Contacts of the strand formed by residues 162 - 166 (chain B) in PDB entry 3KTC
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 LYS 162 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ASN* 3.6 24.3 + - + +
122B TYR* 3.2 5.1 - - + -
123B VAL 2.8 25.1 + - - -
161B VAL* 1.3 79.0 - - - +
163B PHE* 1.3 60.4 + - - +
194B ASP 5.8 0.2 - - - -
195B ASN* 3.4 4.7 - - - +
226B PHE* 3.7 45.1 - - + -
340B EDO 3.0 41.3 + - - +
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Residues in contact with PHE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B MSE 4.8 1.3 - - - -
112B ALA* 4.1 5.2 - - + -
123B VAL* 3.4 35.4 - - + +
125B VAL* 4.0 9.2 - - + -
151B MSE 4.9 4.7 - - - -
154B LEU* 3.5 37.5 - - + -
155B ALA* 3.8 17.7 - - + -
158B ASN* 3.7 38.4 - - + -
161B VAL* 3.3 29.8 - - + -
162B LYS* 1.3 70.1 - - - +
164B ALA* 1.3 59.9 + - - +
165B ILE* 3.9 1.0 + - - -
195B ASN* 2.8 18.6 + - - +
196B VAL* 3.4 13.5 - - + +
197B GLY 2.8 27.7 + - - +
226B PHE* 3.6 3.0 - - - -
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TYR* 3.9 30.1 - - + -
123B VAL 2.9 7.9 + - - -
124B LYS* 3.6 4.2 - - - +
125B VAL* 2.8 30.5 + - - -
162B LYS 4.1 1.2 - - - -
163B PHE* 1.3 70.3 - - - +
165B ILE* 1.3 59.6 + - - +
166B GLU 3.5 1.0 + - - -
197B GLY 3.6 5.8 - - - -
199B LEU* 4.0 20.6 - - + +
226B PHE* 3.9 19.5 - - + -
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Residues in contact with ILE 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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125B VAL* 3.5 9.4 - - + +
127B PRO* 5.2 1.3 - - + -
151B MSE 3.6 31.6 - - + -
163B PHE 4.8 1.3 - - - +
164B ALA* 1.3 70.8 - - - +
166B GLU* 1.3 64.4 + - - +
167B TYR 3.4 5.1 + - - +
178B TRP* 3.8 61.5 - - + -
184B THR* 4.2 7.9 - - + +
188B ILE* 4.4 5.8 - - + -
196B VAL* 3.5 29.4 - - + -
197B GLY 2.9 17.2 + - - +
198B VAL* 3.4 9.2 - - - +
199B LEU 2.9 16.7 + - - -
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Residues in contact with GLU 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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124B LYS* 3.2 30.0 + - + +
125B VAL 2.9 14.0 + - - +
126B TRP* 3.2 22.6 - - + +
164B ALA 3.5 1.4 + - - -
165B ILE* 1.3 72.0 - - - +
167B TYR* 1.3 70.9 + - - +
176B MSE 3.6 6.4 - - - +
199B LEU* 3.5 20.9 - - + +
201B ASP* 3.2 9.7 - - + +
204B HIS* 3.3 8.0 - - + +
229B ASP* 3.1 6.8 - - - +
334B FE 2.0 30.2 - - - -
337B UNL 2.6 29.5 + - - -
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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
------------------------------------------------------------
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