Contacts of the strand formed by residues 4164 - 4168 (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 VAL4164 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4121D ILE* 4.0 21.1 - - + -
4122D TYR 3.5 10.5 - - - +
4123D THR* 3.6 22.7 - - - +
4124D PRO* 4.3 0.2 - - - -
4133D LEU* 4.2 14.6 - - + -
4134D PRO 2.9 11.3 + - - +
4135D VAL* 3.4 8.6 - - + +
4136D MET* 2.8 28.4 + - - +
4163D VAL* 1.3 73.1 - - - +
4165D VAL* 1.3 60.2 + - - +
4166D VAL* 4.3 4.9 - - + -
4205D ILE* 4.1 20.2 - - + -
4208D PHE 4.0 4.5 - - - +
4209D GLY 4.2 0.7 - - - -
4210D GLY* 3.9 24.2 - - - +
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Residues in contact with VAL4165 (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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4121D ILE* 3.5 1.7 - - - +
4122D TYR* 2.8 52.4 + - + +
4136D MET* 3.5 9.9 - - + +
4154D GLY* 4.0 19.3 - - - +
4157D LEU* 3.9 26.0 - - + -
4158D ALA* 3.9 29.6 - - + +
4163D VAL* 4.0 7.6 - - + -
4164D VAL* 1.3 75.3 - - - +
4166D VAL* 1.3 65.4 + - - +
4167D THR* 4.3 14.6 - - + -
4218D PHE* 5.0 5.2 - - + -
4476D PHE* 4.7 7.0 - - + -
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Residues in contact with VAL4166 (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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4119D LEU* 4.1 23.8 - - + -
4120D ASN 3.3 9.4 - - - +
4121D ILE* 4.3 5.2 - - + -
4135D VAL* 3.9 25.1 - - + -
4136D MET 2.9 8.1 + - - +
4137D VAL* 3.3 10.6 - - + +
4138D TRP* 2.7 33.4 + - - +
4164D VAL* 4.3 4.5 - - + -
4165D VAL* 1.3 79.1 - - - +
4167D THR* 1.3 60.0 + - - +
4168D ILE* 4.0 19.3 - - + -
4201D VAL* 4.5 10.1 - - + -
4205D ILE* 4.1 18.6 - - + -
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Residues in contact with THR4167 (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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4119D LEU* 3.2 3.8 - - - -
4120D ASN* 2.8 54.4 + - - +
4122D TYR* 4.3 7.9 - - + -
4138D TRP* 3.8 26.7 - - + -
4149D ALA* 3.6 22.1 + - - +
4152D TYR* 4.0 21.7 + - + +
4154D GLY 5.4 0.4 - - - +
4165D VAL* 4.5 12.8 - - + -
4166D VAL* 1.3 77.9 - - - +
4168D ILE* 1.3 61.0 + - - +
4476D PHE* 4.9 2.2 - - + -
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Residues in contact with ILE4168 (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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4055D PHE* 4.8 0.4 - - + -
4118D TYR 4.0 3.8 - - - +
4119D LEU* 4.0 8.1 - - + -
4137D VAL* 3.7 24.2 - - + -
4138D TRP* 3.3 17.3 + - - +
4139D ILE* 4.0 24.2 - - + -
4140D HIS* 3.7 14.0 + - - -
4149D ALA* 3.5 9.2 - - - +
4166D VAL* 4.0 12.3 - - + -
4167D THR* 1.3 79.1 - - - +
4169D GLN* 1.3 68.5 + - - +
4170D TYR* 4.4 2.1 - - + -
4194D GLN* 4.0 26.9 - - + +
4197D ALA* 3.9 34.5 - - + -
4198D LEU* 5.7 1.3 - - + -
4201D VAL* 5.7 0.7 - - + -
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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