Contacts of the strand formed by residues 163 - 168 (chain B) in PDB entry 3K2H
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 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU* 4.3 9.9 - - + -
138B CYS* 3.0 39.0 - - + -
139B ASP 3.8 11.4 - - - -
140B LYS 4.0 2.5 - - - -
141B ILE* 4.4 8.5 - - + -
159B ILE* 3.5 32.0 - - + +
160B PRO* 2.9 21.3 + - + +
161B ASP* 3.8 9.5 - - - +
162B THR* 1.3 92.9 - - - +
164B GLU* 1.3 62.1 + - - +
184B TYR* 4.2 14.8 - - + -
185B GLU* 3.4 13.0 - - - -
186B ARG* 3.3 45.8 - - - -
187B LYS* 4.2 4.3 + - - -
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Residues in contact with GLU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B PHE* 1.3 76.3 - - - +
165B ILE* 1.3 71.0 + - - +
166B THR* 3.5 11.9 + - + +
184B TYR* 3.2 8.1 - - - -
185B GLU 2.9 33.5 + - - +
187B LYS* 3.6 36.9 + - + +
190B LYS* 5.0 6.1 - - + +
220B GLY* 3.9 24.2 - - - -
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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
----------------------------------------------------------
145B ARG* 4.3 14.8 - - - +
164B GLU* 1.3 76.5 - - - +
166B THR* 1.3 60.0 + - - +
167B ALA 3.6 9.2 - - - +
168B ILE* 3.6 34.8 - - + -
182B VAL* 4.3 6.5 - - + -
183B ILE 3.3 4.7 - - - +
184B TYR* 3.6 45.7 - - + +
220B GLY* 3.6 7.4 - - - +
221B VAL* 3.3 20.0 - - + +
470B ILE* 4.1 32.0 - - + +
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Residues in contact with THR 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B GLU* 3.7 22.9 - - + +
165B ILE* 1.3 76.6 - - - +
167B ALA* 1.3 61.1 + - - +
183B ILE* 2.8 19.1 + - - +
185B GLU* 2.9 41.6 + - + +
190B LYS* 4.9 6.3 - - + -
220B GLY 3.5 17.9 - - - +
221B VAL* 4.0 3.6 - - - -
222B ARG* 2.7 32.8 + - - +
223B ILE* 3.0 6.4 + - - +
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Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A MET* 4.1 8.1 - - + -
165B ILE* 3.6 2.2 - - - +
166B THR* 1.3 83.5 + - - +
168B ILE* 1.3 68.9 + - - +
182B VAL* 3.1 7.1 - - - +
183B ILE* 3.0 53.0 + - + -
221B VAL* 4.4 0.2 - - - -
223B ILE* 3.4 27.1 - - + -
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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
----------------------------------------------------------
203A MET* 4.5 1.8 - - - -
145B ARG* 3.9 7.2 - - - +
165B ILE* 3.6 13.9 - - + -
167B ALA* 1.3 81.8 - - - +
169B SER* 1.3 73.8 + - - +
180B ASP* 3.6 19.3 - - - +
181B PHE 3.5 3.6 - - - -
182B VAL* 3.9 5.4 - - + -
221B VAL* 4.2 6.7 - - + -
223B ILE* 2.9 10.4 + - - +
225B ASN* 3.0 28.6 + - - +
226B HIS* 3.5 16.6 + - + -
229B PHE* 4.1 25.6 - - + -
470B ILE* 3.6 30.7 - - + -
471B PRO* 4.2 9.6 - - + +
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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