Contacts of the strand formed by residues 31 - 36 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C LEU* 3.7 2.0 - - - +
30C SER* 1.3 87.3 + - - +
32C GLY* 1.3 59.2 + - - +
62C ARG 5.0 0.4 - - - -
63C GLY 3.5 12.8 + - - +
64C VAL* 3.8 14.6 - - + -
65C LYS 3.1 14.8 + - - -
132C ILE* 4.0 13.2 - - + -
133C ILE 3.3 19.5 - - - -
134C GLY* 4.0 2.7 - - - -
135C PRO* 3.6 26.9 - - + +
140C LYS* 3.8 32.1 - - + -
160C ILE* 5.5 2.7 - - + -
163C LEU* 3.8 39.7 - - + -
164C GLN* 3.7 41.9 - - + +
167C ALA* 4.7 11.7 - - + -
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Residues in contact with GLY 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C PHE* 6.2 0.9 - - - -
26C TRP* 5.6 0.7 - - - -
27C LEU* 3.6 19.0 - - - +
30C SER 3.7 1.0 + - - -
31C TRP* 1.3 76.9 - - - +
33C VAL* 1.3 68.4 + - - +
34C LEU 4.2 0.4 - - - -
64C VAL* 4.1 1.1 - - - -
65C LYS 3.2 10.5 - - - -
132C ILE* 3.6 2.1 - - - +
133C ILE* 2.8 38.0 + - - +
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Residues in contact with VAL 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 6.2 0.4 - - - -
26C TRP* 6.0 0.2 - - - -
32C GLY* 1.3 79.7 - - - +
34C LEU* 1.3 64.1 + - - +
35C PHE* 4.2 7.6 - - + -
59C PHE* 4.6 3.6 - - + -
64C VAL* 3.5 19.1 - - + -
65C LYS 2.7 10.1 + - - +
66C LEU* 3.5 20.0 - - + -
67C ILE* 2.9 29.0 + - - +
130C VAL* 3.5 30.3 - - + -
131C PHE 3.4 4.0 - - - +
132C ILE* 4.3 15.3 - - + -
153C PHE* 6.3 1.6 - - + -
156C ILE* 4.7 7.4 - - + -
160C ILE* 4.2 16.4 - - + -
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C PHE* 3.6 35.9 - - + -
12C PHE* 4.3 10.3 - - + -
23C PHE* 4.7 3.3 - - + -
32C GLY 4.2 0.6 - - - -
33C VAL* 1.3 72.2 - - - +
35C PHE* 1.3 63.1 + - - +
36C SER* 6.3 0.4 - - - -
67C ILE* 3.2 34.7 - - + +
69C LEU* 4.2 18.8 - - + -
99C ILE* 3.7 21.5 - - + -
110C LEU* 3.9 15.0 - - + -
112C MET* 5.8 1.6 - - + -
130C VAL* 3.5 1.2 - - - -
131C PHE* 2.8 45.4 + - + +
133C ILE* 4.4 10.5 - - + +
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Residues in contact with PHE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 4.2 12.6 - - + -
34C LEU* 1.3 77.0 - - - +
36C SER* 1.3 61.8 + - - +
37C HIS* 5.3 0.2 - - - -
49C LEU* 3.8 24.9 - - + -
52C VAL* 4.0 23.1 - - + -
66C LEU* 4.3 15.5 - - + -
67C ILE 3.0 33.8 + - - -
68C ALA* 3.1 25.3 - - + +
69C LEU* 3.1 22.8 + - - +
96C TYR* 4.0 17.0 - + - -
129C ALA 3.1 13.7 - - - +
130C VAL* 4.0 13.2 - - + -
131C PHE* 5.5 0.4 - - - -
151C ARG* 3.6 24.0 - - - +
153C PHE* 4.6 11.4 - + + -
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Residues in contact with SER 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 6.3 0.4 - - - -
35C PHE* 1.3 74.7 - - - +
37C HIS* 1.3 62.5 + - - +
69C LEU* 3.1 19.7 - - - -
112C MET* 3.9 19.9 - - - -
126C THR* 3.7 12.8 - - - -
127C CYS 2.6 24.3 + - - -
128C ARG* 3.5 2.8 - - - -
129C ALA* 3.0 25.1 + - - +
131C PHE* 6.1 0.4 - - - -
151C ARG* 2.9 26.7 + - - -
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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