Contacts of the strand formed by residues 111 - 119 (chain C) in PDB entry 1KWV
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 PHE 111 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 4.8 4.0 - - + -
100C ALA* 4.2 9.6 - - + -
103C MET* 3.3 43.7 - - + -
104C GLY 5.3 0.7 - - - -
105C LYS* 3.3 50.0 - - + +
109C LYS 3.7 0.2 + - - -
110C LYS* 1.3 76.7 - - - +
112C PHE* 1.3 66.4 + - - +
113C VAL* 3.2 30.3 - - + -
217C CYS 3.9 0.5 - - - +
218C GLU* 3.6 2.6 - - - -
219C PHE* 3.1 70.4 + + + +
220C PRO 5.1 0.7 - - - -
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Residues in contact with PHE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C MET 5.2 3.8 - - - +
110C LYS* 3.3 37.2 - - + -
111C PHE* 1.3 77.8 - - - +
113C VAL* 1.3 68.3 + - - +
136C ALA* 3.8 14.6 - - + -
137C ILE 4.4 2.0 - - - -
143C GLU* 4.1 11.7 - - + -
146C ALA* 4.0 25.4 - - + -
147C ILE* 3.8 34.8 - - + -
150C VAL* 3.8 31.0 - - + +
216C VAL* 4.0 9.4 - - + -
217C CYS 3.4 2.7 - - - -
218C GLU* 3.6 40.4 - - + -
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Residues in contact with VAL 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 4.9 1.6 - - + -
101B PHE* 3.5 17.0 - - + -
102B SER* 3.7 36.8 - - - -
103C MET* 4.1 9.4 - - + +
111C PHE* 3.2 38.6 - - + -
112C PHE* 1.3 78.3 - - - +
114C THR* 1.3 65.8 + - - +
150C VAL* 4.2 4.9 - - - -
216C VAL* 3.4 2.4 - - - -
217C CYS 2.9 31.0 + - - -
219C PHE* 4.1 16.6 - - + -
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Residues in contact with THR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PHE* 3.7 13.4 - - - +
102B SER 4.1 7.6 - - - +
113C VAL* 1.3 79.5 - - - +
115C ASN* 1.3 61.5 + - - +
116C HIS* 3.0 36.3 + - + +
150C VAL* 3.6 31.8 - - + +
151C ALA* 4.8 1.6 - - - -
214C THR* 3.3 10.7 - - - +
215C ALA 2.6 24.7 + - - -
216C VAL* 4.1 10.3 - - - -
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Residues in contact with ASN 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PHE* 3.1 49.0 - - + +
104B GLY* 3.9 10.2 - - - -
105B LYS 2.9 26.9 + - - +
106B LYS* 3.2 22.6 + - - +
107B SER 4.5 0.6 - - - +
114C THR* 1.3 73.5 + - - +
116C HIS* 1.3 70.7 + - - +
117C GLU* 3.0 44.6 + - - +
119C MET* 4.8 0.2 - - - +
127C LEU* 4.7 3.4 - - - +
215C ALA* 4.3 4.2 - - - +
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Residues in contact with HIS 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLY* 5.6 4.0 - - - -
106B LYS* 4.1 9.3 - - - +
114C THR* 3.0 37.5 + - + +
115C ASN* 1.3 83.6 - - - +
117C GLU* 1.3 60.9 + - - +
118C ARG* 3.9 8.3 + - - +
150C VAL 3.9 11.7 - - - -
151C ALA 4.3 9.7 + - - -
152C LYS* 4.2 21.4 - - + +
214C THR* 4.2 9.1 + - - +
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Residues in contact with GLU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LYS* 3.5 20.9 - - + +
107B SER* 3.0 47.8 + - - +
114C THR* 4.5 0.2 + - - -
115C ASN* 3.0 27.7 + - - +
116C HIS* 1.3 78.1 - - - +
118C ARG* 1.3 70.8 + - - +
119C MET* 3.3 21.1 - - + +
214C THR* 3.3 1.3 - - - -
215C ALA* 2.9 29.1 + - - +
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Residues in contact with ARG 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C HIS 3.9 6.7 + - - +
117C GLU* 1.3 80.8 - - - +
119C MET* 1.3 63.7 + - - +
153C THR* 3.4 15.8 + - - +
154C SER* 2.7 35.4 + - - -
212C SER* 3.4 22.1 + - - -
213C HIS* 3.0 30.4 + - - +
214C THR* 2.9 32.7 + - - +
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Residues in contact with MET 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B SER* 4.2 4.5 - - - +
117C GLU* 3.3 48.0 - - + +
118C ARG* 1.3 75.6 - - - +
120C PRO* 1.3 77.9 - - + +
123C LYS* 3.8 35.9 - - + +
124C VAL* 3.4 22.9 - - + -
127C LEU* 4.0 15.0 - - + -
156C PHE* 3.2 6.1 - - - -
212C SER* 3.6 10.5 - - - -
213C HIS 2.9 26.9 + - - +
215C ALA* 3.9 16.2 - - + -
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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