Contacts of the strand formed by residues 87 - 99 (chain A) in PDB entry 2GYZ
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 TRP 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A SER* 3.7 22.3 - - - -
80A PHE 4.0 6.3 - - - -
81A MET* 2.5 34.6 - - + +
85A SER 4.1 1.0 + - - -
86A THR* 1.3 78.5 - - - +
88A ARG* 1.3 75.2 + - - +
89A THR* 3.5 38.4 - - + -
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Residues in contact with ARG 88 (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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21A HIS* 4.9 12.5 - - + +
78A VAL 4.6 0.2 - - - -
79A SER* 3.2 5.9 - - - -
80A PHE* 2.9 55.8 + - + -
82A ASP* 2.7 39.9 + - + +
84A ASN* 5.2 3.6 - - - +
86A THR* 2.8 42.7 + - - +
87A TRP* 1.3 84.2 + - - +
89A THR* 1.3 63.0 + - - +
90A VAL* 5.6 0.2 - - + -
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Residues in contact with THR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA* 3.3 23.2 - - - +
78A VAL 3.4 4.0 + - - -
79A SER* 3.4 9.4 + - - -
87A TRP* 3.5 34.7 - - + -
88A ARG* 1.3 76.0 - - - +
90A VAL* 1.3 69.4 + - - +
91A ASP* 4.2 11.2 + - - +
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Residues in contact with VAL 90 (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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17A LEU* 5.9 0.7 - - + -
19A LEU* 3.6 17.0 - - + -
21A HIS* 3.6 33.2 - - + +
77A ALA* 3.2 2.4 - - - -
78A VAL 2.9 34.4 + - - +
80A PHE* 4.4 11.9 - - + -
88A ARG* 5.6 0.7 - - + -
89A THR* 1.3 78.4 + - - +
91A ASP* 1.3 69.4 + - - +
93A LEU* 3.5 38.5 - - + +
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Residues in contact with ASP 91 (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 ALA* 4.2 8.2 - - - +
89A THR* 4.2 12.8 + - - +
90A VAL* 1.3 79.9 - - - +
92A ARG* 1.3 80.0 + - + +
93A LEU* 3.0 10.7 + - - +
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Residues in contact with ARG 92 (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 TYR* 3.7 60.7 - - + +
76A GLU 3.7 10.4 + - - -
77A ALA* 4.0 3.6 - - - +
90A VAL 3.6 1.2 + - - -
91A ASP* 1.3 81.6 - - + +
93A LEU* 1.3 62.6 + - - +
94A SER 3.5 2.2 - - - -
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Residues in contact with LEU 93 (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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17A LEU* 4.1 35.0 - - + +
19A LEU* 4.4 15.5 - - + -
29A PHE* 3.1 25.6 - - + -
75A TYR* 4.9 2.5 - - - -
76A GLU 3.2 2.8 + - - -
78A VAL* 4.1 16.6 - - + -
90A VAL* 3.5 44.2 + - + +
91A ASP 3.0 6.1 + - - +
92A ARG* 1.3 80.3 - - - +
94A SER* 1.3 60.1 + - - +
95A ALA 4.2 0.2 + - - -
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Residues in contact with SER 94 (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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28A ARG 4.3 2.2 + - - -
29A PHE* 3.8 5.7 - - - -
30A ARG* 2.9 40.2 + - - +
75A TYR* 3.2 6.3 - - - -
76A GLU* 2.8 49.5 + - - -
78A VAL* 3.7 22.0 - - - -
93A LEU* 1.3 78.4 - - - +
95A ALA* 1.3 62.9 + - - +
96A THR* 3.8 0.2 - - - +
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Residues in contact with ALA 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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7A LEU* 3.5 19.7 - - + +
30A ARG* 2.9 44.1 + - - +
31A PHE* 4.0 6.7 - - - -
32A CYS* 4.1 1.8 - - - -
72A PRO* 3.7 27.6 - - + -
74A ARG 3.5 6.5 - - - -
75A TYR* 4.3 3.9 - - - -
93A LEU 4.2 0.8 + - - -
94A SER* 1.3 74.1 + - - +
96A THR* 1.3 63.9 + - - +
97A ALA 4.5 0.4 - - - +
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Residues in contact with THR 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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7A LEU* 4.0 15.8 - - - +
30A ARG* 5.7 0.7 - - - +
74A ARG* 2.8 75.0 + - - +
75A TYR 3.6 1.3 + - - -
76A GLU* 3.5 50.3 - - + +
95A ALA* 1.3 79.3 - - - +
97A ALA* 1.3 55.6 + - - +
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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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7A LEU* 4.1 4.3 - - - +
32A CYS* 3.7 2.4 - - - -
72A PRO* 3.2 9.7 - - - +
73A THR* 2.9 36.8 + - - +
74A ARG* 3.8 25.3 + - + +
95A ALA 3.7 1.0 - - - -
96A THR* 1.3 81.0 + - - +
98A CYS* 1.3 65.2 + - - +
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Residues in contact with CYS 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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5A CYS* 4.0 14.1 - - - +
6A ARG* 3.7 6.3 - - - -
7A LEU* 3.5 41.2 - - - +
32A CYS* 2.0 47.3 - - + -
71A ARG 3.3 6.1 - - - -
73A THR* 4.2 7.3 + - - +
97A ALA* 1.3 74.6 - - - +
99A GLY* 1.3 59.5 + - - +
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Residues in contact with GLY 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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5A CYS* 3.9 8.7 - - - -
69A CYS 3.4 2.3 - - - +
70A CYS* 3.6 0.9 - - - -
71A ARG* 2.9 34.5 + - - +
73A THR* 3.8 11.9 - - - +
98A CYS* 1.3 76.0 - - - +
100A CYS* 1.3 62.5 + - - -
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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