Contacts of the helix formed by residues 96 - 103 (chain B) in PDB entry 1KNY
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 TRP 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ALA 4.6 3.2 + - - -
91B GLN 3.6 11.9 - - - +
92B VAL* 3.8 15.1 - - + +
93B GLU 2.9 26.7 + - - +
95B ASP* 1.3 78.4 + - - +
97B PRO* 1.4 77.9 - - + +
99B THR* 2.9 7.6 - - - -
100B HIS* 2.6 72.7 + + + +
104B PHE* 4.4 13.9 - + - -
123B ALA 4.9 8.4 + - - -
126B VAL* 5.2 1.2 - - - +
131B PHE* 3.2 43.4 - + - -
178B GLY 4.3 2.5 - - - -
179B LEU* 4.3 3.4 - - + -
182B ARG* 3.7 23.1 - - + -
183B ILE 2.9 23.6 - - - -
184B CYS* 3.8 14.2 - - - -
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Residues in contact with PRO 97 (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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94B SER 4.1 4.3 - - - +
95B ASP* 3.4 3.6 - - - -
96B TRP* 1.4 98.8 - - + +
98B LEU* 1.3 61.4 + - - +
175B MET* 3.7 17.5 - - - +
178B GLY* 4.0 1.8 - - - -
179B LEU* 3.7 34.8 - - + +
183B ILE 3.3 21.8 - - - +
184B CYS* 3.2 4.6 - - - +
185B TYR* 2.6 53.6 + - + -
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Residues in contact with LEU 98 (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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95B ASP* 2.9 11.0 + - + +
97B PRO* 1.3 79.7 - - - +
99B THR* 1.3 66.8 + - + +
101B GLY 4.2 1.6 + - - -
171B MET* 5.5 9.2 - - + -
175B MET* 3.8 24.2 - - + +
185B TYR* 4.1 11.2 - - + +
187B THR* 4.9 2.0 - - - -
188B SER* 4.1 20.9 - - - +
191B VAL* 3.8 20.2 - - + -
557B APC 3.6 53.3 + - + +
559B KAN 4.4 18.6 - - - +
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Residues in contact with THR 99 (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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88B TYR* 4.6 7.9 - - - +
95B ASP* 2.3 47.4 + - - +
96B TRP* 2.9 15.9 + - - -
98B LEU* 1.3 81.1 - - + +
100B HIS* 1.3 74.1 + - - -
101B GLY 3.1 4.3 + - - -
102B GLN* 3.4 26.6 + - - +
557B APC 3.3 36.2 - - + +
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Residues in contact with HIS 100 (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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88B TYR* 2.8 50.7 + + - -
89B ALA 3.1 23.1 + - - -
91B GLN 3.2 19.5 + - - -
96B TRP* 2.6 52.9 + + + +
99B THR* 1.3 81.3 + - - +
101B GLY* 1.3 60.5 + - - +
102B GLN 2.9 7.7 + - - -
103B PHE* 2.9 24.2 + + - +
104B PHE* 2.7 26.5 - - + -
123B ALA* 5.2 0.9 - - + -
184B CYS* 3.5 2.7 - - - -
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Residues in contact with GLY 101 (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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98B LEU 4.2 2.8 + - - -
99B THR 3.1 3.6 + - - -
100B HIS* 1.3 76.1 - - - +
102B GLN* 1.3 56.9 + - - +
104B PHE* 2.8 29.4 + - - +
105B SER* 3.0 17.4 + - - -
184B CYS* 3.3 20.3 - - - +
185B TYR 4.5 8.1 - - - -
186B THR 5.6 0.7 - - - -
557B APC 4.2 8.7 - - - -
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Residues in contact with GLN 102 (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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37B TYR* 3.9 39.4 + - + +
54B MET* 4.4 10.8 - - + +
78B ASN* 4.6 0.5 - - - +
80B TYR* 4.0 14.4 + - - -
88B TYR* 4.0 19.9 + - - -
99B THR 3.4 16.9 + - - +
100B HIS 2.9 0.2 + - - -
101B GLY* 1.3 78.3 - - - +
103B PHE* 1.3 87.4 + - + +
104B PHE 3.1 5.0 + - - -
105B SER* 3.3 14.3 + - - -
106B ILE* 3.1 23.0 - - - +
557B APC 3.7 25.0 + - + -
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Residues in contact with PHE 103 (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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54B MET* 4.7 6.1 - - - -
80B TYR* 5.3 1.1 - - - -
85B LEU* 3.2 25.8 - - + -
88B TYR* 3.2 42.2 - + - -
89B ALA* 4.2 8.5 - - + -
100B HIS* 2.9 44.4 + + - +
102B GLN* 1.3 100.4 - - + +
104B PHE* 1.3 60.5 + - - +
106B ILE* 3.6 16.1 - - + +
119B VAL* 3.5 21.5 - - + +
120B TYR* 3.4 23.6 + - - -
123B ALA* 3.4 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