Contacts of the strand formed by residues 56 - 59 (chain A) in PDB entry 2V40
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 ILE 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A ALA* 4.1 0.9 - - - +
55A ASP* 1.3 87.5 - - + +
57A VAL* 1.3 69.0 + - - +
58A CYS* 3.9 22.0 - - - -
92A THR* 3.3 20.2 - - - +
94A PHE* 4.1 11.2 - - + -
237A PHE* 4.1 19.3 - - + -
238A LEU* 5.6 1.8 - - + -
241A ALA* 3.6 30.7 - - + -
247A LYS* 3.7 22.0 - - + +
248A LYS 3.2 3.0 + - - +
249A ILE* 3.4 17.7 - - + -
250A LEU* 2.9 25.8 + - - +
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Residues in contact with VAL 57 (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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51A ALA* 4.3 3.4 - - + -
54A ALA* 4.0 13.2 - - + -
56A ILE* 1.3 78.4 - - - +
58A CYS* 1.3 55.2 + - - +
83A PRO* 3.9 15.0 - - + +
85A GLY* 3.9 32.1 - - - -
86A ILE 3.9 1.8 - - - +
91A VAL* 4.2 10.0 - - + +
92A THR 3.0 10.4 + - - +
93A ALA* 3.3 10.7 - - - -
94A PHE* 2.7 32.7 + - - +
250A LEU* 3.3 28.5 - - + +
252A GLU* 4.0 10.8 - - - +
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Residues in contact with CYS 58 (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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56A ILE* 3.9 19.7 - - - -
57A VAL* 1.3 79.6 - - - +
59A ARG* 1.3 66.3 + - - +
83A PRO* 4.4 3.4 - - - -
94A PHE* 3.2 23.8 - - - +
238A LEU* 5.3 3.8 - - - -
249A ILE* 3.9 15.0 - - - -
250A LEU 2.8 18.4 + - - +
251A VAL* 3.6 15.3 - - + +
252A GLU* 2.9 32.4 + - - +
283A LEU* 4.3 14.4 - - + -
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Residues in contact with ARG 59 (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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58A CYS* 1.3 76.5 - - - +
60A CYS* 1.3 60.3 + - - +
61A GLN 2.8 27.0 + - - -
62A GLY 3.3 11.9 + - - -
63A GLY 2.9 29.5 + - - +
80A HIS 3.3 12.5 + - - -
81A LEU* 3.2 35.1 + - - +
82A LEU 5.3 0.6 + - - -
83A PRO* 4.2 19.0 - - + +
94A PHE 3.0 6.7 + - - +
95A ILE* 4.1 9.9 - - + -
96A GLY* 2.9 27.5 + - - -
99A VAL* 3.6 14.3 - - + +
252A GLU* 3.6 23.0 + - - -
253A GLY 5.4 0.4 - - - -
254A ALA* 3.6 22.4 - - - +
283A LEU* 3.7 4.2 - - - +
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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