Contacts of the strand formed by residues 96 - 101 (chain B) in PDB entry 3GYQ
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 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B GLU* 3.6 0.3 - - - -
36B ASP 2.6 29.0 + - - -
37B VAL* 4.3 13.8 - - + +
40B LEU* 3.5 20.0 - - + -
53B VAL* 4.6 0.2 - - + -
54B TYR 3.5 15.9 - - - +
55B GLY* 4.7 1.7 - - - -
61B PHE* 4.5 5.8 - - + -
62B PRO* 4.1 17.3 - - - +
65B LEU* 3.5 22.7 - - + -
94B ALA* 2.6 13.5 + - - +
95B LYS* 1.3 85.2 + - - +
97B PHE* 1.3 66.7 + - - +
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Residues in contact with PHE 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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19B ILE* 3.9 19.7 - - + -
33B LEU* 3.8 22.7 - - + -
34B ILE 3.2 14.6 - - - +
35B GLU* 4.0 6.7 - - + -
40B LEU* 3.8 8.3 - - - -
53B VAL* 3.6 2.1 - - - +
54B TYR* 2.7 71.6 + + + +
55B GLY* 4.8 3.4 - - - -
79B ILE* 3.8 15.0 - - + -
84B VAL* 4.7 15.7 - - + -
87B LEU* 4.7 6.1 - - + -
88B PHE* 3.5 37.5 - + + -
94B ALA* 4.1 3.6 - - + -
95B LYS 5.1 1.3 - - - -
96B THR* 1.3 88.5 - - - +
98B GLY* 1.3 54.2 + - - +
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Residues in contact with GLY 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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32B THR 3.7 0.2 - - - +
33B LEU* 3.5 7.7 - - - +
34B ILE* 2.9 34.4 + - - +
40B LEU* 3.8 10.9 - - - +
50B PHE* 4.1 6.7 - - - -
52B GLU 3.4 11.0 - - - -
53B VAL* 4.0 4.9 - - - -
54B TYR* 4.5 2.5 - - - -
97B PHE* 1.3 75.9 - - - +
99B ILE* 1.3 64.3 + - - -
100B ALA 3.7 0.9 + - - -
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Residues in contact with ILE 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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18B ILE* 3.9 26.5 - - + -
19B ILE* 3.9 20.0 - - + +
22B THR* 4.4 11.4 - - + +
31B THR* 4.1 15.5 - - + -
32B THR 3.6 5.8 - - - +
33B LEU* 4.3 11.9 - - + -
50B PHE* 3.4 4.6 - - - -
51B ILE* 2.7 63.6 + - + -
52B GLU* 2.9 12.5 + - + +
54B TYR* 3.8 30.3 - - + +
98B GLY* 1.3 73.6 - - - -
100B ALA* 1.3 56.8 + - - +
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Residues in contact with ALA 100 (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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31B THR* 3.3 5.1 - - - -
32B THR* 2.8 44.4 + - + +
34B ILE* 4.2 9.6 - - + -
48B VAL* 3.8 16.8 - - + -
49B GLU 3.3 14.1 - - - +
50B PHE* 3.5 23.3 - - + -
51B ILE* 5.2 0.4 - - - -
98B GLY 3.7 0.4 + - - -
99B ILE* 1.3 75.4 - - - +
101B ARG* 1.3 63.4 + - - +
102B VAL 3.5 0.2 + - - -
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Residues in contact with ARG 101 (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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30B LYS 3.3 11.4 - - - +
31B THR* 4.3 3.6 - - + +
32B THR* 5.2 0.4 - - - -
48B VAL* 4.2 5.5 - - - +
49B GLU* 2.9 69.9 + - + +
50B PHE 3.5 17.6 + - - +
51B ILE* 4.0 21.9 - - + +
100B ALA* 1.3 71.8 - - - +
102B VAL* 1.3 67.7 + - - +
103B PRO* 3.1 11.3 - - - +
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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