Contacts of the helix formed by residues 311 - 319 (chain B) in PDB entry 2WHQ
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303B VAL* 3.8 18.0 - - + +
310B ASP* 1.3 88.7 + - - +
312B PRO* 1.3 74.4 - - - +
313B GLU* 3.7 12.6 + - - +
314B ALA* 3.0 24.3 + - - +
315B LEU* 2.9 20.1 + - - +
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Residues in contact with PRO 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B MET* 4.9 0.2 - - + -
214B LEU* 4.0 20.6 - - + -
232B PRO* 3.3 39.0 - - + +
233B ASN* 3.8 6.5 - - + +
238B THR* 3.7 27.6 - - + +
303B VAL* 4.3 5.8 - - + -
308B LEU* 4.7 9.6 - - + -
310B ASP 4.0 3.8 - - - +
311B THR* 1.3 86.2 - - - +
313B GLU* 1.3 62.6 + - - +
315B LEU* 3.6 3.5 - - + -
316B ILE* 2.8 37.4 + - - +
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Residues in contact with GLU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ASN* 3.5 14.8 - - + +
234B GLY* 2.8 33.5 + - - +
238B THR* 5.2 2.3 + - - -
311B THR* 3.1 10.0 - - - +
312B PRO* 1.3 89.4 - - - +
314B ALA* 1.3 62.5 + - - +
316B ILE* 3.4 8.3 - - + +
317B ASN* 3.1 35.7 + - - +
413B GLN* 4.4 13.9 + - - +
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Residues in contact with ALA 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ASP* 3.6 27.4 - - - +
311B THR* 3.0 22.7 + - - +
313B GLU* 1.3 75.8 - - - +
315B LEU* 1.3 62.8 + - - +
317B ASN* 3.4 7.7 + - - +
318B THR* 3.1 31.6 + - + +
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B LEU* 4.0 41.3 - - + +
308B LEU* 4.4 8.3 - - + -
309B SER* 3.3 27.1 - - - +
310B ASP* 3.3 38.1 - - + +
311B THR 2.9 17.0 + - - +
312B PRO* 3.1 4.7 + - + +
314B ALA* 1.3 75.3 - - - +
316B ILE* 1.3 61.3 + - - +
318B THR* 3.9 6.0 + - - +
319B GLY* 3.0 27.7 + - - -
321B PHE* 4.0 3.5 - - - -
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Residues in contact with ILE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B LEU* 4.0 23.1 - - + -
232B PRO* 5.2 0.9 - - + -
233B ASN* 4.1 31.0 - - + +
312B PRO 2.8 22.8 + - - +
313B GLU* 3.4 14.6 - - - +
315B LEU* 1.3 70.4 - - - +
317B ASN* 1.3 69.5 + - - +
318B THR 3.5 0.3 + - - -
319B GLY 4.2 0.4 - - - -
321B PHE* 3.9 18.6 - - + -
413B GLN* 4.4 11.0 - - + +
414B LEU* 3.8 25.6 - - + -
417B ARG* 3.7 30.0 - - + +
418B LEU* 5.1 0.9 - - + -
421B GLN* 2.9 21.8 + - - -
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Residues in contact with ASN 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B GLU* 3.1 26.3 + - - +
314B ALA* 3.7 8.5 - - - +
315B LEU 3.3 0.2 - - - -
316B ILE* 1.3 86.4 - - - +
318B THR* 1.3 66.9 + - + +
413B GLN* 6.0 1.2 - - - -
417B ARG* 3.1 48.2 + - - +
421B GLN* 3.4 9.0 + - - +
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Residues in contact with THR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B ALA* 3.1 19.5 + - + +
315B LEU* 3.9 8.3 + - - +
317B ASN* 1.3 87.1 - - + +
319B GLY* 1.3 68.4 + - - +
320B ASP* 5.3 0.3 - - - +
421B GLN* 4.9 0.2 - - - -
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Residues in contact with GLY 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B LEU 3.0 18.8 + - - -
316B ILE 4.1 1.8 + - - -
317B ASN 3.7 0.8 - - - -
318B THR* 1.3 82.0 - - - +
320B ASP* 1.3 60.5 + - - -
321B PHE* 3.7 18.2 - - - -
421B GLN* 2.9 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