Contacts of the helix formed by residues 331 - 339 (chain A) in PDB entry 1NVD
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 331 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A PRO* 3.8 13.2 - - + +
327A THR 4.7 1.1 + - - +
328A SER* 3.0 20.7 + - - +
329A LEU 3.3 1.0 - - - -
330A LYS* 1.3 78.6 - - - +
332A ALA* 1.3 67.1 + - - +
333A ARG* 2.8 64.1 + - - +
334A ILE* 3.1 29.5 + - + +
335A ARG* 3.1 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LYS 3.1 3.4 + - - -
331A ASP* 1.3 73.2 + - - +
333A ARG* 1.3 62.2 + - - +
335A ARG* 3.2 26.1 + - - +
336A LYS* 3.1 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLU* 4.9 8.9 + - - -
324A GLY* 3.8 20.5 + - - -
325A LEU 4.3 1.6 + - - -
326A PRO* 3.6 31.5 - - - +
331A ASP* 2.8 38.4 + - - +
332A ALA* 1.3 72.3 - - - +
334A ILE* 1.3 70.4 + - - +
336A LYS* 3.5 6.2 + - - +
337A LEU* 3.2 46.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU* 4.0 23.8 - - + -
285A ILE* 3.7 36.8 - - + -
289A GLU* 4.9 4.5 - - - +
293A ILE* 4.7 6.7 - - + -
326A PRO* 3.9 26.5 - - + -
328A SER 4.4 3.8 - - - +
329A LEU 4.7 11.4 - - - +
331A ASP* 3.1 31.2 + - + +
333A ARG* 1.3 86.8 - - + +
335A ARG* 1.3 62.9 + - + +
337A LEU* 3.4 2.6 + - + +
338A THR* 2.9 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A LEU 4.4 12.3 - - - +
330A LYS* 2.7 35.5 + - - +
331A ASP 3.1 6.1 + - - +
332A ALA* 3.2 27.4 + - - +
334A ILE* 1.3 74.8 - - + +
336A LYS* 1.3 66.1 + - - +
338A THR* 3.2 7.6 + - - -
339A ALA* 3.0 20.1 + - - -
340A GLY* 3.2 18.7 + - - +
341A LYS 6.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ALA 3.1 15.6 + - - +
333A ARG* 4.0 7.0 - - - +
334A ILE 3.4 0.4 - - - -
335A ARG* 1.3 78.0 - - - +
337A LEU* 1.3 65.0 + - + +
339A ALA* 3.5 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ARG* 3.4 38.6 - - - +
284A GLN* 3.3 23.4 - - + +
285A ILE* 4.0 15.9 - - + -
289A GLU* 5.2 2.2 - - - +
333A ARG* 3.2 35.6 + - + +
334A ILE* 3.8 4.9 - - + +
336A LYS* 1.3 81.8 - - + +
338A THR* 1.3 59.1 + - - +
339A ALA* 3.3 2.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU* 3.8 17.2 - - + +
284A GLN* 4.2 13.0 - - + -
285A ILE* 3.4 31.2 - - + -
334A ILE* 2.9 20.6 + - + +
335A ARG* 3.2 10.2 + - - -
337A LEU* 1.3 75.5 - - - +
339A ALA* 1.3 68.9 + - - +
340A GLY 3.1 1.7 + - - -
341A LYS* 3.2 47.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ARG 3.0 6.2 + - - -
336A LYS* 3.5 6.6 + - - +
337A LEU 3.3 5.1 - - - +
338A THR* 1.3 79.6 - - - +
340A GLY* 1.3 57.2 + - - +
341A LYS 3.5 0.6 + - - -
----------------------------------------------------------
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