Contacts of the strand formed by residues 80 - 85 (chain A) in PDB entry 3KCN
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 VAL 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A SER 2.9 17.0 + - - +
53A VAL* 3.5 6.1 - - + +
54A ILE 3.0 22.7 + - - +
78A ASN 4.0 4.5 - - - +
79A SER* 1.3 75.4 - - - +
81A TYR* 1.3 60.4 - - - +
82A LEU* 3.8 5.7 + - + -
103A PHE* 3.5 42.2 - - + -
122A GLY* 3.5 31.9 - - - +
125A GLN* 3.7 18.4 - - + -
126A TYR* 3.8 11.9 - - - +
129A VAL* 5.6 1.6 - - + -
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Residues in contact with TYR 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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54A ILE* 3.3 36.5 - - + +
56A VAL* 5.1 0.2 - - + -
69A ILE* 3.7 39.3 - - + -
72A ALA* 3.1 39.8 + - + +
73A ARG* 3.4 29.2 - - + -
76A SER* 2.9 23.3 + - - -
77A PRO 5.0 0.4 - - - -
79A SER* 3.5 30.7 - - - -
80A VAL* 1.3 75.2 - - - +
82A LEU* 1.3 63.4 + - - +
101A GLN 3.8 10.5 + - - +
102A VAL* 3.7 4.4 - - - -
103A PHE* 2.9 29.4 + - - +
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Residues in contact with LEU 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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53A VAL* 3.8 20.9 - - + -
54A ILE 3.0 5.7 + - - +
55A MSE 3.1 20.6 - - + -
56A VAL 3.0 23.6 + - - -
69A ILE* 4.4 2.8 - - - +
80A VAL* 3.9 24.0 - - + +
81A TYR* 1.3 80.9 - - - +
83A MSE 1.3 63.9 + - - +
103A PHE* 4.1 4.7 - - + -
104A ARG* 3.2 30.1 - - + +
106A LEU* 4.7 7.9 - - + -
118A ALA* 3.7 39.9 - - + +
119A ILE* 3.9 8.7 - - + +
122A GLY* 5.0 0.2 - - - -
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Residues in contact with MSE 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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56A VAL 3.3 6.7 - - - +
57A ASP 3.7 2.9 - - - -
58A MSE 3.1 63.5 - - + +
65A GLY* 3.4 27.8 - - - +
66A THR* 3.7 10.3 - - - +
69A ILE* 3.4 25.4 - - + -
82A LEU* 1.3 73.2 - - - +
84A LEU* 1.3 65.1 + - - +
85A THR* 4.9 2.0 - - - -
93A ALA* 5.4 6.1 - - - -
96A ALA* 5.5 0.9 - - - -
102A VAL* 4.0 17.3 - - + -
104A ARG 3.1 8.1 + - - -
105A PHE* 3.3 15.2 - - + +
106A LEU* 2.8 28.7 + - - +
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Residues in contact with LEU 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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13A ASP* 4.6 3.1 - - + +
18A LEU* 4.6 17.5 - - + -
22A LEU* 5.0 1.6 - - + -
55A MSE 3.3 42.4 - - + +
56A VAL 2.9 14.9 + - - +
57A ASP* 3.7 18.7 - - + +
58A MSE 3.0 30.3 + - - +
83A MSE 1.3 73.4 - - - +
85A THR* 1.3 59.3 + - - +
106A LEU* 3.5 20.0 - - + +
108A LYS* 3.9 15.3 + - + +
110A CYS* 4.0 26.0 - - + -
115A ILE* 5.0 6.3 - - + -
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Residues in contact with THR 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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58A MSE 4.2 8.5 - - - +
83A MSE 4.4 4.7 - - - -
84A LEU* 1.3 76.4 - - - +
86A GLY* 1.3 61.2 + - - +
89A ASP* 3.2 25.6 + - - +
90A LEU* 5.6 1.6 - - - -
93A ALA* 3.8 17.2 - - + +
105A PHE* 3.5 38.1 - - + -
106A LEU 2.9 17.4 + - - +
107A ASN* 3.3 16.0 - - - +
108A LYS* 2.9 27.9 + - - +
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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