Contacts of the strand formed by residues 101 - 108 (chain B) in PDB entry 1KCX
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 THR 101 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLY 3.5 10.1 - - - +
71B ASP* 4.0 12.1 - - + +
96B ALA* 2.9 44.4 + - + +
97B LEU* 3.3 11.5 + - - +
99B GLY 3.4 2.0 + - - -
100B GLY* 1.3 76.6 - - - +
102B THR* 1.3 60.1 + - - +
103B MET 3.3 27.6 - - - +
104B ILE* 4.4 0.9 - - + -
133B CYS* 5.0 0.7 - - - -
358B ILE 4.3 8.4 + - - +
361B ARG* 3.0 30.0 + - - +
362B MET* 4.1 6.6 + - - +
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Residues in contact with THR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLY* 3.0 33.0 + - - -
69B GLY 3.1 4.8 + - - -
97B LEU* 4.0 11.7 - - + -
100B GLY 3.7 2.2 + - - +
101B THR* 1.3 75.5 - - - +
103B MET* 1.3 62.6 + - - +
133B CYS* 3.5 19.1 - - - +
134B ASP* 4.0 5.9 + - - +
408B ASP* 3.5 27.2 + - + +
410B VAL* 4.7 1.8 - - + -
446B VAL* 4.0 20.2 - - + -
447B ILE 3.7 23.3 - - - +
448B SER* 4.6 4.1 + - - -
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Residues in contact with MET 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLY 3.2 6.8 + - - +
70B ILE* 3.4 18.5 - - + -
71B ASP 2.8 25.4 + - - -
101B THR* 3.3 7.5 - - - +
102B THR* 1.3 81.0 - - - +
104B ILE* 1.3 65.6 + - - +
105B ILE* 5.0 1.1 - - + -
133B CYS* 4.4 1.9 - - - -
134B ASP* 3.3 24.2 - - + +
135B TYR 3.7 10.5 - - - -
136B SER* 3.4 30.5 - - - +
394B LEU* 4.0 23.3 - - + -
398B LYS* 4.0 26.9 - - + -
408B ASP* 5.2 1.1 - - - +
469B ILE* 3.6 25.1 - - + -
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Residues in contact with ILE 104 (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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71B ASP* 3.5 10.5 - - + -
74B THR* 3.9 20.6 - - + +
76B LEU* 3.8 20.2 - - + -
89B PHE* 4.1 14.8 - - + -
93B THR* 3.8 24.9 - - + -
96B ALA* 4.5 5.4 - - + -
101B THR* 4.4 6.7 - - + -
103B MET* 1.3 83.3 - - - +
105B ILE* 1.3 66.6 + - - +
106B ASP* 4.5 2.0 - - + +
133B CYS* 4.7 6.1 - - - -
134B ASP 3.6 3.0 + - - +
135B TYR* 3.3 18.9 - - + -
136B SER 3.0 21.5 + - - -
358B ILE* 4.1 23.1 - - + -
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Residues in contact with ILE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 4.4 13.5 - - + -
71B ASP 3.1 9.6 + - - +
72B VAL* 3.5 14.7 - - - +
74B THR* 3.5 17.4 + - - -
103B MET* 5.0 2.9 - - + -
104B ILE* 1.3 78.7 - - - +
106B ASP* 1.3 58.7 + - - +
136B SER* 3.3 27.6 - - - +
138B HIS* 3.2 48.0 + - + +
392B PHE* 3.8 34.1 - - + -
394B LEU* 4.4 13.9 - - + -
471B ARG* 4.1 9.2 - - - +
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Residues in contact with ASP 106 (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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74B THR* 2.8 23.6 + - - +
76B LEU* 2.8 34.4 + - - +
77B GLN 4.4 0.3 + - - -
89B PHE* 3.6 27.6 - - + -
104B ILE* 3.9 4.3 - - + -
105B ILE* 1.3 74.0 - - - +
107B HIS* 1.3 66.5 + - - +
108B VAL 3.7 0.3 + - - -
123B TRP* 3.3 28.6 + - - -
135B TYR* 6.1 0.2 - - + -
136B SER 3.1 6.8 + - - +
137B LEU* 3.4 13.9 - - + +
138B HIS* 2.7 32.7 + - - +
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Residues in contact with HIS 107 (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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73B ASN* 3.5 22.9 + - - -
74B THR 2.9 24.7 + - - +
75B TYR* 3.2 45.7 + + + -
77B GLN 5.6 0.5 + - - -
78B LYS 5.7 0.2 + - - -
106B ASP* 1.3 75.8 - - - +
108B VAL* 1.3 61.7 + - - +
109B VAL* 3.6 7.4 + - - +
123B TRP* 3.4 13.2 + - - -
138B HIS* 3.3 35.6 + + + +
140B ASP* 2.6 23.3 + - - +
165B GLN* 3.0 28.2 + - + -
196B LEU* 3.9 13.3 - - + +
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B HIS* 1.3 71.4 - - - +
109B VAL* 1.3 61.1 + - - +
110B PRO* 3.2 8.9 - - + +
116B LEU 5.2 0.9 - - - +
119B SER* 3.6 28.5 - - - +
120B PHE* 3.9 11.7 - - + +
123B TRP* 3.4 48.9 - - + -
137B LEU* 4.3 19.1 - - + -
138B HIS 3.0 19.2 + - - +
139B VAL* 4.4 8.3 - - + -
140B ASP* 3.0 25.8 + - - +
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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