Contacts of the helix formed by residues 365 - 381 (chain D) in PDB entry 1F9E
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 ASP 365 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363D GLY 3.8 1.8 + - - -
364D ASP* 1.3 75.5 + - - +
366D ILE* 1.3 69.8 + - - +
367D LEU* 3.2 23.4 + - - +
368D THR* 2.7 42.0 + - - +
369D ILE* 3.0 21.9 + - - +
397D LYS* 3.9 41.6 + - + +
398D LEU 3.6 21.7 + - - +
399D VAL* 4.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 366 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C VAL* 6.0 0.2 - - + -
281C PHE* 4.4 13.7 - - + -
328D LEU* 3.3 28.9 - - + -
353D LEU* 5.4 2.7 - - + -
357D LEU* 5.1 3.6 - - + -
364D ASP 4.0 0.6 + - - -
365D ASP* 1.3 73.3 - - - +
367D LEU* 1.3 60.7 + - + +
369D ILE* 3.1 18.4 + - + +
370D LEU* 2.7 58.8 + - + +
394D LEU* 4.1 8.1 - - + -
398D LEU* 2.8 40.6 + - + +
399D VAL* 4.9 0.2 - - - +
400D PHE* 4.4 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 367 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B LEU* 4.2 22.9 - - + -
368B THR* 5.9 0.2 - - - -
371B THR* 3.7 16.2 - - - +
392B PHE* 4.0 14.6 - - + -
328D LEU* 4.9 2.0 - - + -
365D ASP* 3.2 17.3 + - - +
366D ILE* 1.3 86.9 - - + +
368D THR* 1.3 66.7 + - - +
370D LEU* 3.2 13.1 + - + +
371D THR* 2.8 27.6 + - - -
392D PHE* 3.5 56.1 - - + -
394D LEU* 4.7 8.5 - - + -
396D LYS 6.0 0.9 - - - +
397D LYS* 6.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 368 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ASP* 4.9 3.1 - - + +
367B LEU* 5.9 0.2 - - - -
397B LYS* 3.5 35.9 + - + +
360D ARG* 3.8 30.5 - - - +
364D ASP* 4.3 11.9 + - + +
365D ASP* 2.7 36.9 + - - +
367D LEU* 1.3 71.7 - - - +
369D ILE* 1.3 64.4 + - - +
371D THR* 3.0 19.0 + - - -
372D GLU* 3.1 11.8 + - - +
397D LYS* 5.3 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 369 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D LEU* 4.7 4.7 - - + +
356D SER* 3.3 27.8 - - - +
357D LEU* 3.9 24.9 - - + +
360D ARG* 3.7 23.1 - - + -
361D CYS* 3.8 25.6 - - - -
364D ASP* 3.7 18.8 - - + +
365D ASP 3.0 19.5 + - - +
366D ILE* 3.3 13.2 - - + +
368D THR* 1.3 76.5 - - - +
370D LEU* 1.3 62.9 + - - +
372D GLU* 3.1 8.8 + - - +
373D VAL* 3.0 26.4 + - + +
400D PHE* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 370 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B PHE* 4.8 1.1 - - + -
281C PHE* 4.4 12.6 - - + -
328D LEU* 4.0 26.9 - - + -
330D GLY* 5.3 1.3 - - - -
349D TYR* 3.6 26.7 - - + +
353D LEU* 4.5 6.1 - - + -
366D ILE* 2.7 43.4 + - + +
367D LEU* 3.2 9.8 + - + +
369D ILE* 1.3 73.1 - - - +
371D THR* 1.3 61.3 + - - +
373D VAL* 3.2 16.6 + - + +
374D ASN* 3.0 26.7 + - - +
389D PRO* 4.0 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 371 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B LEU* 3.7 10.9 - - - +
392B PHE* 3.7 14.5 - - - -
394B LEU* 3.8 6.9 - - - +
395B ARG 3.7 3.9 - - - +
396B LYS* 3.7 41.6 + - - +
397B LYS* 4.4 7.2 - - + +
367D LEU 2.8 16.3 + - - -
368D THR* 3.0 12.1 + - - -
370D LEU* 1.3 74.5 - - - +
372D GLU* 1.3 62.5 + - - +
374D ASN* 2.9 25.5 + - - +
375D TYR* 2.9 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 372 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ARG 5.4 0.2 - - - -
356D SER* 2.8 26.2 + - - +
359D GLU* 3.7 15.9 - - - +
360D ARG* 2.5 48.6 + - - +
362D ARG* 5.4 0.3 - - - +
368D THR 3.1 6.5 + - - +
369D ILE* 3.1 11.3 + - - +
371D THR* 1.3 80.3 - - - +
373D VAL* 1.3 62.4 + - - +
375D TYR* 3.2 9.2 + - + +
376D GLU* 3.0 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349D TYR* 3.7 33.2 - - + +
352D SER* 3.6 22.9 - - - +
353D LEU* 4.1 19.3 - - + +
356D SER* 4.2 10.8 - - - -
369D ILE* 3.0 20.3 + - + +
370D LEU* 3.3 19.3 - - + +
371D THR 3.1 0.2 - - - -
372D GLU* 1.3 77.3 - - - +
374D ASN* 1.3 63.8 + - - +
376D GLU* 3.4 0.4 + - - -
377D VAL* 2.9 39.7 + - + +
387D PRO* 4.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 374 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B PHE* 3.7 24.7 + - - -
393B THR 3.9 5.3 - - - -
394B LEU 3.2 24.0 + - - +
395B ARG* 4.1 2.7 - - - -
370D LEU 3.0 12.3 + - - +
371D THR* 2.9 9.7 + - - +
373D VAL* 1.3 76.9 - - - +
375D TYR* 1.3 58.4 + - - +
377D VAL* 3.6 1.2 + - - +
378D SER* 2.6 34.3 + - - -
386D MET* 3.5 16.1 - - + +
387D PRO* 3.0 36.5 - - - +
389D PRO* 3.8 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 375 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LYS* 3.2 48.5 + - + -
319B ARG* 3.2 16.1 + - - -
395B ARG* 3.3 42.3 - - - +
396B LYS* 4.5 2.2 - - + -
299C ASP* 2.8 31.2 + - + -
371D THR 2.9 8.0 + - - +
372D GLU* 3.4 13.2 - - + +
374D ASN* 1.3 75.4 - - - +
376D GLU* 1.3 77.4 + - + +
378D SER* 2.9 26.7 + - - -
379D ASN* 3.0 34.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 376 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352D SER* 3.8 17.3 - - - +
356D SER* 6.5 0.4 - - - -
372D GLU* 3.0 30.2 + - + +
373D VAL 3.8 2.7 - - - +
375D TYR* 1.3 95.3 - - - +
377D VAL* 1.3 62.3 + - - +
378D SER 3.1 1.0 + - - -
379D ASN* 3.2 17.3 + - - +
381D LYS* 3.5 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 377 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D TRP* 4.0 20.0 - - + +
349D TYR* 4.5 3.1 - - - -
352D SER* 4.0 14.6 - - - +
373D VAL* 2.9 39.0 + - + +
376D GLU* 1.3 73.0 - - - +
378D SER* 1.3 60.7 + - - +
379D ASN 3.4 0.2 - - - -
381D LYS* 3.4 23.2 + - + +
385D GLN* 3.5 50.6 + - + +
387D PRO* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 378 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B TYR 3.5 4.5 - - - +
321B ILE* 4.6 2.7 - - - -
322B PRO* 3.6 27.0 - - - +
395B ARG* 3.2 27.1 - - - +
374D ASN 2.6 18.0 + - - -
375D TYR 2.9 13.6 + - - -
377D VAL* 1.3 77.7 - - - +
379D ASN* 1.3 61.8 + - - +
381D LYS 3.1 0.4 + - - -
384D LYS* 2.9 32.9 + - - -
385D GLN 4.2 2.1 + - - -
386D MET* 4.0 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 379 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ARG* 2.7 51.0 + - - +
320B TYR 4.4 6.9 - - - +
321B ILE* 5.3 0.9 - - - +
395B ARG* 4.5 2.9 + - - -
375D TYR* 3.0 33.6 - - - +
376D GLU* 3.2 10.2 + - - +
378D SER* 1.3 77.4 - - - +
381D LYS* 1.3 75.8 + - + +
384D LYS* 4.1 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 381 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D TRP* 3.4 70.5 - - + +
351D GLN* 6.4 1.1 - - - -
352D SER* 5.3 5.4 - - - -
355D GLN* 5.6 7.1 - - - +
376D GLU* 3.5 15.7 + - - +
377D VAL* 3.6 13.3 - - - +
378D SER 3.1 3.4 - - - +
379D ASN* 1.3 78.6 - - - +
381D ASP* 1.3 60.7 + - - +
384D LYS* 2.8 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 381 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B TYR* 5.7 2.3 - - + -
340D TYR* 3.4 39.8 - + + +
348D TRP* 3.5 13.7 - - + -
379D ASN 3.6 12.7 - - - +
381D LYS* 1.3 236.9 - - + +
382D MET* 2.5 40.1 + - - +
383D GLY 2.9 23.6 + - - +
384D LYS* 3.6 14.8 - - + +
4201R ASP* 3.5 17.2 - - - +
----------------------------------------------------------
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