Contacts of the strand formed by residues 163 - 168 (chain B) in PDB entry 3TKR
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 ARG 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B PHE 3.8 2.2 - - - -
80B PRO* 3.5 19.2 - - + +
84B THR* 5.3 0.6 + - - -
85B PHE 5.8 0.2 - - - +
86B VAL* 3.4 24.8 - - - +
87B CYS* 3.2 37.8 - - - +
90B GLU* 2.8 29.3 + - - -
162B LEU* 1.3 79.9 - - - +
164B GLY* 1.3 54.4 + - - +
178B THR 3.4 4.5 - - - +
180B ASN* 2.9 39.5 + - + +
181B ASP 4.2 2.2 - - - +
182B LEU* 2.8 31.6 + - - +
184B VAL 3.5 21.7 + - - -
186B ARG* 3.2 27.6 + - - +
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Residues in contact with GLY 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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77B PHE* 3.4 1.2 - - - -
78B PHE* 2.8 37.1 + - - +
153B VAL* 4.1 7.9 - - - -
162B LEU* 3.2 11.0 + - - +
163B ARG* 1.3 72.6 - - - +
165B LEU* 1.3 59.8 + - - -
166B PHE* 3.8 5.8 - - - -
178B THR 3.3 5.8 - - - -
179B LEU* 3.6 18.2 - - - -
186B ARG* 3.1 6.7 + - - +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 3.8 16.4 - - + -
76B PHE 3.8 2.7 - - - -
77B PHE* 3.8 16.2 - - + -
94B PHE* 3.7 31.6 - - + -
164B GLY* 1.3 73.2 - - - +
166B PHE* 1.3 70.0 + - - +
167B ILE* 3.9 27.8 - - + -
176B GLN* 4.2 9.2 - - - +
177B ILE* 3.5 4.5 - - - +
178B THR* 2.7 47.4 + - + +
186B ARG* 3.7 19.5 - - + +
191B THR* 3.7 13.5 - - + +
194B LEU* 6.2 0.7 - - + -
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Residues in contact with PHE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 4.1 7.6 - - + -
74B LEU 3.6 2.1 - - - +
75B VAL* 3.6 2.9 - - - -
76B PHE* 2.8 51.8 + + + +
78B PHE* 3.6 30.3 - + - -
151B TYR* 3.4 52.9 - + + -
153B VAL* 3.5 14.4 - - + -
164B GLY 3.8 8.5 - - - -
165B LEU* 1.3 78.1 - - - +
167B ILE* 1.3 63.9 + - - +
168B ILE* 4.0 2.7 - - + -
174B LEU* 3.7 17.5 - - + -
176B GLN 3.4 3.6 - - - -
177B ILE* 3.7 34.5 - - + -
179B LEU* 4.3 7.9 - - + -
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Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 3.9 28.7 - - + -
74B LEU 3.6 5.2 - - - +
75B VAL* 4.5 9.4 - - + -
165B LEU* 3.9 15.9 - - + -
166B PHE* 1.3 75.9 - - - +
168B ILE* 1.3 62.0 + - - +
169B ASP 4.3 0.2 - - - -
174B LEU* 3.5 2.8 - - - +
175B ARG* 2.8 34.0 + - + +
176B GLN* 3.0 34.3 + - + +
191B THR* 4.2 6.1 - - + +
194B LEU* 3.7 33.4 - - + -
195B VAL* 4.2 19.5 - - + +
198B PHE* 4.9 4.9 - - + -
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Residues in contact with ILE 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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48B ALA* 3.6 26.5 - - + -
66B LEU* 4.1 22.9 - - + -
73B TYR* 3.4 6.5 - - - -
74B LEU* 2.8 45.9 + - + +
76B PHE* 4.1 26.2 - - + -
151B TYR* 4.1 11.0 - - + +
166B PHE* 4.6 1.8 - - + +
167B ILE* 1.3 78.9 - - - +
169B ASP* 1.3 72.4 + - - +
172B GLY* 3.7 26.9 - - - +
173B ILE 3.5 3.8 - - - +
174B LEU* 4.0 9.9 - - + -
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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