Contacts of the strand formed by residues 80 - 85 (chain A) in PDB entry 4CNI
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 SER 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A SER* 5.9 1.3 - - - -
22A CYS 3.1 11.6 + - - -
23A ALA* 4.5 6.9 - - - +
29A PHE* 3.5 9.2 - - - -
74A ARG* 3.3 3.1 - - - -
75A ASP 2.8 34.6 + - - -
78A LYS* 2.9 22.2 + - - +
79A ASN* 1.3 75.9 + - - +
81A LEU* 1.3 58.8 + - - +
82A TYR* 3.5 30.7 + - - -
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A SER* 3.4 4.5 - - - -
22A CYS* 2.8 40.2 + - + +
29A PHE* 3.9 8.2 - - + -
34A MET* 3.7 29.6 - - + -
35A ASN 3.9 10.1 - - - +
36A TRP* 3.4 21.7 - - + +
51A MET* 3.9 14.1 - - + -
72A ILE* 3.7 25.1 - - + -
73A SER 3.3 18.4 - - - +
74A ARG* 4.4 1.6 - - + +
80A SER* 1.3 73.9 - - - +
82A TYR* 1.3 65.8 + - - +
98A CYS* 3.7 22.9 - - - -
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Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG* 3.6 46.1 + - + +
20A LEU 3.2 7.2 - - - +
21A SER* 3.3 30.1 - - - -
36A TRP* 3.7 4.5 - - - +
71A THR 4.4 0.2 - - - -
72A ILE* 3.3 10.6 - - - +
73A SER* 2.7 61.4 + - - +
74A ARG* 4.3 2.0 - - - -
75A ASP* 3.8 32.4 + - + +
78A LYS* 4.2 12.8 + - - +
80A SER* 3.5 25.5 + - - -
81A LEU* 1.3 77.4 - - - +
83A LEU* 1.3 61.3 + - - +
84A GLN* 4.1 1.8 - - + +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU 3.5 4.2 - - - +
19A ARG* 4.5 1.6 - - - -
20A LEU* 3.0 39.4 + - + +
36A TRP* 3.5 42.6 - - + +
48A VAL* 4.3 10.1 - - + -
49A ALA* 4.5 3.6 - - + -
70A PHE* 4.0 31.0 - - + -
71A THR 3.6 13.2 - - - +
72A ILE* 4.4 6.7 - - + +
82A TYR* 1.3 73.5 - - - +
84A GLN* 1.3 59.9 + - - +
85A MET* 3.6 16.1 + - + +
96A TYR* 3.9 27.8 - - + -
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Residues in contact with GLN 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER* 3.8 10.7 - - - -
18A LEU 3.6 13.4 + - - -
19A ARG* 3.5 27.5 + - + +
69A ARG 4.1 0.9 - - - +
70A PHE* 3.3 4.9 - - - +
71A THR* 2.7 54.0 + - - +
82A TYR* 4.1 1.8 - - + +
83A LEU* 1.3 71.3 - - - +
85A MET* 1.3 77.9 + - - +
86A ASN* 3.5 25.2 + - - +
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Residues in contact with MET 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER* 3.1 7.1 - - - -
18A LEU* 2.8 40.8 + - - +
20A LEU* 3.9 31.6 - - - -
69A ARG 4.1 2.5 - - - -
70A PHE* 3.7 23.8 - - + -
83A LEU* 4.0 8.1 - - + +
84A GLN* 1.3 76.8 + - - +
86A ASN* 1.3 65.3 + - - +
88A LEU* 3.3 39.5 - - + -
92A ASP* 4.6 1.6 - - + -
96A TYR* 3.3 38.6 - - + +
116A VAL* 4.1 16.4 - - + -
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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