Contacts of the strand formed by residues 111 - 119 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 4.5 9.2 - - + -
99B HIS* 4.2 18.2 - + - -
100B ALA* 4.0 24.2 - - + -
103B MET* 3.6 39.9 - - + -
104B GLY 5.2 0.4 - - - -
105B LYS* 3.8 37.9 - - + +
109B LYS 3.7 0.6 + - - -
110B LYS* 1.3 70.8 - - - +
112B PHE* 1.3 71.9 + - - +
113B VAL* 4.0 16.8 - - + -
218B GLU* 3.2 4.0 - - - -
219B PHE* 2.8 71.2 + + + +
220B PRO 4.3 0.6 + - - -
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Residues in contact with PHE 112 (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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103B MET 4.9 3.6 - - - +
110B LYS* 3.7 39.4 + - + -
111B PHE* 1.3 80.5 - - - +
113B VAL* 1.3 63.7 + - - +
136B ALA* 4.0 9.2 - - + -
143B GLU* 4.0 13.7 - - + -
146B ALA* 3.8 28.3 - - + -
147B ILE* 3.6 38.8 - - + -
150B VAL* 3.7 31.5 - - + +
216B VAL* 4.5 4.3 - - + -
217B CYS 3.4 2.2 - - - +
218B GLU* 3.4 38.1 - - + -
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.3 4.3 - - + -
101A PHE* 3.5 14.8 - - + -
102A SER* 3.8 35.4 - - - -
103B MET* 4.5 11.2 - - + -
111B PHE* 4.0 17.5 - - + -
112B PHE* 1.3 76.2 - - - +
114B THR* 1.3 67.3 + - - +
150B VAL* 3.9 8.2 - - - +
216B VAL* 3.5 1.7 - - - +
217B CYS* 3.0 29.4 + - + +
219B PHE* 3.6 34.3 - - + -
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Residues in contact with THR 114 (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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101A PHE* 3.6 13.2 - - - +
102A SER 4.4 6.2 - - - +
103B MET* 5.8 0.5 - - - +
113B VAL* 1.3 82.6 - - - +
115B ASN* 1.3 60.7 + - - +
116B HIS* 3.0 34.3 + - + +
150B VAL* 3.5 32.3 - - + +
151B ALA* 4.6 2.5 - - - -
214B THR* 3.3 9.7 - - - +
215B ALA 2.4 27.1 + - - -
216B VAL* 3.9 10.3 - - + -
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Residues in contact with ASN 115 (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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101A PHE* 3.1 52.8 - - + +
104A GLY* 3.9 8.1 - - - -
105A LYS 2.9 25.5 + - - +
106A LYS* 3.3 22.3 + - - +
107A SER* 4.5 0.8 + - - +
114B THR* 1.3 73.8 + - - +
116B HIS* 1.3 70.0 + - - +
117B GLU* 2.9 45.0 + - - +
127B LEU* 4.6 4.6 - - - +
215B ALA* 4.2 3.1 - - - +
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Residues in contact with HIS 116 (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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104A GLY* 5.7 3.6 - - - -
106A LYS* 4.0 11.1 - - - +
114B THR* 3.0 34.5 + - + +
115B ASN* 1.3 84.7 + - - +
117B GLU* 1.3 61.0 + - - +
118B ARG* 4.0 5.5 + - - +
150B VAL 3.9 11.4 - - - -
151B ALA 4.1 11.2 + - - -
152B LYS* 4.7 11.1 - - + +
214B THR* 4.2 9.7 + - - +
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Residues in contact with GLU 117 (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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106A LYS* 3.2 18.1 - - + -
107A SER* 2.8 47.7 + - - +
114B THR* 4.6 0.2 + - - -
115B ASN* 2.9 28.2 + - - +
116B HIS* 1.3 78.8 - - - +
118B ARG* 1.3 70.4 + - - +
119B MET* 3.5 21.6 - - + +
214B THR* 4.1 0.4 - - - -
215B ALA* 2.9 29.8 + - - +
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Residues in contact with ARG 118 (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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116B HIS 4.0 5.1 + - - +
117B GLU* 1.3 81.6 - - - +
119B MET* 1.3 65.4 + - - +
153B THR* 4.0 11.1 + - - -
154B SER* 2.8 46.5 + - - +
212B SER* 3.2 23.0 + - - -
213B HIS* 3.1 28.2 + - - +
214B THR* 3.5 17.6 + - - +
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Residues in contact with MET 119 (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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107A SER* 4.3 4.3 - - - +
117B GLU* 3.5 45.3 - - + +
118B ARG* 1.3 74.1 - - - +
120B PRO* 1.3 79.1 - - + +
123B LYS* 3.5 30.5 - - + +
124B VAL* 3.4 32.5 - - + -
127B LEU* 3.9 21.3 - - + -
156B PHE* 3.0 19.9 - - - -
212B SER* 3.6 10.8 - - - -
213B HIS 2.8 13.6 + - - +
215B ALA* 4.0 8.5 - - + -
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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