Contacts of the strand formed by residues 31 - 36 (chain D) in PDB entry 2V32
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 TRP 31 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D LEU* 3.8 2.0 - - - +
30D SER* 1.3 88.5 + - - +
32D GLY* 1.3 58.3 + - - +
62D ARG 4.9 0.9 - - - -
63D GLY 3.6 11.3 + - - +
64D VAL* 4.2 13.9 - - + -
65D LYS 3.0 15.3 + - - -
132D ILE* 4.1 12.3 - - + -
133D ILE 3.4 20.2 - - - -
134D GLY* 3.8 2.9 - - - -
135D PRO* 3.5 27.4 - - + +
140D LYS* 4.0 30.1 - - + -
160D ILE* 5.5 3.6 - - + -
163D LEU* 3.8 39.5 - - + -
164D GLN* 3.5 43.8 - - + +
167D ALA* 4.7 11.4 - - + -
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Residues in contact with GLY 32 (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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23D PHE* 6.1 0.7 - - - -
26D TRP* 5.3 1.3 - - - -
27D LEU* 3.7 20.4 - - - +
31D TRP* 1.3 75.1 - - - +
33D VAL* 1.3 69.3 + - - +
34D LEU 4.2 0.2 - - - -
64D VAL* 4.2 1.3 - - - -
65D LYS 3.3 10.1 - - - -
131D PHE 4.5 0.2 - - - -
132D ILE* 3.5 2.6 - - - +
133D ILE* 2.9 38.1 + - - +
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Residues in contact with VAL 33 (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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32D GLY* 1.3 77.7 - - - +
34D LEU* 1.3 59.7 + - - +
35D PHE* 4.1 10.5 + - + -
59D PHE* 4.5 4.0 - - + -
64D VAL* 3.6 19.7 - - + -
65D LYS 2.8 10.3 + - - +
66D LEU* 3.6 20.3 - - + -
67D ILE* 2.9 30.1 + - - +
130D VAL* 3.6 29.4 - - + -
131D PHE 3.4 3.4 - - - -
132D ILE* 4.3 15.7 - - + -
133D ILE* 5.3 0.2 - - - -
153D PHE* 6.5 0.4 - - + -
156D ILE* 4.6 6.7 - - + -
160D ILE* 4.1 18.2 - - + -
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Residues in contact with LEU 34 (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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9D PHE* 3.7 31.6 - - + -
12D PHE* 4.3 13.5 - - + -
23D PHE* 4.7 2.9 - - + -
32D GLY 4.2 0.8 - - - -
33D VAL* 1.3 71.3 - - - +
35D PHE* 1.3 63.6 + - - +
36D SER* 6.3 0.7 - - - -
67D ILE* 3.2 35.7 - - + +
69D LEU* 4.3 19.3 - - + -
99D ILE* 3.9 22.0 - - + -
110D LEU* 4.2 12.8 - - + -
112D MET* 5.6 1.6 - - + -
130D VAL* 3.4 2.8 - - - +
131D PHE* 2.8 44.0 + - + +
133D ILE* 4.4 12.4 - - + +
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Residues in contact with PHE 35 (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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33D VAL* 4.1 17.5 - - + -
34D LEU* 1.3 78.7 - - - +
36D SER* 1.3 61.3 + - - +
49D LEU* 3.8 26.7 - - + -
52D VAL* 4.1 23.6 - - + -
66D LEU* 4.2 16.4 - - + -
67D ILE 2.9 35.1 + - - -
68D ALA* 3.3 22.2 - - + -
69D LEU* 3.0 24.6 + - - +
96D TYR* 3.9 15.0 - + - -
129D ALA 3.1 11.4 - - - +
130D VAL* 4.1 10.8 - - + -
131D PHE* 5.8 0.4 - - - -
151D ARG* 3.8 22.0 - - - +
153D PHE* 4.6 11.9 - + + -
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Residues in contact with SER 36 (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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34D LEU* 6.3 0.4 - - - -
35D PHE* 1.3 76.0 - - - +
37D HIS* 1.3 61.7 + - - +
69D LEU* 3.1 18.8 - - - -
112D MET* 3.7 21.5 - - - -
126D THR* 3.9 8.9 - - - -
127D CYS 2.6 23.3 + - - -
128D ARG* 3.5 3.6 - - - -
129D ALA* 2.8 26.5 + - - +
131D PHE* 6.1 0.6 - - - -
151D ARG* 2.7 26.3 + - - -
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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