Contacts of the strand formed by residues 82 - 88 (chain B) in PDB entry 2Q2L
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 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B HIS* 3.7 5.4 - - + -
62B HIS* 3.1 6.4 + - - -
70B HIS* 3.1 10.1 + - + -
71B GLY 3.2 26.1 + - - +
73B PRO* 3.2 25.5 - - - +
78B ARG* 3.4 12.8 + - + +
79B HIS* 2.7 36.3 + - - +
80B ALA 3.2 4.2 - - - -
81B GLY* 1.3 73.0 - - - +
83B LEU* 1.3 59.8 + - - +
84B GLY 3.4 4.9 - - - +
123B ASP* 5.5 0.2 - - - +
1002B ZN 2.0 35.8 - - - -
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Residues in contact with LEU 83 (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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20B PHE* 5.2 0.7 - - + -
30B VAL* 4.6 5.2 - - + -
44B PHE* 3.0 45.5 + - + +
46B VAL* 3.7 30.7 - - + +
73B PRO* 3.8 12.2 - - + +
78B ARG* 4.2 2.2 - - - +
81B GLY 3.2 4.7 + - - +
82B ASP* 1.3 80.5 - - - +
84B GLY* 1.3 60.9 + - - +
85B ASN 3.7 3.8 + - - +
98B ILE* 3.8 31.0 - - + +
100B ASP* 4.1 28.0 - - + +
103B ILE* 4.1 25.6 - - + -
116B VAL* 4.8 2.5 - - + -
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Residues in contact with GLY 84 (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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43B GLY* 3.4 4.7 - - - -
44B PHE* 2.7 34.4 + - - +
45B HIS* 4.6 1.4 - - - -
72B SER* 5.4 0.2 - - - -
73B PRO* 3.6 19.4 - - - +
82B ASP* 3.4 5.1 - - - +
83B LEU* 1.3 77.4 - - - +
85B ASN* 1.3 61.0 + - - -
123B ASP* 4.0 13.0 + - - +
125B LEU* 4.4 8.1 - - - -
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Residues in contact with ASN 85 (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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41B LEU* 4.1 31.3 - - + +
42B HIS 3.2 18.5 - - - +
43B GLY 3.4 0.8 - - - +
83B LEU 3.7 3.5 + - - +
84B GLY* 1.3 75.3 - - - -
86B ILE* 1.3 68.0 + - - +
87B THR* 4.3 2.0 + - - -
98B ILE* 5.4 1.4 - - - +
122B PRO* 3.4 6.1 - - - +
123B ASP* 2.6 49.9 - - - +
125B LEU* 3.8 12.2 - - - +
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Residues in contact with ILE 86 (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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34B ILE* 4.1 15.9 - - + -
37B LEU* 4.8 6.3 - - + -
40B GLY 3.5 1.9 - - - +
41B LEU* 3.3 5.1 - - - -
42B HIS* 2.9 45.2 + - + +
44B PHE* 3.9 37.0 - - + -
85B ASN* 1.3 80.4 - - - +
87B THR* 1.3 61.6 + - - +
88B VAL* 3.7 1.9 + - + -
94B ALA* 4.6 9.0 - - + -
96B PHE* 3.9 46.9 - - + -
98B ILE* 4.3 6.7 - - + -
118B VAL* 4.5 12.8 - - + -
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Residues in contact with THR 87 (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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40B GLY* 3.5 5.2 - - - +
41B LEU* 3.2 25.0 - - + +
85B ASN 5.1 1.6 + - - -
86B ILE* 1.3 74.2 - - - +
88B VAL* 1.3 68.0 + - - +
89B GLY* 3.9 1.9 + - - +
94B ALA* 3.5 16.5 - - - +
95B CYS 5.1 0.5 + - - -
96B PHE* 6.1 1.2 - - - +
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Residues in contact with VAL 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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37B LEU* 3.3 50.9 - - + +
38B LYS 3.4 14.4 - - - +
39B PRO* 3.6 0.9 - - + +
40B GLY* 2.5 37.9 + - - +
42B HIS* 3.4 22.9 - - + +
86B ILE* 3.7 4.5 + - + +
87B THR* 1.3 78.2 - - - +
89B GLY* 1.3 67.3 + - - +
92B GLY 3.5 18.6 - - - +
93B THR 3.6 3.1 - - - +
94B ALA* 4.1 9.6 - - + -
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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