Contacts of the helix formed by residues 331 - 342 (chain D) in PDB entry 1S77
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 ASN 331 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D LYS* 3.7 1.0 + - - -
330D ILE* 1.3 72.3 - - - +
332D LYS* 1.3 61.8 + - - +
333D LYS* 3.3 12.3 + - - +
334D VAL* 3.1 32.3 + - - +
335D LEU* 2.9 20.3 + - - +
442D GLY 3.6 13.1 + - - +
443D LEU 2.7 19.9 + - - +
444D LEU 5.4 0.4 + - - -
445D THR* 4.0 23.8 + - + +
513D ALA* 4.1 13.1 - - - +
516D PHE* 4.6 2.3 - - - -
517D GLU* 5.0 7.9 + - - +
532D LEU* 4.6 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D ILE* 3.2 10.1 + - + +
331D ASN* 1.3 71.9 + - - +
333D LYS* 1.3 60.2 + - + +
335D LEU* 3.5 9.6 - - + +
336D ALA* 2.8 28.2 + - - +
409D ALA* 3.8 16.4 - - + -
410D ASN* 3.1 51.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 333 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D ASN* 3.2 6.5 + - - +
332D LYS* 1.3 74.4 - - + +
334D VAL* 1.3 67.4 + - - +
336D ALA* 3.1 22.0 - - - +
337D VAL* 3.2 13.3 + - - +
493D ALA 6.1 0.2 - - - -
516D PHE* 3.3 48.5 - - + +
517D GLU* 5.9 0.8 + - - -
528D TYR* 5.7 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D ASN* 3.0 31.6 + - - +
333D LYS* 1.3 73.0 - - - +
335D LEU* 1.3 60.1 + - - +
337D VAL* 3.4 5.2 + - - +
338D ALA* 2.9 27.0 + - - +
442D GLY* 3.1 34.3 - - - +
443D LEU* 3.8 7.2 - - + -
509D PHE* 3.9 26.0 - - + +
512D LEU* 4.9 2.5 - - + -
513D ALA* 3.7 23.8 - - - +
516D PHE* 4.0 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D ILE* 3.9 12.1 - - + -
331D ASN 2.9 12.9 + - - +
332D LYS* 3.5 14.4 - - + +
334D VAL* 1.3 75.8 - - - +
336D ALA* 1.3 58.8 + - - +
339D ASN* 2.8 47.2 + - - +
402D LEU* 3.9 14.1 - - + -
405D ALA* 3.8 23.1 - - + +
406D ASN* 3.1 33.7 - - - +
409D ALA* 3.8 27.1 - - + -
443D LEU* 3.5 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D LYS 2.8 14.7 + - - +
333D LYS* 3.1 15.3 - - - +
335D LEU* 1.3 78.8 - - - +
337D VAL* 1.3 65.0 + - + +
339D ASN* 3.7 7.4 + - - +
340D VAL* 3.6 16.1 + - - +
497D LEU* 5.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 337 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D LYS 3.2 13.9 + - - +
334D VAL 3.5 6.3 - - - +
336D ALA* 1.3 75.0 - - + +
338D ALA* 1.3 69.1 + - - +
340D VAL* 2.9 28.5 - - + +
341D ILE* 3.0 13.9 + - + +
496D PRO* 3.5 37.5 - - + -
497D LEU* 5.4 6.5 - - + +
502D TRP* 4.0 10.5 - - + -
509D PHE* 3.8 13.9 - - + -
512D LEU* 3.3 28.9 - - + -
516D PHE* 4.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D VAL 2.9 15.7 + - - +
335D LEU* 3.8 2.5 - - - +
337D VAL* 1.3 84.4 - - - +
339D ASN* 1.3 57.9 + - - +
341D ILE* 4.6 0.9 - - - -
342D THR* 2.8 34.0 + - - +
402D LEU* 3.8 12.8 - - + +
439D MET* 4.5 6.5 - - + -
443D LEU* 4.0 17.0 - - + -
509D PHE* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 339 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D LEU* 2.8 28.5 + - - +
336D ALA* 4.0 6.0 - - - +
337D VAL 3.2 0.2 - - - -
338D ALA* 1.3 73.7 - - - +
340D VAL* 1.3 62.2 + - + +
342D THR* 3.2 14.5 + - - -
343D LYS* 3.7 23.5 - - - +
402D LEU* 3.5 19.1 - - - +
403D GLU* 5.1 2.0 + - - -
406D ASN* 2.8 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 340 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D ALA 3.6 13.2 - - - +
337D VAL* 2.9 17.3 - - + +
339D ASN* 1.3 74.0 - - + +
341D ILE* 1.3 67.0 + - + +
342D THR 3.0 1.8 - - - -
343D LYS* 2.6 43.3 + - - +
344D TRP* 3.4 16.5 + - - +
497D LEU* 4.1 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 341 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D VAL* 3.0 16.8 + - + +
338D ALA* 4.5 0.7 - - - +
340D VAL* 1.3 80.6 - - + +
342D THR* 1.3 64.7 + - + +
343D LYS 3.0 1.8 + - - -
344D TRP* 3.4 42.8 + - + +
347D CYS* 3.3 27.7 - - - +
348D PRO* 3.3 36.8 - - + -
349D VAL* 4.2 8.1 - - + -
496D PRO 5.2 0.9 - - - +
497D LEU* 5.3 3.8 - - + -
500D THR* 4.8 3.1 - - + -
502D TRP* 3.6 28.3 - - + -
509D PHE* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 342 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D ALA* 2.8 30.1 + - - +
339D ASN 3.2 10.4 + - - -
340D VAL 2.8 2.8 + - - -
341D ILE* 1.3 81.8 - - + +
343D LYS* 1.3 60.3 + - - +
344D TRP 4.6 2.1 - - - +
347D CYS* 5.5 0.8 - - - +
352D ILE* 4.6 18.4 - - + +
354D ALA* 5.6 0.7 - - - -
355D ILE* 3.8 2.8 + - - +
395D ARG* 3.0 36.3 + - - -
398D LEU* 4.4 15.5 - - + -
402D LEU* 3.6 12.0 - - + +
439D MET* 4.3 22.7 - - - -
509D PHE* 4.8 2.7 - - + -
----------------------------------------------------------
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