Contacts of the strand formed by residues 128 - 133 (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 ARG 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B SER 3.4 6.7 - - - -
37B HIS* 4.2 1.0 - - - +
38B PRO* 3.4 20.3 - - + +
44B VAL* 3.7 11.3 - - - +
45B SER* 3.0 25.3 + - - +
48B GLU* 2.9 32.4 + - - -
127B CYS* 1.3 72.1 - - - +
129B ALA* 1.3 60.5 + - - +
143B ILE* 4.0 1.9 - - - +
145B TYR* 2.8 40.5 + - + +
146B PRO 3.4 8.1 - - - +
147B ALA 2.7 32.7 + - - -
149B THR 3.5 20.8 + - - -
151B ARG* 3.5 23.6 - - - +
1220B BEZ 2.9 32.3 + - - -
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Residues in contact with ALA 129 (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 4.5 0.2 - - - -
35B PHE* 3.2 3.4 - - - -
36B SER* 3.0 31.0 + - - +
112B MET* 3.9 11.2 - - + -
127B CYS* 4.0 2.5 - - - -
128B ARG* 1.3 73.6 - - - +
130B VAL* 1.3 62.7 + - - +
131B PHE* 3.8 18.8 - - + -
143B ILE 3.3 4.7 - - - -
144B LEU* 3.7 26.7 - - + -
151B ARG* 2.9 17.0 + - - -
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Residues in contact with VAL 130 (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* 3.6 28.3 - - + -
34B LEU 3.5 3.6 - - - +
35B PHE* 4.3 4.9 - - + -
129B ALA* 1.3 78.2 - - - +
131B PHE* 1.3 68.6 + - - +
132B ILE* 4.2 11.2 - - + +
141B LEU* 6.1 1.6 - - + -
142B SER* 3.1 10.0 - - - -
143B ILE* 2.9 61.5 + - + +
151B ARG* 3.5 19.1 - - - +
153B PHE* 5.0 0.9 - - + -
156B ILE* 4.4 22.2 - - + -
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Residues in contact with PHE 131 (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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3B ILE* 3.8 17.7 - - + -
9B PHE* 3.7 28.9 - + + -
32B GLY 3.6 1.4 - - - +
33B VAL* 3.4 3.8 - - - -
34B LEU* 2.8 47.3 + - + +
35B PHE* 5.8 0.4 - - - -
110B LEU* 3.7 37.7 - - + -
112B MET* 4.0 8.1 - - + -
129B ALA* 3.8 27.4 - - + -
130B VAL* 1.3 74.4 - - - +
132B ILE* 1.3 62.4 + - - +
133B ILE* 3.7 7.0 - - + +
139B LEU* 3.7 18.4 - - + -
141B LEU 3.8 2.2 - - - -
142B SER* 3.6 25.8 - - - -
144B LEU* 4.4 9.2 - - + -
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Residues in contact with ILE 132 (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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31B TRP* 4.0 23.1 - - + -
32B GLY 3.4 8.3 - - - +
33B VAL* 4.4 12.3 - - + +
64B VAL* 5.8 0.7 - - + -
130B VAL* 4.5 10.1 - - + -
131B PHE* 1.3 75.6 - - - +
133B ILE* 1.3 62.2 + - - +
134B GLY 4.2 0.2 - - - -
139B LEU* 3.5 3.6 - - - +
140B LYS* 2.9 28.8 + - - +
141B LEU* 3.1 36.4 + - + +
156B ILE* 4.6 8.1 - - + -
159B VAL* 3.9 19.3 - - + -
160B ILE* 4.2 20.6 - - + -
163B LEU* 4.0 22.0 - - + -
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Residues in contact with ILE 133 (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* 4.0 33.2 - - + -
23B PHE* 3.7 29.4 - - + -
27B LEU* 3.6 24.0 - - + -
31B TRP* 3.3 7.0 - - - -
32B GLY 2.8 39.7 + - - +
34B LEU* 4.2 9.4 - - + +
131B PHE* 3.7 20.4 - - + +
132B ILE* 1.3 77.8 - - - +
134B GLY* 1.3 72.8 + - - +
137B LYS* 3.8 22.0 - - - +
138B LYS 3.6 4.0 - - - +
139B LEU* 4.6 2.0 - - + -
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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