Contacts of the strand formed by residues 83 - 88 (chain B) in PDB entry 3KJR
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 ARG 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 4.5 5.5 + - - +
42B ARG* 3.9 28.2 - - - +
45B THR* 3.0 46.7 + - - +
46B THR* 3.5 11.9 - - + +
60B GLN* 3.9 10.5 - - - +
61B ASN* 3.6 14.1 - - + +
63B VAL* 4.0 15.7 - - + +
80B LEU* 3.3 41.9 + - + +
81B LYS* 3.2 26.8 + - - +
82B ASN* 1.3 82.3 - - - +
84B ILE* 1.3 62.4 + - - +
85B ASN* 2.9 20.8 + - - +
123B LEU* 5.4 0.6 - - - +
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Residues in contact with ILE 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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60B GLN* 3.9 24.2 + - + +
61B ASN 2.8 14.9 + - - +
62B VAL* 3.5 19.1 - - + +
63B VAL* 2.7 32.7 + - - +
83B ARG* 1.3 71.4 - - - +
85B ASN* 1.3 59.5 + - - +
86B VAL* 3.8 10.3 + - + -
99B LEU* 3.9 27.6 - - + -
111B LEU* 5.0 0.4 - - + -
115B VAL* 4.0 15.5 - - + -
116B PRO 3.9 22.4 - - - +
117B HIS* 4.3 3.1 - - + -
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Residues in contact with ASN 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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63B VAL* 3.6 5.9 - - - +
65B PHE* 4.0 14.8 - - + -
78B LEU* 3.2 10.6 - - - +
79B PRO* 3.4 6.2 - - + +
80B LEU* 2.7 49.6 + - - +
83B ARG* 2.9 22.8 + - - +
84B ILE* 1.3 75.9 + - - +
86B VAL* 1.3 61.2 + - - +
87B ILE* 6.0 0.4 - - + -
97B GLY 5.0 3.6 + - - +
98B CYS* 3.4 27.1 - - - -
99B LEU* 3.1 22.3 + - - +
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Residues in contact with VAL 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 VAL* 3.7 22.9 - - + -
63B VAL 2.8 13.1 + - - +
64B ILE* 3.3 17.4 - - + -
65B PHE* 2.9 28.4 + - - -
84B ILE* 4.1 7.0 - - + -
85B ASN* 1.3 79.1 - - - +
87B ILE* 1.3 63.5 + - - +
88B LEU* 4.0 14.4 - - + -
99B LEU* 3.2 25.1 - - + +
101B TYR* 3.7 22.4 - - + -
107B ALA* 5.0 0.2 - - + -
111B LEU* 4.0 14.8 - - + -
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Residues in contact with ILE 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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65B PHE* 3.5 11.7 - - + +
67B ARG* 3.8 20.4 - - + -
70B TYR* 3.7 32.3 - - + -
78B LEU* 6.3 0.7 - - + -
85B ASN* 6.0 0.2 - - + -
86B VAL* 1.3 76.0 - - - +
88B LEU* 1.3 69.8 + - - +
92B VAL* 4.2 16.2 - - + -
95B VAL* 4.1 31.0 - - + -
98B CYS* 4.1 24.0 - - + -
99B LEU 2.9 6.9 + - - +
100B VAL* 3.3 10.4 - - + +
101B TYR 3.2 22.5 + - - -
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Residues in contact with LEU 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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64B ILE* 4.0 7.9 - - + -
65B PHE 2.9 16.2 + - - +
66B GLY* 3.8 0.8 - - - -
67B ARG* 3.1 22.3 + - - +
86B VAL* 4.0 13.0 - - + -
87B ILE* 1.3 83.8 - - - +
89B SER* 1.3 65.9 + - - +
101B TYR* 3.5 16.2 - - + +
102B GLU 4.8 2.9 - - - +
103B ASP 4.6 1.6 - - - +
104B LEU* 3.9 29.8 - - + +
107B ALA* 3.8 24.9 - - + -
128B LEU* 3.7 29.8 - - + -
512B NAP 3.4 23.5 - - + +
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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