Contacts of the helix formed by residues 329 - 344 (chain A) in PDB entry 4N9W
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 329 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A GLY 3.1 16.7 + - - +
326A ILE 3.5 9.2 - - - +
327A LEU 3.4 0.8 - - - -
328A GLU* 1.3 74.7 - - + +
330A ASP* 1.3 62.3 + - - +
331A GLN* 3.1 16.3 + - - +
332A LEU* 2.9 35.9 + - + +
333A ARG* 3.0 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ARG* 3.8 12.5 + - - -
327A LEU 4.1 2.1 - - - +
328A GLU 3.7 6.8 + - - +
329A ASP* 1.3 71.6 + - - +
331A GLN* 1.3 58.2 + - - +
333A ARG* 3.0 35.4 + - - +
334A ALA* 2.8 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ASP* 3.1 10.5 + - - +
330A ASP* 1.3 78.1 - - - +
332A LEU* 1.3 63.7 + - - +
334A ALA* 3.4 5.2 + - - +
335A GLY* 3.0 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ARG* 5.7 4.5 - - - +
325A GLY 4.5 15.9 - - - +
326A ILE* 4.1 13.0 - - + -
329A ASP* 2.9 28.3 + - + +
331A GLN* 1.3 77.7 - - - +
333A ARG* 1.3 64.6 + - - +
335A GLY* 3.2 3.3 + - - -
336A TYR* 3.1 60.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
189A ARG* 3.5 19.7 - - - +
264A ASP* 3.9 22.7 + - - +
289A ALA* 3.6 19.5 - - + -
326A ILE* 2.8 48.7 + - + +
327A LEU* 3.1 21.3 + - - +
329A ASP 3.0 13.8 + - - +
330A ASP* 3.0 30.4 + - - +
332A LEU* 1.3 80.6 - - - +
334A ALA* 1.3 61.0 + - - +
336A TYR* 3.3 10.9 + - - +
337A VAL* 3.1 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ASP 2.8 21.1 + - - +
331A GLN* 3.7 6.7 - - - +
333A ARG* 1.3 73.5 - - - +
335A GLY* 1.3 56.6 + - - +
337A VAL* 3.4 7.7 + - - +
338A ALA* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLN 3.0 14.5 + - - -
332A LEU* 3.2 4.7 + - - -
334A ALA* 1.3 74.0 - - - +
336A TYR* 1.3 64.5 + - - +
338A ALA* 3.3 6.0 + - - +
339A ARG* 3.1 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ALA* 4.7 13.5 - - + -
290A VAL 5.4 0.2 - - - -
305A GLY 3.5 23.1 + - - -
306A ASP 3.9 10.8 - - - -
307A ALA 3.9 3.1 - - - +
308A GLY* 3.4 34.5 + - - -
309A ARG* 3.8 24.7 - - + +
326A ILE* 3.4 35.2 - - + -
332A LEU* 3.1 44.7 + - + +
333A ARG* 3.7 6.7 - - - +
335A GLY* 1.3 74.6 - - - +
337A VAL* 1.3 58.7 + - - +
339A ARG* 3.3 1.4 + - - +
340A ALA* 2.8 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLY* 3.6 39.5 - - - +
288A THR 4.2 0.7 - - - -
289A ALA* 3.7 26.5 - - + +
333A ARG* 3.1 21.0 + - + +
334A ALA* 3.7 7.6 - - - +
336A TYR* 1.3 75.2 - - - +
338A ALA* 1.3 58.6 + - - +
340A ALA* 3.3 6.0 + - - +
341A SER* 2.8 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ALA 3.0 17.9 + - - +
335A GLY* 3.6 6.3 - - - +
336A TYR 3.2 0.2 - - - -
337A VAL* 1.3 79.7 - - - +
339A ARG* 1.3 83.9 - - - +
341A SER* 4.0 5.1 - - - -
342A GLU* 3.2 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ASP* 3.5 30.1 - - + +
307A ALA* 4.1 6.4 - - + +
335A GLY* 3.1 25.5 + - - +
336A TYR 3.9 1.6 - - - +
338A ALA* 1.3 93.7 - - - +
340A ALA* 1.3 57.4 + - - +
342A GLU* 3.0 41.0 + - - +
343A ARG* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A MET* 3.7 40.7 - - + +
288A THR 5.9 2.0 - - - +
289A ALA* 6.5 0.9 - - - -
307A ALA* 3.7 17.7 - - - +
336A TYR 2.8 18.7 + - - +
337A VAL* 3.6 6.7 - - - +
339A ARG* 1.3 75.2 - - - +
341A SER* 1.3 59.6 + - - +
344A VAL* 3.0 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A MET 3.8 11.3 + - - -
285A ALA 5.3 1.2 + - - -
287A GLY* 4.3 5.9 - - - -
337A VAL* 2.8 31.6 + - - +
338A ALA* 4.0 5.6 - - - -
340A ALA* 1.3 72.8 - - - +
342A GLU* 1.3 61.5 + - - +
344A VAL* 3.4 16.2 - - - +
345A HIS* 3.3 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ALA* 3.2 9.4 + - - +
339A ARG* 3.0 47.0 + - - +
341A SER* 1.3 77.3 - - - +
343A ARG* 1.3 65.0 + - - +
344A VAL 3.4 0.5 + - - -
345A HIS* 3.6 20.9 + - - +
346A ARG* 5.8 0.3 + - - -
402A EDO 4.7 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A MET* 4.1 11.2 - - + -
300A ARG* 3.0 22.2 + - - +
301A VAL 3.0 25.9 + - - -
303A ALA* 3.9 25.4 - - - +
307A ALA* 4.3 4.9 - - + -
339A ARG 3.0 17.5 + - - +
340A ALA 3.8 4.0 - - - +
342A GLU* 1.3 78.9 - - - +
344A VAL* 1.3 62.0 + - - +
345A HIS 3.1 1.9 + - - -
346A ARG* 3.2 63.0 + - - +
347A TYR* 3.6 20.9 + - + -
402A EDO 5.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A VAL* 3.8 21.0 - - + +
281A VAL* 3.7 40.8 - - + +
284A MET* 4.1 9.4 - - + -
285A ALA* 3.9 25.1 - - + +
340A ALA 3.0 15.3 + - - +
341A SER* 3.4 22.9 - - - +
343A ARG* 1.3 72.3 - - - +
345A HIS* 1.3 67.5 + - + +
346A ARG 3.0 3.1 - - - -
347A TYR* 3.0 25.2 + - + +
348A ASP 3.7 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