - - - +
368B LYS* 1.3 57.8 + - + +
370B MET* 3.2 7.7 + - + +
371B ILE* 2.9 47.3 + - + +
378B ALA* 3.1 36.3 - - + +
380B PRO* 3.9 20.9 - - + -
397B ILE* 3.6 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLU* 5.0 18.6 + - - +
24B LEU* 3.9 26.2 - - + -
355B PRO 4.8 4.5 + - - -
356B GLY* 4.6 5.7 - - - -
360B GLU* 2.8 40.3 + - - -
364B ARG* 3.3 16.4 + - - +
365B ARG* 3.6 11.4 - - - +
366B PHE 3.3 0.2 - - - -
367B VAL* 1.3 78.1 - - + +
369B TRP* 1.3 62.5 + - - +
371B ILE* 3.4 1.0 + - - +
372B LYS* 3.1 47.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B PHE* 4.8 3.6 - + - -
351B MET* 3.8 29.5 - - + -
354B LEU* 3.8 24.7 - - + +
355B PRO* 6.1 2.0 - - + -
365B ARG 3.1 13.3 + - - +
366B PHE* 3.5 42.8 - + - +
368B LYS* 1.3 76.4 - - - +
370B MET* 1.3 72.5 + - + +
372B LYS* 3.6 11.2 - - - +
373B ASN* 3.0 59.7 + - + +
374B LYS* 3.5 37.2 - - + -
418B TRP* 3.8 20.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B LEU* 5.1 0.4 - - - -
366B PHE* 2.8 28.0 + - + +
367B VAL* 3.7 9.2 - - - +
369B TRP* 1.3 85.5 - - + +
371B ILE* 1.3 59.5 + - - +
374B LYS* 2.9 33.4 + - + +
375B GLY 2.9 8.8 + - - -
376B LEU* 3.4 30.3 + - + +
377B VAL 4.1 0.2 - - - -
378B ALA* 3.7 33.4 - - + +
397B ILE* 4.0 12.3 - - + -
399B PHE* 4.1 11.7 - - + -
418B TRP* 3.7 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PHE* 5.3 4.0 - - - +
24B LEU* 3.8 37.2 - - + +
25B ALA* 4.6 6.1 - - + +
28B HIS* 4.1 20.2 - - + +
29B ASP 4.6 0.7 - - - +
30B VAL* 3.8 20.4 - - + +
367B VAL* 2.9 38.4 + - + +
368B LYS 3.8 3.8 - - - +
370B MET* 1.3 79.2 - - - +
372B LYS* 1.3 63.7 + - - +
375B GLY* 3.4 15.8 + - - -
376B LEU 3.5 18.8 - - - +
377B VAL* 4.0 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 4.7 11.2 - - + -
28B HIS* 3.6 39.2 + - + +
355B PRO* 5.9 5.3 - - - +
368B LYS* 3.1 45.3 + - - +
369B TRP* 3.6 9.5 - - - +
371B ILE* 1.3 81.5 - - + +
373B ASN* 1.3 72.3 + - - +
375B GLY 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B TRP* 3.0 55.1 + - - +
372B LYS* 1.3 92.9 - - - +
374B LYS* 1.3 75.0 + - + +
375B GLY 3.7 0.4 - - - -
417B LYS* 5.9 1.0 + - - -
421B GLU* 4.7 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B TRP* 3.5 35.1 - - + -
370B MET* 2.9 27.2 + - + +
373B ASN* 1.3 87.8 + - + +
375B GLY* 1.3 63.7 + - - +
376B LEU* 3.3 2.0 + - + +
414B LYS* 3.5 27.4 - - - +
417B LYS* 4.7 4.7 + - - +
418B TRP* 3.7 54.8 - - + +
421B GLU* 3.1 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASP 3.5 20.4 - - - -
30B VAL* 3.3 6.8 - - - -
31B VAL 2.9 24.3 + - - -
370B MET 2.9 4.2 + - - -
371B ILE 3.4 10.8 + - - -
372B LYS 4.8 0.4 - - - -
373B ASN 3.7 1.2 - - - -
374B LYS* 1.3 78.6 - - - +
376B LEU* 1.3 59.8 + - - +
414B LYS* 3.6 18.7 - - - +
----------------------------------------------------------
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