Contacts of the strand formed by residues 163 - 169 (chain B) in PDB entry 5GKI
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 163 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B GLU* 3.3 52.9 - - + +
157B LYS 3.4 5.6 - - - +
158B ALA* 4.1 11.9 - - + +
162B GLY* 1.3 80.4 - - - +
164B VAL* 1.3 61.4 + - - +
165B ALA 3.8 1.4 + - - -
179B GLU* 5.0 1.2 - - - +
196B TYR* 3.4 20.9 + - - -
103C MPD 5.1 11.9 - - + -
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Residues in contact with VAL 164 (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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156B GLU* 3.2 5.4 - - - -
157B LYS* 2.8 32.5 + - + +
159B ILE* 3.6 40.2 - - + -
163B ILE* 1.3 76.1 - - - +
165B ALA* 1.3 66.8 + - - +
166B VAL 3.9 23.3 - - - +
167B LEU* 3.9 20.2 - - + +
177B VAL* 4.2 13.2 - - + -
196B TYR* 3.8 25.4 - - + -
200B LEU* 5.2 0.4 - - + -
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Residues in contact with ALA 165 (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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132B GLU* 4.5 7.0 - - - +
155B ARG* 3.4 5.9 - - - +
156B GLU* 2.8 33.7 + - - +
163B ILE 3.8 2.0 + - - -
164B VAL* 1.3 70.8 - - - +
166B VAL* 1.3 67.3 + - - +
178B LEU 3.4 16.1 + - - +
179B GLU* 4.1 2.8 + - - +
180B LEU* 4.0 34.1 - - + +
196B TYR* 4.8 0.4 - - - -
301B MG 4.0 17.1 - - - -
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Residues in contact with VAL 166 (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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136B ALA* 4.5 10.8 - - + -
139B ILE* 5.1 4.7 - - + -
140B PHE* 3.8 27.4 - - + -
150B PHE* 4.5 8.5 - - + -
152B PRO* 4.5 4.3 - - + -
154B PHE 3.4 9.2 - - - +
155B ARG* 4.8 0.9 - - + -
164B VAL* 3.9 6.3 - - - +
165B ALA* 1.3 86.9 - - - +
167B LEU* 1.3 72.1 + - - +
176B VAL 3.8 0.2 - - - +
177B VAL* 3.7 3.1 - - - -
178B LEU* 3.0 58.2 + - + +
180B LEU* 4.3 19.3 - - + -
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Residues in contact with LEU 167 (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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153B LEU* 2.9 24.5 + - + +
154B PHE* 2.9 39.1 + - + +
157B LYS* 4.2 20.0 - - + +
159B ILE* 4.9 5.8 - - + -
164B VAL* 3.9 13.4 - - + +
166B VAL* 1.3 80.0 - - - +
168B GLY* 1.3 60.2 + - - +
175B ILE* 3.7 28.0 - - + -
176B VAL 3.0 20.4 - - - +
177B VAL* 4.0 13.9 - - + -
200B LEU* 4.1 12.6 - - + -
204B TYR* 5.9 4.5 - - + +
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Residues in contact with GLY 168 (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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150B PHE* 4.3 5.6 - - - -
151B LYS 3.1 15.5 - - - -
152B PRO* 4.2 1.8 - - - -
153B LEU* 3.7 9.4 - - - -
167B LEU* 1.3 77.7 - - - +
169B ARG* 1.3 65.2 + - - +
175B ILE* 3.6 6.4 - - - +
176B VAL* 2.8 36.7 + - - -
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Residues in contact with ARG 169 (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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150B PHE* 3.4 6.8 - - - -
151B LYS* 2.6 49.2 + - + +
153B LEU* 4.0 16.8 - - + +
168B GLY* 1.3 80.2 - - - +
170B ASP* 1.3 64.4 + - - +
173B GLY* 2.6 38.1 + - - -
174B ASN 3.1 7.9 - - - +
175B ILE* 3.3 35.2 - - + +
176B VAL* 4.2 1.8 - - - -
204B TYR* 3.9 16.8 + - - -
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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