Contacts of the strand formed by residues 83 - 89 (chain A) in PDB entry 2KJD
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 GLU 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A THR* 4.7 14.1 - - + +
15A MET 3.1 14.6 - - - +
16A LYS* 3.4 19.9 + - + +
22A TYR* 3.1 6.5 + - - -
61A ASN* 4.2 1.2 - - - +
80A GLY* 3.3 26.8 + - - +
82A ASP* 1.3 99.4 - - - +
84A THR* 1.3 62.6 + - - +
85A LYS* 4.8 12.8 - - - +
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Residues in contact with THR 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 CYS 3.6 0.3 - - - +
14A THR* 3.8 0.7 - - - +
15A MET* 2.8 57.9 + - + +
22A TYR* 4.0 12.8 - - + -
24A PHE* 5.5 0.4 - - + -
60A VAL* 3.5 15.1 - - - +
61A ASN* 2.8 25.2 + - - -
77A ILE* 3.8 28.8 - - + +
83A GLU* 1.3 75.9 - - - +
85A LYS* 1.3 63.9 + - - +
86A LEU* 4.2 10.3 - - + +
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Residues in contact with LYS 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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12A LEU* 4.1 25.6 - - + +
13A CYS 3.1 6.1 - - - +
14A THR* 3.9 32.8 - - + +
59A GLU 3.7 0.9 - - - +
60A VAL* 3.2 5.2 - - - -
61A ASN* 2.7 48.1 + - - +
62A GLY 4.5 0.8 + - - +
83A GLU* 4.8 12.3 - - - +
84A THR* 1.3 76.1 + - - +
86A LEU* 1.3 62.9 + - - +
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Residues in contact with LEU 86 (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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12A LEU* 3.6 3.0 - - - -
13A CYS* 2.6 52.0 + - + +
15A MET* 3.9 24.5 - - + -
24A PHE* 4.2 21.5 - - + -
51A LEU* 4.1 11.4 - - + -
57A ILE* 4.0 35.0 - - + -
59A GLU 3.4 0.4 - - - -
60A VAL* 3.6 33.7 - - + -
77A ILE* 4.3 11.2 - - + -
84A THR* 4.1 12.1 - - + +
85A LYS* 1.3 73.7 - - - +
87A LEU* 1.3 60.0 + - - +
88A VAL* 4.0 0.9 - - + -
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Residues in contact with LEU 87 (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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10A PRO* 3.7 14.4 - - + -
11A ARG 3.4 16.4 - - - +
12A LEU* 4.2 11.0 - - + +
56A ARG 3.5 0.7 - - - +
57A ILE* 3.6 1.0 - - - -
58A VAL* 2.7 41.4 + - + +
59A GLU* 2.7 55.8 + - + +
86A LEU* 1.3 73.1 - - - +
88A VAL* 1.3 59.8 + - - +
104A PRO 3.9 7.2 - - - +
105A SER* 3.5 22.0 - - - +
106A GLN* 4.0 1.1 - - + +
109A LEU* 3.4 31.2 - - + -
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Residues in contact with VAL 88 (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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10A PRO* 3.4 6.4 - - - +
11A ARG* 3.2 50.6 + - + +
13A CYS* 3.7 13.0 - - - -
37A ILE* 4.7 1.3 - - + -
50A GLY 4.0 5.8 - - - +
51A LEU* 3.7 26.0 - - + -
52A ARG 4.9 0.4 - - - +
55A ASP* 3.7 25.4 - - + +
56A ARG 3.1 15.0 - - - +
57A ILE* 3.8 14.6 - - + -
86A LEU* 4.7 0.7 - - + -
87A LEU* 1.3 80.2 - - - +
89A VAL* 1.3 64.1 + - - +
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Residues in contact with VAL 89 (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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10A PRO* 3.6 21.1 - - + -
54A GLN 4.7 0.3 - - - +
55A ASP* 3.3 23.8 - - - -
56A ARG* 3.5 18.5 + - + +
58A VAL* 4.1 12.1 - - + -
88A VAL* 1.3 80.2 - - - +
90A ASP* 1.3 68.5 + - - +
93A THR* 4.0 17.7 - - + -
94A ASP* 3.7 30.1 - - + +
97A PHE* 4.0 1.3 - - + -
104A PRO* 3.6 25.1 - - + -
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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