Contacts of the helix formed by residues 311 - 319 (chain A) in PDB entry 2H9Y
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 THR 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A VAL* 3.6 19.6 - - + +
310A ASP* 1.3 87.8 + - - +
312A PRO* 1.4 72.5 - - - +
313A GLU* 3.7 11.0 + - - +
314A ALA* 3.0 22.7 + - - +
315A LEU* 3.0 18.7 + - - +
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Residues in contact with PRO 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A MET* 5.0 0.4 - - + -
214A LEU* 4.0 21.3 - - + -
232A PRO* 3.4 39.3 - - + +
233A ASN* 3.8 6.7 - - + +
238A THR* 3.8 19.3 - - + +
303A VAL* 4.1 14.4 - - + -
308A LEU* 4.5 10.8 - - + -
310A ASP 3.5 4.4 - - - +
311A THR* 1.4 84.7 - - - +
313A GLU* 1.3 55.8 + - - +
315A LEU* 4.4 3.1 - - + +
316A ILE* 2.9 37.0 + - - +
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ASN* 4.6 10.4 - - + +
311A THR* 3.1 10.3 + - - +
312A PRO* 1.3 78.7 - - - +
314A ALA* 1.3 64.2 + - - +
316A ILE* 3.5 9.1 - - + +
317A ASN* 3.1 45.0 + - - +
413A GLN* 5.0 14.2 + - + +
537A PRO* 5.6 7.4 - - - +
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Residues in contact with ALA 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ASP* 3.5 27.1 - - + +
311A THR* 3.0 23.3 + - - +
313A GLU* 1.3 77.4 + - - +
315A LEU* 1.3 61.5 + - + +
317A ASN* 3.3 6.1 + - - +
318A THR* 3.1 33.7 + - + +
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU* 3.9 43.1 - - + +
308A LEU* 4.6 7.4 - - + -
309A SER* 3.5 24.7 - - - +
310A ASP* 3.6 36.3 - - + +
311A THR 3.0 15.9 + - - +
312A PRO* 4.0 4.0 - - + +
314A ALA* 1.3 76.8 - - + +
316A ILE* 1.3 57.7 + - - +
318A THR* 4.3 6.5 - - - +
319A GLY* 2.9 29.5 + - - -
321A PHE* 3.7 4.0 - - - -
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Residues in contact with ILE 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU* 3.9 24.5 - - + -
232A PRO* 5.0 1.6 - - + -
233A ASN* 4.0 28.0 - - + +
312A PRO 2.9 23.5 + - - +
313A GLU* 3.5 10.1 - - + +
315A LEU* 1.3 74.4 - - - +
317A ASN* 1.3 62.5 + - - +
321A PHE* 3.9 10.7 - - + -
413A GLN* 4.2 14.1 - - + -
414A LEU* 4.0 26.9 - - + -
417A ARG* 3.5 29.4 - - + +
418A LEU* 5.0 1.3 - - + -
421A GLN* 2.5 33.8 + - - -
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Residues in contact with ASN 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A GLU* 3.1 39.8 + - - +
314A ALA* 3.3 5.9 + - - +
316A ILE* 1.3 80.3 - - - +
318A THR* 1.3 63.4 + - + +
413A GLN* 5.4 3.8 - - - -
417A ARG* 3.2 56.2 + - - +
421A GLN* 3.3 9.2 - - - +
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Residues in contact with THR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A ALA* 3.1 21.3 + - + +
315A LEU* 4.1 7.4 + - - +
317A ASN* 1.3 85.4 - - + +
319A GLY* 1.3 68.0 + - - +
320A ASP* 3.9 0.9 + - - +
421A GLN* 5.1 0.9 - - - -
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Residues in contact with GLY 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A LEU 2.9 19.7 + - - -
316A ILE 4.0 1.8 + - - -
317A ASN 3.7 1.4 - - - -
318A THR* 1.3 82.7 - - - +
320A ASP* 1.3 60.1 + - - -
321A PHE* 3.6 16.2 - - - -
421A GLN* 3.4 26.0 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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