Contacts of the strand formed by residues 94 - 106 (chain A) in PDB entry 2ZHV
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 THR 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A LEU* 3.7 36.6 - - + +
85A VAL 3.4 15.9 - - - +
86A SER* 3.8 11.0 + - - -
93A VAL* 1.3 80.2 + - - +
95A VAL* 1.3 70.5 + - - +
143A GLN* 4.9 0.7 - - - +
144A THR* 5.0 1.6 - - - +
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Residues in contact with VAL 95 (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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84A LEU* 3.2 6.7 - - - -
85A VAL 2.6 42.1 + - - +
93A VAL* 4.7 0.2 - - + -
94A THR* 1.3 81.5 - - - +
96A ARG* 1.3 64.8 + - - +
97A ALA* 3.7 2.6 + - + -
136A PHE* 3.9 31.0 - - + -
139A SER 4.8 0.7 - - - -
140A LEU* 3.8 32.8 - - + +
143A GLN* 3.4 19.5 - - + +
144A THR* 3.6 28.0 - - + -
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Residues in contact with ARG 96 (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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59A THR* 2.9 46.5 + - - +
61A ARG* 3.3 47.9 - - - +
82A THR* 2.9 41.7 + - + +
83A ASP* 3.2 8.6 - - - +
84A LEU* 3.9 20.7 - - + +
95A VAL* 1.3 70.7 - - - +
97A ALA* 1.3 60.4 + - - +
139A SER* 4.0 2.3 + - - -
143A GLN* 2.8 38.9 + - - +
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Residues in contact with ALA 97 (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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38A PHE* 4.9 0.4 - - + -
82A THR* 3.2 6.4 - - - -
83A ASP 3.0 29.5 + - - +
85A VAL* 4.2 10.8 - - + -
95A VAL* 3.7 2.8 + - + -
96A ARG* 1.3 75.4 - - - +
98A ASN* 1.3 71.3 + - - +
99A ILE* 3.6 2.4 - - - +
136A PHE* 3.8 34.8 - - + -
139A SER* 4.4 15.0 - - - +
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Residues in contact with ASN 98 (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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38A PHE* 3.5 20.3 - - - +
63A LEU* 3.8 7.2 - - + +
80A LEU* 5.8 0.4 - - + -
81A GLY 3.4 6.3 - - - +
82A THR* 3.4 18.9 - - - +
97A ALA* 1.3 79.0 - - - +
99A ILE* 1.3 64.4 + - - +
132A SER 5.2 0.2 + - - -
133A LEU* 3.4 33.7 - - + +
134A GLU* 3.0 52.0 + - - +
136A PHE* 5.9 0.4 - - - +
139A SER* 5.0 1.2 + - - -
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Residues in contact with ILE 99 (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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20A VAL* 3.3 31.4 - - + -
38A PHE* 3.5 24.7 - - + +
40A VAL* 3.8 28.5 - - + -
52A TYR* 4.0 14.1 - - + +
79A GLU 3.6 0.3 - - - +
80A LEU* 4.6 2.9 - - - +
81A GLY* 2.7 37.4 + - - +
82A THR 5.3 0.4 - - - -
83A ASP* 3.7 20.6 - - + +
85A VAL* 3.7 14.6 - - + -
97A ALA 3.6 6.7 - - - +
98A ASN* 1.3 81.4 - - - +
100A ALA* 1.3 65.9 + - - +
101A ALA* 3.5 3.2 + - - +
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Residues in contact with ALA 100 (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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37A ASN* 5.1 3.6 - - - +
38A PHE 3.0 9.6 + - - +
39A ALA* 3.4 6.5 - - + +
40A VAL 3.0 24.9 + - - -
67A VAL* 4.2 2.9 - - + -
76A TRP* 3.7 35.9 - - + -
78A GLY* 5.1 0.2 - - - -
79A GLU 3.6 5.4 - - - +
80A LEU* 3.7 20.4 - - + +
99A ILE* 1.3 73.6 - - - +
101A ALA* 1.3 60.8 + - - +
102A ILE 3.3 3.1 + - - -
133A LEU* 5.9 0.2 - - + -
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Residues in contact with ALA 101 (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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40A VAL* 3.7 9.0 - - - -
42A ALA* 3.5 19.1 - - + -
52A TYR* 4.6 7.0 - - + -
54A ARG* 3.6 34.8 - - - +
78A GLY* 2.9 4.0 - - - -
79A GLU 2.8 39.3 + - - +
99A ILE 3.5 2.7 + - - +
100A ALA* 1.3 68.8 - - - +
102A ILE* 1.3 64.6 + - - +
103A THR* 3.2 4.9 + - - +
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Residues in contact with ILE 102 (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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39A ALA* 3.9 12.3 - - + +
40A VAL* 2.8 42.7 + - - +
41A GLY* 3.9 4.7 - - - -
42A ALA* 3.0 24.3 + - - +
43A ALA* 3.8 4.9 + - - +
76A TRP* 4.0 25.1 - - + -
77A GLU 3.4 13.9 - - - +
78A GLY* 4.0 0.7 - - - -
100A ALA 3.9 3.1 - - - +
101A ALA* 1.3 68.5 - - - +
103A THR* 1.3 59.0 + - - +
104A GLU 3.8 14.8 - - - +
105A SER* 4.2 2.5 - - - -
108A PHE* 3.6 29.8 - - + -
109A PHE* 3.8 20.6 - - + -
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Residues in contact with THR 103 (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 ALA* 5.0 2.9 - - + +
43A ALA* 4.7 15.7 - - + +
54A ARG* 4.0 13.2 - - - +
77A GLU* 3.0 13.5 + - - +
78A GLY* 4.0 5.9 - - - -
79A GLU* 3.7 31.1 + - - +
101A ALA 3.2 13.7 + - - +
102A ILE* 1.3 75.1 - - - +
104A GLU* 1.3 65.5 + - - +
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Residues in contact with GLU 104 (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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68A TYR* 5.6 0.3 - - - -
75A LYS* 3.7 23.5 + - - -
77A GLU* 2.7 57.2 + - + +
102A ILE* 3.6 3.6 - - - +
103A THR* 1.3 86.0 - - - +
105A SER* 1.3 65.8 + - - +
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Residues in contact with SER 105 (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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45A HIS* 4.3 16.3 + - - -
75A LYS* 3.2 21.4 - - - +
76A TRP* 3.9 8.7 - - - -
102A ILE* 4.2 5.8 - - - -
104A GLU* 1.3 81.1 - - - +
106A ASP* 1.3 65.0 + - - +
108A PHE* 4.0 13.3 + - - +
109A PHE* 3.5 26.7 + - - -
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Residues in contact with ASP 106 (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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73A GLN 3.8 5.7 - - - +
74A GLY* 2.8 14.3 - - - -
75A LYS* 2.7 50.9 + - + +
105A SER* 1.3 76.4 - - - +
107A LYS* 1.3 93.7 + - - +
108A PHE 3.0 3.0 + - - -
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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