Contacts of the strand formed by residues 81 - 90 (chain B) in PDB entry 2CGA
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 GLN 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B VAL 3.5 1.7 - - - +
67B VAL* 3.4 5.3 - - - +
68B ALA* 2.7 49.7 + - + +
79B LYS* 5.3 2.0 - - + +
80B ILE* 1.3 82.0 - - - +
82B LYS* 1.3 62.6 + - - +
83B LEU* 4.0 13.4 - - + +
111B ALA 4.9 0.2 - - - +
112B ALA* 3.7 7.8 - - - +
113B SER* 2.7 54.7 + - - +
115B SER* 5.1 1.8 + - - -
118B VAL* 3.6 22.2 - - + +
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Residues in contact with LYS 82 (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 GLN* 3.6 22.0 + - - -
38B GLY* 6.4 0.2 - - - -
65B VAL* 4.0 17.3 - - + +
66B VAL 3.6 2.9 - - - -
67B VAL* 4.3 13.3 - - + +
80B ILE* 4.3 20.1 - - + +
81B GLN* 1.3 74.1 - - - +
83B LEU* 1.3 64.6 + - - +
84B LYS* 4.1 3.2 + - - +
110B THR* 4.7 3.5 - - - +
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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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46B LEU* 5.2 2.0 - - + -
65B VAL* 3.5 7.4 - - - +
66B VAL* 2.7 63.2 + - + +
68B ALA* 4.4 12.6 - - + -
81B GLN* 4.2 20.4 - - + +
82B LYS* 1.3 79.2 - - - +
84B LYS* 1.3 62.7 + - - +
85B ILE 3.9 0.2 + - - -
108B LEU* 3.9 24.2 - - + -
110B THR* 3.5 36.1 - - + +
111B ALA 4.3 0.9 - - - +
112B ALA* 4.1 25.1 - - + +
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Residues in contact with LYS 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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64B ASP 4.8 5.8 - - - +
65B VAL* 5.1 5.2 - - + +
82B LYS 4.1 2.4 + - - +
83B LEU* 1.3 75.7 - - - +
85B ILE* 1.3 57.6 - - - +
108B LEU* 3.4 7.4 - - - +
109B SER* 2.5 47.5 + - - +
110B THR* 3.6 12.2 + - + +
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Residues in contact with ILE 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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33B LEU* 5.5 0.7 - - + -
60B VAL* 3.6 28.5 - - + -
61B THR 3.7 4.9 - - - +
62B THR* 4.0 22.3 + - + +
64B ASP* 3.4 31.2 + - + +
65B VAL 4.2 0.4 - - - +
66B VAL* 3.9 24.0 - - + -
83B LEU 4.4 1.1 - - - +
84B LYS* 1.3 76.5 - - - +
86B ALA* 1.3 62.6 + - - +
87B LYS 3.9 15.5 - - - +
88B VAL* 4.0 18.4 - - + -
106B LEU* 4.1 16.6 - - + -
107B LYS 3.7 11.2 - - - +
108B LEU* 4.2 4.3 - - + +
109B SER* 3.9 3.2 - - - -
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Residues in contact with ALA 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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62B THR* 3.5 13.7 - - - +
85B ILE* 1.3 74.1 - - - +
87B LYS* 1.3 72.1 + - + +
107B LYS* 2.8 22.3 + - + +
108B LEU 3.9 3.4 - - - +
109B SER* 3.4 26.9 - - - +
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Residues in contact with LYS 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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62B THR* 4.3 4.5 - - - -
85B ILE* 3.5 2.2 - - - +
86B ALA* 1.3 90.6 - - + +
88B VAL* 1.3 65.0 + - - +
89B PHE* 3.3 41.8 - - + -
106B LEU* 3.6 2.3 - - - -
107B LYS* 2.9 34.8 + - + +
245B ASN* 5.8 0.6 + - - +
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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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60B VAL* 3.4 28.7 - - + +
61B THR* 3.9 21.5 - - - +
62B THR* 4.2 7.7 - - + +
85B ILE* 4.0 7.4 - - + -
87B LYS* 1.3 75.6 + - - +
89B PHE* 1.3 64.8 + - - +
90B LYS* 4.0 6.0 + - + +
104B THR* 3.5 27.1 - - + -
105B LEU 3.6 3.1 - - - -
106B LEU* 3.6 15.3 - - + -
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Residues in contact with PHE 89 (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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51B TRP* 3.8 26.5 - + - -
87B LYS* 3.3 57.4 - - + -
88B VAL* 1.3 74.0 - - - +
90B LYS* 1.3 63.2 + - - +
104B THR* 3.2 5.7 - - - -
105B LEU* 2.8 48.2 + - + +
107B LYS* 4.3 3.4 - - + -
237B TRP* 3.5 8.3 - - + -
241B THR* 4.0 24.0 - - + -
245B ASN* 3.7 34.5 - - + -
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Residues in contact with LYS 90 (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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56B ALA* 4.1 13.7 - - + +
88B VAL* 3.9 7.7 + - + +
89B PHE* 1.3 73.1 - - - +
91B ASN* 1.3 75.7 + - - +
92B SER* 3.3 6.9 + - - +
94B TYR* 3.7 32.5 + - + +
104B THR* 3.6 18.1 - - + +
237B TRP* 3.9 5.1 + - - -
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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