Contacts of the strand formed by residues 158 - 162 (chain B) in PDB entry 1GKU
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 ILE 158 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B SER* 3.7 19.3 - - - +
93B LEU* 3.7 31.4 - - + +
96B ALA* 3.3 27.1 - - + -
102B CYS* 3.3 4.9 - - + +
104B VAL* 4.7 1.6 - - + -
119B ILE* 4.2 20.6 - - + -
133B LEU* 3.1 26.7 + - + +
134B ILE* 3.4 7.6 - - + +
135B GLY 3.0 25.5 + - - +
156B PHE* 4.1 0.7 - - - +
157B LYS* 1.3 77.7 - - - +
159B VAL* 1.3 66.7 + - - +
160B ILE* 4.1 20.9 - - + -
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Residues in contact with VAL 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ARG* 4.3 18.2 - - - +
102B CYS 2.9 8.9 + - - +
103B TYR* 3.3 16.3 - - + -
104B VAL* 2.7 33.3 + - - +
135B GLY 3.2 3.6 - - - +
149B PHE* 3.7 15.5 - - + -
153B LEU* 4.4 11.2 - - + +
156B PHE* 3.8 24.2 - - + +
157B LYS 5.2 0.2 - - - -
158B ILE* 1.3 77.7 - - - +
160B ILE* 1.3 59.3 + - - +
161B THR* 3.5 23.1 - - + -
173B LEU* 4.7 5.2 - - + -
176B PHE* 4.3 9.9 - - + -
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Residues in contact with ILE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 3.1 16.6 - - + +
106B PHE* 3.4 39.0 - - + -
112B VAL* 3.7 10.6 - - + +
115B ALA* 4.0 5.6 - - + -
116B ALA* 4.0 28.9 - - + +
119B ILE* 3.8 26.0 - - + -
134B ILE* 4.6 9.2 - - + -
135B GLY 3.2 6.6 + - - +
136B TYR* 3.0 31.4 - - + +
137B TYR 3.1 1.0 + - - -
158B ILE* 4.1 12.1 - - + -
159B VAL* 1.3 78.7 - - - +
161B THR* 1.3 63.0 + - - +
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Residues in contact with THR 161 (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 TYR* 3.0 20.8 + - + -
104B VAL 3.0 6.1 + - - +
105B ILE* 3.5 2.9 - - - -
106B PHE* 2.8 25.5 + - - +
112B VAL* 3.8 9.0 - - - +
137B TYR* 3.8 21.3 - - + -
149B PHE* 4.1 3.4 - - + -
159B VAL* 3.5 24.0 - - + -
160B ILE* 1.3 82.6 - - - +
162B THR* 1.3 72.6 + - - +
165B PHE* 3.5 28.7 - - + +
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Residues in contact with THR 162 (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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105B ILE* 3.9 4.5 - - - +
106B PHE 2.9 10.1 - - - -
107B PRO 5.1 3.4 - - - -
108B THR* 4.0 18.6 - - - -
109B SER* 4.0 11.9 - - - +
112B VAL* 3.9 17.7 - - + -
137B TYR* 4.0 15.5 + - + +
138B HIS* 4.8 3.6 - - - -
161B THR* 1.3 93.0 + - - +
163B THR* 1.3 62.5 + - - +
164B GLN* 3.7 11.7 + - - +
165B PHE* 3.4 22.3 + - - +
166B LEU 3.7 2.1 + - - -
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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