Contacts of the strand formed by residues 76 - 83 (chain A) in PDB entry 2V5Y
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 CYS 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A HIS* 1.3 77.4 - - - +
77A ILE* 1.3 63.1 + - - +
78A ASP* 3.9 4.6 + - - +
124A GLU* 3.6 19.3 - - - -
125A LEU 3.8 2.2 - - - -
156A LYS 3.4 4.0 - - - +
157A VAL* 4.7 0.4 - - - -
158A LEU* 2.8 37.2 + - + +
160A HIS* 3.4 9.2 - - + +
161A PRO 3.8 0.9 - - - +
162A CYS* 2.0 65.5 - - - +
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Residues in contact with ILE 77 (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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66A LEU* 4.6 10.8 - - + -
69A LEU* 5.0 4.7 - - + -
75A HIS* 4.6 2.9 - - + -
76A CYS* 1.3 74.8 - - - +
78A ASP* 1.3 64.7 + - - +
79A PHE* 5.3 3.4 - - + -
124A GLU* 3.1 3.6 - - - +
125A LEU* 2.7 54.9 + - + +
127A ILE* 3.7 9.4 - - + -
135A TYR* 3.5 26.2 - - + +
137A VAL* 3.5 29.4 - - + -
139A PHE* 6.3 1.8 - - + -
155A VAL* 4.3 21.5 - - + -
156A LYS 3.4 9.0 - - - +
157A VAL* 4.4 15.7 - - + +
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Residues in contact with ASP 78 (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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76A CYS* 4.9 3.9 - - - +
77A ILE* 1.3 77.7 - - - +
79A PHE* 1.3 66.6 + - - +
80A HIS* 4.8 2.6 + - - -
122A ARG* 3.1 33.2 + - + +
123A ALA 3.3 11.2 - - - +
124A GLU* 3.7 11.2 - - + +
154A GLU 3.3 2.6 - - - +
155A VAL* 3.4 0.9 - - - -
156A LYS* 2.6 76.0 + - - +
158A LEU* 4.0 12.3 - - - +
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Residues in contact with PHE 79 (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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77A ILE* 5.3 2.9 - - + -
78A ASP* 1.3 78.3 - - - +
80A HIS* 1.3 75.5 + - - +
81A TYR* 3.9 24.0 - + + -
96A VAL* 4.8 1.1 - - + -
110A TRP* 4.0 24.2 - + - -
121A ASN 3.6 0.3 - - - +
122A ARG* 3.5 4.7 - - - +
123A ALA* 2.9 60.2 + - + +
125A LEU* 4.4 24.9 - - + -
139A PHE* 3.6 37.5 - + + -
152A ILE* 4.2 7.2 - - + -
154A GLU 3.5 8.1 - - - +
155A VAL* 4.0 24.7 - - + +
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Residues in contact with HIS 80 (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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78A ASP* 4.8 5.1 + - - -
79A PHE* 1.3 83.1 - - - +
81A TYR* 1.3 61.6 + - - +
120A TRP* 4.0 29.6 - - + -
121A ASN* 3.2 6.1 - - - -
122A ARG* 3.3 45.0 + - + +
152A ILE* 3.4 5.4 - - - -
153A ASP* 3.1 25.4 + - + +
154A GLU* 3.4 47.4 + - + +
156A LYS* 5.7 2.2 - - - -
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Residues in contact with TYR 81 (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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79A PHE* 3.9 11.4 - + + -
80A HIS* 1.3 74.5 - - - +
82A PHE* 1.3 65.2 + - - +
83A VAL* 4.6 5.4 - - + -
94A LEU* 4.0 7.6 - - + -
110A TRP* 3.4 32.3 - + - -
112A ILE* 3.5 44.5 - - + +
119A THR 3.8 1.2 - - - +
120A TRP* 3.3 9.6 - - - -
121A ASN* 3.0 70.9 + - + +
122A ARG 4.2 1.7 + - - -
123A ALA* 4.1 8.1 - - + -
151A ALA 3.2 11.4 - - - +
152A ILE* 3.9 12.6 - - + -
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Residues in contact with PHE 82 (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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42A TRP 4.1 4.9 - - - -
43A MET 5.2 0.7 - - - -
44A PRO* 3.7 43.1 - - + -
81A TYR* 1.3 77.8 - - - +
83A VAL* 1.3 68.2 + - - +
84A SER* 4.0 22.2 - - - -
118A ARG* 3.2 26.9 - - + -
119A THR* 3.2 41.3 - - - -
120A TRP* 3.5 33.7 - + + -
121A ASN* 5.6 0.4 - - - +
149A TYR* 5.5 3.1 - - + -
150A LEU* 3.4 3.8 - - - +
151A ALA* 2.8 41.1 + - + +
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Residues in contact with VAL 83 (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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81A TYR* 4.6 7.0 - - + -
82A PHE* 1.3 80.8 - - - +
84A SER* 1.3 64.3 + - - +
91A PRO* 3.6 20.2 - - + -
112A ILE* 3.6 25.1 - - + -
114A GLY 3.2 21.3 - - - +
115A ASP 4.0 9.9 - - - +
116A PRO* 4.0 5.8 - - - -
117A THR* 3.2 27.1 + - - +
118A ARG* 3.4 10.4 + - - -
149A TYR 3.5 2.5 - - - -
150A LEU* 3.3 32.3 - - + -
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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