Contacts of the strand formed by residues 4346 - 4351 (chain D) in PDB entry 2H7C
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 TYR4346 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4227D VAL* 4.2 1.6 - - + -
4228D SER* 3.4 25.4 + - - -
4231D VAL* 4.5 14.1 - - + -
4243D ALA* 3.4 25.4 - - + -
4245D SER* 2.7 34.1 + - - -
4249D VAL* 4.2 4.0 - - - +
4344D VAL* 3.8 1.1 - - + +
4345D PRO* 1.3 75.6 - - - +
4347D MET* 1.3 70.0 + - - +
4348D VAL* 3.8 19.7 - - + -
4433D VAL* 3.8 21.3 - - + -
4437D HIS* 3.4 46.7 - + + +
4443D PRO 3.0 7.5 + - - -
4444D THR* 3.4 7.4 - - + +
4445D TYR 3.0 24.3 + - - +
4503D PHE* 3.7 4.4 - - - -
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Residues in contact with MET4347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4243D ALA 2.8 8.7 + - - +
4244D ILE* 3.2 25.0 - - + +
4245D SER 2.8 26.2 + - - +
4346D TYR* 1.3 72.2 - - - +
4348D VAL* 1.3 63.7 + - - +
4445D TYR* 3.3 13.2 - - + +
4447D TYR* 4.1 12.6 - - + -
4499D PHE 4.6 0.2 - - - +
4500D TRP* 3.9 24.0 - - + -
4503D PHE* 3.6 47.0 - - + -
4509D PRO* 4.2 7.4 - - + -
4517D TRP* 3.6 37.0 - - + -
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Residues in contact with VAL4348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4245D SER* 3.5 5.6 - - - +
4249D VAL* 4.0 14.6 - - + -
4346D TYR* 3.8 38.1 - - + +
4347D MET* 1.3 79.4 - - - +
4349D GLY* 1.3 62.7 + - - +
4430D SER* 3.7 38.6 - - - +
4433D VAL* 4.8 3.1 - - + -
4434D ALA* 4.6 13.7 - - + -
4444D THR* 5.2 0.7 - - + -
4445D TYR 2.7 12.5 + - - +
4446D MET* 3.0 38.7 - - + +
4447D TYR* 3.3 2.9 + - - -
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Residues in contact with GLY4349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4245D SER 3.0 10.8 + - - +
4247D SER* 2.9 24.3 + - - -
4248D GLY 4.7 0.2 + - - -
4348D VAL* 1.3 77.7 - - - +
4350D ILE* 1.3 69.4 + - - +
4430D SER* 4.5 2.1 + - - -
4446D MET* 5.1 1.1 - - - -
4447D TYR* 3.2 35.8 - - - -
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Residues in contact with ILE4350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4247D SER* 4.1 2.7 - - - -
4349D GLY* 1.3 79.5 - - - +
4351D ASN* 1.3 73.0 + - - +
4354D GLU* 3.4 14.8 - - + +
4426D PHE* 3.9 14.1 - - + +
4427D GLY* 4.0 11.7 - - - +
4430D SER* 3.4 30.1 - - - +
4446D MET* 5.5 1.6 - - + -
4447D TYR* 3.0 11.1 + - - +
4448D GLU* 3.2 23.4 - - + +
4449D PHE 2.8 23.0 + - - -
4539D LEU* 4.4 10.1 - - + -
4540D LYS* 3.7 34.1 - - + -
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Residues in contact with ASN4351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4247D SER* 3.9 10.2 + - - -
4350D ILE* 1.3 86.6 - - - +
4352D LYS* 1.3 65.3 + - - +
4353D GLN 3.3 1.3 + - - -
4354D GLU* 2.7 29.6 + - - +
4447D TYR* 4.3 3.3 - - - -
4448D GLU* 4.5 2.7 - - - -
4449D PHE* 3.2 30.2 - - - +
4466D GLY 3.1 17.9 - - - +
4467D ASP 3.0 20.3 + - - +
4468D HIS* 4.1 0.8 - - - +
4469D GLY 3.5 7.3 - - - +
4470D ASP* 3.7 3.0 - - - +
4471D GLU* 2.8 32.6 + - - +
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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