Contacts of the strand formed by residues 75 - 84 (chain A) in PDB entry 2ZB8
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 ASP 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A TYR* 5.1 0.3 + - - -
52A MET* 4.3 0.3 - - - +
55A ARG* 3.1 16.9 + - - -
68A TRP* 3.1 38.1 + - - +
73A VAL* 4.9 3.4 - - + +
74A VAL* 1.3 79.8 - - - +
76A GLY* 1.3 60.6 + - - +
100A TYR* 3.4 35.5 - - - +
101A TRP 3.0 21.1 - - - +
102A PRO* 3.9 4.7 - - + -
103A TRP* 3.6 8.9 + - - -
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Residues in contact with GLY 76 (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 TYR* 4.2 5.8 - - - -
52A MET* 4.0 13.9 - - - -
55A ARG* 5.5 1.3 - - - -
75A ASP* 1.3 77.2 - - - +
77A GLY* 1.3 68.5 + - - -
99A PHE 3.0 16.7 - - - +
101A TRP* 2.8 30.7 + - - +
103A TRP* 3.7 4.0 - - - +
800A IMN 5.8 0.2 - - - -
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Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.6 6.6 - - - +
47A SER* 3.1 32.7 + - - +
49A ASP* 5.0 1.4 + - - -
51A TYR* 4.4 6.3 + - - -
52A MET* 4.5 5.5 - - - +
76A GLY* 1.3 72.0 - - - +
78A GLY* 1.3 59.4 + - - -
97A THR* 5.8 0.2 - - - -
98A SER 3.4 8.3 - - - -
99A PHE* 3.5 10.5 + - - +
103A TRP* 5.2 0.3 + - - -
130A LEU* 4.1 10.5 - - - -
800A IMN 5.9 0.2 - - - -
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Residues in contact with GLY 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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45A TYR 3.4 11.2 - - - -
46A LEU* 4.0 3.6 - - - -
76A GLY 3.4 0.6 + - - -
77A GLY* 1.3 74.0 - - - -
79A ILE* 1.3 60.9 + - - -
97A THR* 2.7 35.4 + - - -
98A SER 3.1 10.1 + - - -
101A TRP* 3.6 20.9 - - - -
130A LEU* 3.8 6.1 - - - +
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Residues in contact with ILE 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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43A THR* 3.9 1.7 - - - +
44A LEU* 2.8 23.4 + - + +
45A TYR* 2.9 23.1 + - + +
78A GLY* 1.3 73.9 - - - +
80A GLY* 1.3 68.6 + - - +
95A PHE* 5.3 0.2 - - + -
96A VAL 3.3 9.9 - - - +
97A THR* 3.3 30.3 - - - +
101A TRP* 3.7 5.6 - - - -
117A VAL* 4.9 9.2 - - + -
126A LEU* 4.0 36.6 - - + +
129A PHE* 3.6 27.6 - - + -
130A LEU* 3.7 24.2 - - + -
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Residues in contact with GLY 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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42A ARG 3.2 14.4 - - - -
44A LEU* 3.8 10.0 - - - +
79A ILE* 1.3 77.9 - - - +
81A ILE* 1.3 61.7 + - - +
95A PHE* 3.5 10.2 - - - -
96A VAL* 2.8 30.9 + - - +
101A TRP* 3.2 14.7 - - - -
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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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41A VAL* 3.3 3.3 - - - -
42A ARG* 2.7 78.1 + - + +
44A LEU* 4.1 14.1 - - + -
80A GLY* 1.3 75.6 - - - +
82A ILE* 1.3 74.0 + - - +
83A GLU* 3.4 1.3 + - + +
93A GLY* 3.9 22.4 - - - +
94A ASP 3.3 11.2 - - - +
95A PHE* 4.1 24.7 - - + -
101A TRP* 4.7 0.4 - - - -
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Residues in contact with ILE 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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39A VAL* 4.5 6.3 - - + -
40A GLN 3.6 4.9 - - - +
41A VAL* 4.3 7.9 - - + +
81A ILE* 1.3 74.7 - - - +
83A GLU* 1.3 62.1 + - - +
84A GLU 3.7 27.8 - - - +
85A SER* 4.1 3.8 - - - -
90A LEU* 3.5 49.4 - - + -
91A THR 3.5 23.3 - - - +
92A LYS* 3.5 2.4 - - - +
93A GLY* 2.8 26.2 + - - -
94A ASP* 2.9 26.0 + - + +
96A VAL* 3.9 17.7 - - + -
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Residues in contact with GLU 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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40A GLN* 2.7 42.5 + - - +
41A VAL 4.5 0.2 - - - -
42A ARG* 2.7 56.8 + - + +
81A ILE* 4.0 9.6 - - + +
82A ILE* 1.3 78.0 - - - +
84A GLU* 1.3 65.7 + - + +
92A LYS* 3.4 26.2 - - - +
106A LYS* 3.8 23.7 + - - +
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Residues in contact with GLU 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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34A ILE* 3.3 28.8 - - + +
39A VAL* 3.1 6.6 - - - +
40A GLN* 2.7 46.4 + - + +
82A ILE* 3.7 2.9 - - - +
83A GLU* 1.3 90.8 - - + +
85A SER* 1.3 61.2 + - - +
92A LYS* 5.2 2.2 - - - -
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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