Contacts of the strand formed by residues 102 - 110 (chain A) in PDB entry 1KP5
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 TYR 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A VAL* 4.3 0.5 - - - -
79A GLN 3.9 7.8 + - - -
80A CYS* 3.9 14.0 + - + +
93A PHE* 4.1 17.7 - + + -
94A PHE* 3.7 39.8 - + + -
97A ALA* 4.2 2.7 - - + -
98A MET* 3.5 25.6 - - + -
101A GLY* 1.3 76.3 - - - +
103A VAL* 1.3 65.1 + - - +
104A GLN* 3.6 12.9 + - + -
120A ALA 3.8 0.2 - - - +
121A GLU* 3.6 1.6 - - - -
122A VAL* 3.0 57.4 + - + +
195A ASN* 3.4 25.4 - - - -
196A THR 3.3 19.3 - - - +
197A PRO* 4.0 2.9 - - + -
198A ILE* 3.7 9.9 - - - +
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Residues in contact with VAL 103 (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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102A TYR* 1.3 72.2 - - - +
104A GLN* 1.3 62.4 + - - +
105A GLU* 4.1 26.2 - - + +
119A ARG* 3.7 35.7 - - + +
120A ALA 3.2 9.2 - - - +
121A GLU* 4.0 10.1 - - + -
194A GLN 3.7 1.1 - - - +
195A ASN* 3.2 7.4 - - - +
196A THR* 2.8 44.9 + - - +
197A PRO 5.6 0.9 - - - +
198A ILE* 3.9 19.3 - - + -
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Residues in contact with GLN 104 (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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73A THR 5.3 0.7 - - - +
76A GYS 3.0 34.7 + - - +
79A GLN* 3.9 8.7 - - - +
102A TYR* 3.6 22.3 + - + -
103A VAL* 1.3 73.4 - - - +
105A GLU* 1.3 63.6 + - - +
106A ARG* 3.2 21.7 + - + +
118A THR* 4.0 2.4 + - - +
119A ARG* 3.6 1.2 - - - -
120A ALA* 2.7 47.6 + - + +
122A VAL* 4.9 2.7 - - + -
193A GLN* 3.7 18.4 - - + +
194A GLN 3.6 2.2 - - - -
195A ASN* 2.8 30.9 + - - +
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Residues in contact with GLU 105 (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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103A VAL* 4.1 13.7 - - + +
104A GLN* 1.3 78.5 - - - +
106A ARG* 1.3 66.2 + - - +
118A THR 3.3 10.8 - - - +
119A ARG* 3.7 34.1 + - + +
192A TYR 3.8 0.5 - - - +
193A GLN* 3.4 0.9 - - - +
194A GLN* 2.8 58.6 + - + +
196A THR* 5.7 2.4 + - - +
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Residues in contact with ARG 106 (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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72A THR* 2.9 31.9 + - - -
73A THR* 4.0 7.1 + - - +
76A GYS 2.8 37.0 + - - +
79A GLN* 3.9 1.4 + - - -
104A GLN* 3.2 19.9 + - + +
105A GLU* 1.3 79.8 - - - +
107A THR* 1.3 65.2 + - - +
108A ILE* 4.1 9.9 - - + -
117A LYS* 3.7 3.8 - - - +
118A THR* 2.9 45.5 + - - +
175A PHE* 3.9 12.7 - - - -
191A HIS* 3.9 22.0 - - - -
192A TYR 3.1 9.2 - - - +
193A GLN* 2.6 41.5 + - + +
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Residues in contact with THR 107 (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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106A ARG* 1.3 73.1 + - - +
108A ILE* 1.3 66.9 + - - +
109A SER* 4.7 6.3 - - - +
115A ASN* 5.1 6.1 - - + +
116A TYR 3.5 9.0 - - - +
117A LYS* 3.4 35.4 + - - +
190A ASP 3.3 4.2 - - - +
191A HIS* 3.7 0.5 - - - -
192A TYR* 3.1 46.3 + - + -
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Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A THR 4.7 3.8 - - - +
72A THR* 3.8 10.1 - - - +
73A THR* 4.0 17.0 - - - +
106A ARG* 4.5 14.1 - - + -
107A THR* 1.3 75.7 - - - +
109A SER* 1.3 59.9 + - - +
110A PHE* 3.8 16.5 + - + -
115A ASN* 3.2 5.1 - - - +
116A TYR* 2.7 57.9 + - + -
118A THR* 5.3 2.7 - - + +
189A ALA* 3.8 16.4 - - + -
190A ASP 3.2 2.7 - - - -
191A HIS* 3.4 49.8 - - + +
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Residues in contact with SER 109 (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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107A THR* 3.9 6.6 - - - -
108A ILE* 1.3 72.0 - - - +
110A PHE* 1.3 68.4 + - - +
111A LYS* 3.7 2.1 + - - -
113A ASP 5.2 1.4 + - - -
114A GLY 4.7 0.2 + - - -
115A ASN* 3.9 13.5 - - - +
189A ALA* 3.3 2.4 - - - -
190A ASP* 2.7 53.7 + - - +
192A TYR* 5.0 7.9 - - - -
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Residues in contact with PHE 110 (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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69A THR* 3.9 20.2 - - + -
108A ILE* 3.8 20.9 - - + -
109A SER* 1.3 74.8 + - - +
111A LYS* 1.3 67.0 + - - +
112A ASP 3.3 0.5 + - - -
113A ASP* 3.0 32.2 + - + +
114A GLY 3.0 20.9 + - - +
116A TYR* 3.6 42.0 - + - -
140A PHE* 3.5 22.2 - + + -
146A ILE* 3.9 20.9 - - + -
179A HIS* 4.4 5.6 - + - -
187A GLN* 3.8 13.7 - - + +
188A LEU 3.3 8.1 - - - -
189A ALA* 3.6 22.4 - - + -
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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