Contacts of the strand formed by residues 87 - 99 (chain B) in PDB entry 2GYR
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B SER* 3.3 33.5 + - - -
80B PHE 3.4 7.4 - - - -
81B MET* 3.0 35.7 - - + +
85B SER 4.0 0.6 + - - -
86B THR* 1.3 80.3 - - - +
88B ARG* 1.3 74.3 + - - +
89B THR* 3.7 28.3 - - + -
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Residues in contact with ARG 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B HIS* 4.0 20.0 + - + +
78B VAL 4.8 0.2 - - - -
79B SER* 3.1 9.5 - - - -
80B PHE* 2.9 58.9 + - + +
82B ASP* 3.2 22.6 + - + +
86B THR* 3.1 32.7 - - - +
87B TRP* 1.3 94.4 + - - +
89B THR* 1.3 63.1 + - - +
90B VAL* 6.0 0.7 - - + -
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Residues in contact with THR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ALA* 3.2 23.4 - - - +
78B VAL 3.4 8.8 + - - -
79B SER* 4.0 4.8 - - - -
80B PHE* 5.5 0.4 - - - -
87B TRP* 3.7 29.9 - - + -
88B ARG* 1.3 80.2 - - - +
90B VAL* 1.3 70.9 + - - +
91B ASP* 4.1 10.4 + - - +
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PRO* 5.6 4.7 - - + -
19B LEU* 4.0 30.3 - - + -
21B HIS* 6.2 1.3 - - + -
77B ALA* 3.2 17.7 - - - -
78B VAL 3.1 14.0 + - - +
80B PHE* 4.7 15.7 - - + -
88B ARG* 6.0 0.4 - - + -
89B THR* 1.3 82.3 + - - +
91B ASP* 1.3 69.6 + - - +
93B LEU* 3.5 34.8 - - + +
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Residues in contact with ASP 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PRO* 4.9 6.8 - - - +
77B ALA* 3.7 11.0 - - - +
89B THR* 4.5 13.3 - - - +
90B VAL* 1.3 83.2 - - - +
92B ARG* 1.3 82.1 + - + +
93B LEU* 3.0 2.9 + - - +
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Residues in contact with ARG 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A SER* 4.5 7.9 - - - -
42A PRO* 4.1 30.1 - - + +
43A HIS* 3.6 19.9 + - - +
75B TYR* 3.5 48.6 - - + +
76B GLU* 4.0 11.0 - - - +
77B ALA 4.0 0.4 - - - +
90B VAL 3.7 0.2 + - - -
91B ASP* 1.3 81.7 - - + +
93B LEU* 1.3 61.1 + - - +
94B SER 3.6 2.2 - - - -
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PRO* 3.5 25.4 - - + +
43A HIS* 2.8 20.9 - - - -
46A SER* 3.1 31.0 - - - +
17B LEU* 4.5 17.0 - - + -
19B LEU* 4.1 11.9 - - + -
29B PHE* 3.4 12.1 - - - -
76B GLU 3.3 3.4 + - - -
78B VAL* 3.5 30.5 - - + -
90B VAL* 3.5 38.6 - - + +
91B ASP 3.0 2.2 + - - -
92B ARG* 1.3 77.6 - - - +
94B SER* 1.3 59.5 + - - +
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Residues in contact with SER 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A HIS* 3.9 3.6 - - - -
28B ARG 4.6 1.6 + - - -
29B PHE* 3.9 6.0 - - - -
30B ARG* 3.0 34.6 + - - +
75B TYR* 3.1 6.2 - - - -
76B GLU* 2.8 51.2 + - - -
78B VAL* 3.7 19.7 - - - -
92B ARG 3.6 0.4 - - - -
93B LEU* 1.3 80.4 - - - +
95B ALA* 1.3 63.3 + - - +
96B THR* 3.7 1.2 - - - +
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A HIS* 3.8 9.7 + - - +
7B LEU* 3.7 19.2 - - + +
30B ARG* 3.0 42.2 + - - +
31B PHE* 4.0 4.0 - - - -
32B CYS* 4.3 2.5 - - - -
72B PRO* 3.7 26.9 - - + -
74B ARG 3.5 6.3 - - - -
75B TYR* 4.3 1.6 - - - -
76B GLU* 3.9 2.8 - - - +
94B SER* 1.3 75.2 + - - +
96B THR* 1.3 62.2 + - - +
97B ALA 3.7 0.7 - - - +
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Residues in contact with THR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 3.8 16.7 - - - +
30B ARG* 5.7 0.2 - - - +
74B ARG* 2.8 61.3 + - - +
75B TYR 3.7 9.8 + - - +
76B GLU* 3.4 45.1 - - + +
95B ALA* 1.3 78.2 - - - +
97B ALA* 1.3 56.6 + - - +
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 4.2 4.7 - - - +
32B CYS* 3.6 1.0 - - - -
72B PRO* 3.2 8.5 - - - +
73B THR* 2.7 46.0 + - - +
74B ARG* 3.6 26.7 + - + +
95B ALA 3.7 0.8 - - - -
96B THR* 1.3 83.8 + - - +
98B CYS* 1.3 62.4 + - - +
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Residues in contact with CYS 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B CYS* 4.3 4.0 - - - +
6B ARG* 3.7 6.7 - - - -
7B LEU* 3.4 34.7 - - - +
32B CYS* 2.0 53.6 - - + -
70B CYS* 4.1 9.9 - - - -
71B ARG 3.2 5.8 - - - -
73B THR* 3.8 10.2 + - - +
97B ALA* 1.3 74.6 - - - +
99B GLY* 1.3 59.8 + - - +
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Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B CYS* 4.1 9.2 - - - -
69B CYS 3.4 2.3 - - - +
71B ARG* 2.9 33.2 + - - +
73B THR* 3.9 9.3 - - - +
98B CYS* 1.3 78.3 - - - +
100B 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