Contacts of the strand formed by residues 76 - 85 (chain A) in PDB entry 2V72
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 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A TRP* 4.7 2.7 - - + -
65A ILE* 5.5 0.7 - - + -
74A GLY 2.9 15.8 + - - +
75A PHE* 1.3 71.3 - - - +
77A THR* 1.3 61.2 + - - +
78A LYS 3.5 25.4 - - - +
79A TYR* 4.1 11.0 - - + -
97A TRP* 3.3 41.0 - - + +
98A GLU 4.4 4.0 - - - +
104A LYS* 5.5 1.2 + - - -
119A ILE* 4.7 6.7 - - + -
121A ALA* 3.8 29.8 - - + -
123A GLN 3.6 7.6 - - - +
124A GLY* 4.1 0.9 - - - -
128A PHE 5.2 0.2 - - - +
129A ALA* 4.2 10.1 - - + -
130A SER 4.1 4.4 + - - +
131A ILE* 4.1 32.5 - - + -
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Residues in contact with THR 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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75A PHE 3.5 11.0 + - - +
76A ILE* 1.3 75.8 - - - +
78A LYS* 1.3 61.8 + - - +
79A TYR* 5.1 0.4 - - - -
96A THR* 3.0 13.8 + - - +
97A TRP* 2.7 40.0 + - - +
98A GLU 5.1 0.4 - - - +
99A GLU* 3.9 32.3 - - + +
123A GLN* 2.9 31.5 + - - +
124A GLY* 3.7 4.7 + - - -
125A VAL* 4.6 3.1 - - + +
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Residues in contact with LYS 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 ILE* 3.5 6.9 - - - +
77A THR* 1.3 80.4 + - - +
79A TYR* 1.3 61.7 + - - +
95A GLY 3.5 15.3 - - - +
96A THR* 4.2 9.2 - - - +
122A ILE* 2.8 55.5 + - + +
123A GLN* 3.3 38.4 + - + +
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Residues in contact with TYR 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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76A ILE* 4.1 11.0 - - + -
78A LYS* 1.3 76.6 - - - +
80A GLU* 1.3 68.5 + - - +
81A ILE* 3.9 24.9 - - + -
93A ALA* 4.4 2.0 - - + +
94A GLU* 3.4 20.9 + - - +
95A GLY* 3.1 59.6 + - - +
96A THR 3.6 4.4 + - - -
97A TRP* 3.3 66.5 + + + -
106A VAL* 4.2 11.0 - - + +
119A ILE* 4.9 3.4 - - + -
120A THR 3.2 12.6 - - - +
122A ILE* 4.0 6.5 - - - +
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Residues in contact with GLU 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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79A TYR* 1.3 77.7 - - - +
81A ILE* 1.3 67.5 + - - +
82A HIS* 3.1 25.7 - - + -
91A LEU* 3.8 19.8 - - + +
93A ALA 3.4 5.8 - - - -
94A GLU* 4.1 8.1 - - + -
118A LYS 3.6 0.7 - - - +
119A ILE* 3.7 1.6 - - - +
120A THR* 3.0 44.7 + - - +
122A ILE* 3.9 19.1 - - + +
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Residues in contact with ILE 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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63A ILE* 4.3 12.1 - - + -
65A ILE* 4.8 7.6 - - + -
79A TYR* 3.9 15.0 - - + -
80A GLU* 1.3 79.4 - - - +
82A HIS* 1.3 58.1 + - - +
91A LEU* 3.7 2.8 - - - +
92A VAL* 2.8 45.0 + - + +
93A ALA* 2.7 28.0 + - + +
97A TRP* 5.0 1.8 - - + -
106A VAL* 3.9 32.3 - - + -
117A ILE* 3.6 28.0 - - + -
118A LYS 3.4 2.5 - - - -
119A ILE* 3.7 21.5 - - + -
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Residues in contact with HIS 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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80A GLU* 3.1 32.6 + - + +
81A ILE* 1.3 78.9 - - - +
83A ALA* 1.3 60.6 + - - +
84A ILE* 4.4 0.8 - - - +
89A GLU* 3.9 32.1 - - + +
90A THR* 3.3 7.0 - - - +
91A LEU* 3.4 40.5 - - + +
92A VAL* 4.5 0.4 - - - -
117A ILE* 3.5 6.1 - - - +
118A LYS* 2.9 46.2 + - + +
120A THR* 4.6 8.4 + - - -
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Residues in contact with ALA 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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82A HIS* 1.3 74.8 - - - +
84A ILE* 1.3 63.3 + - - +
85A ASN 4.1 0.4 - - - -
88A VAL 3.4 2.3 - - - +
89A GLU* 3.2 2.8 - - - +
90A THR* 2.9 43.8 + - + +
92A VAL* 4.4 4.2 - - + +
112A ILE* 4.0 20.6 - - + -
113A ASP 4.4 4.9 - - - +
114A ALA* 3.7 23.8 - - + -
116A GLU 3.5 4.5 - - - +
117A ILE* 5.2 2.9 - - + -
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Residues in contact with ILE 84 (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 SER* 5.9 0.2 - - - +
82A HIS 4.4 5.2 - - - +
83A ALA* 1.3 79.0 - - - +
85A ASN* 1.3 57.5 + - - +
87A GLY* 4.0 19.3 - - - +
88A VAL 3.2 2.5 - - - +
89A GLU* 3.4 33.2 - - + +
114A ALA* 3.6 0.6 - - - -
115A GLU* 2.8 47.5 + - - +
116A GLU* 2.9 54.0 + - + +
117A ILE 4.6 0.7 - - - +
118A LYS* 4.6 9.6 - - + -
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Residues in contact with ASN 85 (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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57A ALA* 4.5 9.9 - - - +
83A ALA 4.1 0.8 - - - -
84A ILE* 1.3 74.1 - - - +
86A ASN* 1.3 67.1 + - - +
88A VAL* 2.7 40.3 + - - +
90A THR* 6.0 3.4 - - + -
113A ASP* 3.4 42.5 - - - +
114A ALA* 3.7 8.1 + - - -
115A GLU* 3.1 17.1 + - - +
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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