Contacts of the strand formed by residues 31 - 36 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B LEU* 4.0 0.7 - - - +
30B SER* 1.3 89.5 + - - +
32B GLY* 1.3 59.9 + - - +
62B ARG 5.0 0.4 - - - -
63B GLY* 3.6 13.3 + - - +
64B VAL* 4.0 13.9 - - + -
65B LYS* 3.0 16.2 + - - +
132B ILE* 4.0 14.1 - - + -
133B ILE 3.3 18.2 - - - -
134B GLY* 3.8 3.1 - - - -
135B PRO* 3.5 29.7 - - + +
140B LYS* 4.0 29.2 - - + -
160B ILE* 5.7 3.1 - - + -
163B LEU* 3.8 39.9 - - + -
164B GLN* 3.5 42.1 - - + +
167B ALA* 4.7 11.7 - - + -
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Residues in contact with GLY 32 (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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23B PHE* 6.1 0.4 - - - -
26B TRP* 5.6 0.4 - - - -
27B LEU* 3.6 19.0 - - - +
30B SER 3.9 0.2 + - - -
31B TRP* 1.3 75.7 - - - +
33B VAL* 1.3 65.4 + - - +
34B LEU 4.1 0.7 - - - -
64B VAL* 4.2 0.4 - - - -
65B LYS 3.2 10.5 - - - -
67B ILE* 6.4 0.2 - - - -
131B PHE 3.6 0.9 - - - +
132B ILE* 3.4 5.4 - - - +
133B ILE* 2.8 39.1 + - - +
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Residues in contact with VAL 33 (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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23B PHE* 6.2 0.2 - - - -
32B GLY* 1.3 76.3 - - - +
34B LEU* 1.3 60.1 + - - +
35B PHE* 4.1 7.0 - - + -
59B PHE* 4.6 3.6 - - + -
64B VAL* 3.4 23.3 - - + -
65B LYS 2.8 9.3 + - - +
66B LEU* 3.4 20.5 - - + -
67B ILE* 2.9 35.1 + - - +
130B VAL* 3.6 29.2 - - + -
131B PHE 3.4 2.9 - - - +
132B ILE* 4.4 12.3 - - + -
153B PHE* 5.6 2.9 - - + -
156B ILE* 4.6 7.6 - - + -
160B ILE* 4.1 16.8 - - + -
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Residues in contact with LEU 34 (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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9B PHE* 3.6 35.2 - - + -
12B PHE* 4.6 9.4 - - + -
23B PHE* 4.7 2.7 - - + -
32B GLY 4.1 0.8 - - - -
33B VAL* 1.3 70.5 - - - +
35B PHE* 1.3 67.0 + - - +
36B SER* 6.3 0.4 - - - -
67B ILE* 3.3 30.7 - - + +
69B LEU* 4.2 19.5 - - + -
99B ILE* 3.9 22.7 - - + -
110B LEU* 3.9 16.2 - - + -
112B MET* 5.7 1.8 - - + -
130B VAL* 3.5 1.7 - - - +
131B PHE* 2.8 44.2 + - + +
133B ILE* 4.2 11.1 - - + +
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Residues in contact with PHE 35 (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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33B VAL* 4.1 13.7 - - + -
34B LEU* 1.3 79.4 - - - +
36B SER* 1.3 62.2 + - - +
37B HIS* 5.9 0.2 - - - -
49B LEU* 3.8 25.6 - - + -
52B VAL* 3.9 29.4 - - + -
66B LEU* 4.1 20.4 - - + -
67B ILE* 2.9 29.4 + - - -
68B ALA* 3.2 21.2 - - + +
69B LEU* 2.8 25.9 + - - +
96B TYR* 4.2 10.5 - + - -
129B ALA 3.2 12.6 - - - +
130B VAL* 4.3 11.9 - - + -
131B PHE* 5.8 0.4 - - - -
151B ARG* 3.7 14.4 - - - +
153B PHE* 4.0 18.4 - + + -
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Residues in contact with SER 36 (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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34B LEU* 6.3 0.4 - - - -
35B PHE* 1.3 75.0 - - - +
37B HIS* 1.3 61.4 + - - +
69B LEU* 3.1 19.1 - - - +
112B MET* 4.0 15.4 - - - -
126B THR* 3.7 17.2 - - - -
127B CYS 2.7 22.5 + - - -
128B ARG* 3.4 3.8 - - - -
129B ALA* 3.0 24.0 + - - +
151B ARG* 2.8 25.9 + - - -
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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