Contacts of the strand formed by residues 128 - 133 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A SER 3.3 7.2 - - - -
37A HIS* 4.1 1.8 - - - +
38A PRO* 3.4 15.1 - - + +
44A VAL* 3.6 12.4 - - - +
45A SER* 2.8 28.3 + - - +
48A GLU* 2.8 41.4 + - - +
127A CYS* 1.3 71.3 - - - +
129A ALA* 1.3 61.2 + - - +
130A VAL 4.0 0.5 + - - -
143A ILE* 4.1 1.4 - - - +
144A LEU* 4.1 0.3 - - - -
145A TYR* 2.8 40.9 + - + +
146A PRO 3.5 10.1 + - - +
147A ALA* 2.6 35.3 + - - +
149A THR 3.5 17.6 + - - -
151A ARG* 3.4 24.5 - - - +
1222A BEZ 3.2 28.3 + - - -
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU 4.6 0.4 - - - -
35A PHE* 3.2 2.7 - - - -
36A SER* 3.0 33.4 + - - +
112A MET* 3.9 10.3 - - + -
127A CYS* 4.2 1.1 - - - -
128A ARG* 1.3 74.2 - - - +
130A VAL* 1.3 61.7 + - - +
131A PHE* 3.7 24.5 - - + -
143A ILE 3.4 6.5 - - - +
144A LEU* 3.8 20.2 - - + -
151A ARG* 2.9 16.5 + - - -
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 3.6 27.6 - - + -
34A LEU 3.6 3.6 - - - +
35A PHE* 4.3 4.5 - - + -
129A ALA* 1.3 79.9 - - - +
131A PHE* 1.3 69.0 + - - +
132A ILE* 4.2 9.2 - - + -
141A LEU* 3.9 1.7 - - + +
142A SER* 3.1 9.7 - - - -
143A ILE* 2.9 60.6 + - + +
151A ARG* 3.5 20.9 - - - +
153A PHE* 5.0 1.6 - - + -
156A ILE* 4.2 21.8 - - + -
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Residues in contact with PHE 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 3.7 20.6 - - + -
9A PHE* 3.8 34.1 - + + -
32A GLY 3.8 0.3 - - - +
33A VAL* 3.4 5.2 - - - +
34A LEU* 2.8 50.1 + - + +
35A PHE* 5.6 0.2 - - - -
36A SER* 6.0 0.2 - - - -
110A LEU* 3.7 29.8 - - + -
112A MET* 4.0 16.4 - - + -
129A ALA* 3.7 27.8 - - + -
130A VAL* 1.3 75.8 - - - +
132A ILE* 1.3 62.3 + - - +
133A ILE* 3.9 6.4 + - + +
139A LEU* 3.9 8.7 - - + -
141A LEU 3.7 2.2 - - - -
142A SER* 3.8 24.5 - - - -
144A LEU* 4.4 9.4 - - + -
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Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TRP* 4.0 17.0 - - + -
32A GLY 3.6 8.5 - - - +
33A VAL* 4.3 7.9 - - + -
64A VAL* 6.1 0.4 - - + -
130A VAL* 4.5 8.7 - - + -
131A PHE* 1.3 75.1 - - - +
133A ILE* 1.3 57.4 + - - +
139A LEU* 3.6 1.9 - - - +
140A LYS* 2.8 33.5 + - - +
141A LEU* 3.0 26.6 + - + +
156A ILE* 4.2 12.8 - - + +
159A VAL* 4.0 23.8 - - + -
160A ILE* 3.9 27.8 - - + -
163A LEU* 3.8 26.9 - - + -
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Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A PHE* 4.0 35.4 - - + -
23A PHE* 3.4 33.2 - - + -
27A LEU* 3.6 20.4 - - + -
31A TRP* 3.4 9.4 - - - -
32A GLY 2.9 35.6 + - - +
34A LEU* 4.3 11.7 - - + +
131A PHE* 4.0 15.3 - - + +
132A ILE* 1.3 76.6 - - - +
134A GLY* 1.3 71.3 + - - +
137A LYS* 3.7 23.3 - - - +
138A LYS 3.6 4.7 - - - +
139A LEU* 4.8 2.5 - - - -
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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