Contacts of the strand formed by residues 76 - 86 (chain B) in PDB entry 3CFV
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 ASN 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B THR* 2.9 32.5 - - + +
71B THR* 3.0 34.9 + - - +
74B GLU 3.3 9.1 + - - -
75B GLN* 1.3 83.1 + - - +
77B HIS* 1.3 68.6 + - - +
122B HIS* 3.0 30.4 + - + +
124B GLY* 3.0 44.0 - - - +
125B GLU* 3.4 2.3 - - - -
126B VAL 5.3 0.2 - - - +
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Residues in contact with HIS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TRP* 6.1 1.4 - - - -
68B GLY* 3.6 2.8 - - - -
69B THR* 3.2 38.9 + - - +
75B GLN* 3.8 30.2 + - + +
76B ASN* 1.3 79.8 - - - +
78B LEU* 1.3 60.4 + - - +
79B VAL* 3.9 3.1 - - + +
119B LYS* 3.7 45.5 - - + -
120B ILE 3.2 15.3 - - - +
121B ASN* 3.7 22.0 + - - -
122B HIS* 4.0 5.8 - - - -
126B VAL* 3.7 2.5 - - - +
160B PRO* 4.2 13.6 - - + +
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Residues in contact with LEU 78 (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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66B VAL* 4.1 9.6 - - + -
67B LEU 3.5 17.9 - - - +
77B HIS* 1.3 71.8 - - - +
79B VAL* 1.3 61.0 + - - +
80B VAL* 5.9 1.6 - - + -
118B ILE* 4.1 1.2 - - - +
119B LYS* 3.6 1.4 - - - -
120B ILE* 2.8 54.0 + - + +
122B HIS* 3.9 15.8 - - + +
126B VAL* 4.4 5.8 - - + -
129B ALA* 3.6 26.9 - - + -
139B ILE* 4.2 20.4 - - + -
141B THR* 3.9 10.8 - - + -
151B PHE* 3.9 34.5 - - + -
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Residues in contact with VAL 79 (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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66B VAL* 3.5 3.8 - - - +
67B LEU* 2.6 65.1 + - + +
68B GLY* 4.2 6.3 - - - +
69B THR* 4.8 3.8 - - - +
77B HIS* 3.9 17.3 - - + +
78B LEU* 1.3 78.5 - - - +
80B VAL* 1.3 73.7 + - - +
81B ALA 3.9 3.1 - - - +
116B CYS* 5.0 1.1 - - - -
118B ILE 3.5 8.5 - - - +
119B LYS* 4.5 13.9 - - + -
412B ARS 3.9 24.2 - - - -
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 3.7 24.7 - - + -
64B TRP* 4.1 11.7 - - + -
65B LEU 3.1 11.2 - - - +
66B VAL* 4.7 4.0 - - + -
78B LEU* 5.9 2.2 - - + -
79B VAL* 1.3 77.5 - - - +
81B ALA* 1.3 60.4 + - - +
116B CYS* 3.8 2.3 - - - -
117B GLU* 2.9 39.0 + - + -
118B ILE* 3.0 34.9 + - + +
120B ILE* 6.4 0.2 - - + -
139B ILE* 4.4 14.4 - - + -
153B TYR* 4.3 22.2 - - + -
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Residues in contact with ALA 81 (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 TRP* 3.2 10.8 - - - +
65B LEU* 2.8 37.7 + - + +
67B LEU* 3.8 24.9 - - + -
79B VAL* 3.9 2.2 - - - +
80B VAL* 1.3 72.6 - - - +
82B ARG* 1.3 60.5 + - - +
83B VAL* 4.1 2.4 + - + +
114B ILE* 3.9 19.5 - - + -
115B GLU 3.2 13.0 - - - +
116B CYS* 4.5 0.2 - - - +
412B ARS 4.1 7.0 - - - -
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Residues in contact with ARG 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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62B LEU* 4.3 21.3 - - + -
63B HIS 3.5 4.5 - - - +
64B TRP* 3.5 30.7 - - + +
80B VAL 4.1 0.8 + - - -
81B ALA* 1.3 72.8 - - - +
83B VAL* 1.3 65.6 + - - +
84B HIS* 4.7 5.5 + - + -
113B LYS 3.8 0.3 - - - +
114B ILE* 3.4 2.3 - - - -
115B GLU* 2.7 83.1 + - - +
116B CYS 4.2 5.1 + - - -
117B GLU* 3.0 42.9 + - + +
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Residues in contact with VAL 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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35B MSE 5.9 1.3 - - + -
48B TRP* 4.1 10.8 - - + -
61B ALA 3.3 3.3 - - - +
62B LEU* 3.5 2.8 - - - -
63B HIS* 2.8 60.7 + - + +
65B LEU* 3.7 21.5 - - + -
81B ALA 4.7 0.9 - - - +
82B ARG* 1.3 83.6 - - - +
84B HIS* 1.3 65.3 + - - +
85B ILE* 4.1 14.1 - - + -
113B LYS 3.1 8.1 - - - +
114B ILE* 3.8 22.7 - - + -
400B ILE* 4.1 14.6 - - + -
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Residues in contact with HIS 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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35B MSE 3.6 7.1 - - - +
60B TYR* 3.5 46.6 + + + -
61B ALA 3.4 4.5 - - - -
62B LEU* 3.3 25.4 - - + +
82B ARG* 4.7 7.7 + - + -
83B VAL* 1.3 74.0 - - - +
85B ILE* 1.3 60.3 + - - +
86B PRO* 3.6 0.6 - - + +
112B GLY* 3.5 24.1 - - - -
113B LYS* 2.8 56.4 + - + +
115B GLU* 3.9 14.1 + - - -
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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* 3.8 20.9 - - + -
35B MSE 4.6 9.2 - - - -
48B TRP* 4.1 21.5 - - + -
60B TYR* 3.9 0.9 - - - -
61B ALA* 2.7 39.6 + - - +
63B HIS* 3.5 40.8 - - + +
83B VAL* 4.1 11.0 - - + -
84B HIS* 1.3 75.0 - - - +
86B PRO* 1.3 76.3 - - + +
87B ASN* 3.5 0.5 + - - -
382B ASN* 4.3 4.0 - - - +
385B GLU* 5.6 7.2 - - + -
388B VAL* 4.5 8.3 - - + -
400B ILE* 4.2 10.3 - - + -
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Residues in contact with PRO 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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33B LEU* 4.6 12.5 - - + +
35B MSE 4.1 13.0 - - - -
59B ASP 3.9 2.7 - - - +
60B TYR* 3.9 11.2 - - + -
84B HIS 3.6 8.0 - - - +
85B ILE* 1.3 100.4 - - + +
87B ASN* 1.3 68.5 + - - +
88B ASP* 3.6 2.3 + - - -
111B THR* 4.7 9.9 - - - -
112B GLY* 4.1 20.2 - - - +
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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