Contacts of the strand formed by residues 221 - 227 (chain B) in PDB entry 2KH2
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 ALA 221 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ARG* 4.2 22.0 - - + +
168B GLN 3.9 1.8 - - - -
169B ALA* 3.5 28.3 - - + +
170B PRO* 4.3 4.9 - - - -
175B GLU* 6.4 0.4 - - - -
218B GLU 5.8 0.2 - - - +
219B ASP 3.1 9.6 + - - +
220B THR* 1.3 77.8 - - - +
222B VAL* 1.3 67.6 + - - +
223B TYR* 3.7 7.6 - - - -
243B LEU* 4.1 3.7 - - - +
244B VAL 3.1 28.4 + - - +
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Residues in contact with VAL 222 (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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167B ARG* 3.1 5.4 - - - +
168B GLN 2.8 43.3 + - - +
170B PRO* 4.4 12.3 - - + -
221B ALA* 1.3 79.1 - - - +
223B TYR* 1.3 63.0 + - - +
224B TYR* 3.8 28.9 - - + +
240B GLN 5.0 1.1 - - - +
241B GLY* 3.8 18.6 - - - +
242B THR 3.5 13.0 - - - +
243B LEU* 3.9 20.4 - - + +
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Residues in contact with TYR 223 (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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135B GLU* 3.8 3.1 - - - +
149B LEU* 3.7 25.1 - - + -
165B TRP* 4.6 9.3 - + + -
166B VAL 3.8 3.4 - - - +
167B ARG* 2.8 49.5 + - + -
177B VAL* 4.0 20.4 - - + -
197B PHE* 3.8 4.9 - + - -
210B LEU* 4.1 11.9 - - + -
212B MET* 3.6 28.4 - - + +
219B ASP* 3.1 20.2 + - - +
221B ALA 3.7 15.7 - - - -
222B VAL* 1.3 75.8 - - - +
224B TYR* 1.3 62.5 + - - +
241B GLY* 3.0 1.6 - - - -
242B THR* 2.8 40.9 + - - +
244B VAL* 3.8 15.7 - - + -
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Residues in contact with TYR 224 (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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38B GLN* 3.5 9.9 + - - -
42B LYS 5.5 3.1 - - - -
43B ALA* 5.5 0.2 - - - -
44B PRO* 4.4 19.1 - - + -
135B GLU* 3.4 4.7 - - - +
165B TRP* 3.9 8.6 - - - -
166B VAL* 2.9 31.6 + - - +
167B ARG* 4.7 0.4 - - - -
168B GLN* 2.8 46.2 + - + -
174B LEU* 4.8 8.1 - - + -
222B VAL* 3.8 33.7 - - + +
223B TYR* 1.3 73.0 - - - +
225B CYS* 1.3 64.2 + - - +
226B ALA* 3.4 3.6 + - - +
238B TRP* 3.8 20.6 - + + -
239B GLY 3.9 11.2 - - - +
240B GLN 3.6 17.7 - - - -
241B GLY* 3.6 13.9 - - - -
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Residues in contact with CYS 225 (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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133B LEU* 3.8 19.9 - - + +
135B GLU* 2.7 23.7 + - + +
151B CYS* 2.0 51.1 - - - -
163B MET* 5.8 0.4 - - - -
164B SER 4.6 0.9 - - - -
165B TRP* 4.5 8.1 - - - -
208B LEU* 3.7 19.1 - - - -
224B TYR* 1.3 71.8 - - - +
226B ALA* 1.3 62.6 + - - +
237B TYR 3.5 1.6 - - - +
238B TRP* 3.2 8.1 - - - -
239B GLY 2.9 24.5 + - - +
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Residues in contact with ALA 226 (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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133B LEU* 4.9 1.3 - - - -
163B MET* 3.0 8.3 - - - +
164B SER 2.9 42.7 + - - +
165B TRP 4.5 0.2 - - - +
166B VAL* 4.0 15.5 - - + -
224B TYR 3.4 2.8 + - - +
225B CYS* 1.3 76.3 - - - +
227B ARG* 1.3 60.8 + - - +
228B GLN* 4.3 0.2 - - - -
235B PHE* 3.5 31.2 - - + -
237B TYR 3.8 3.6 - - - -
238B TRP* 4.7 6.3 - - + +
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Residues in contact with ARG 227 (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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131B VAL* 3.9 15.4 - - - +
133B LEU* 4.3 11.9 - - + -
156B PHE* 3.6 58.9 - - + +
161B TYR* 3.9 26.8 + - + -
162B ASP 3.8 12.1 - - - +
163B MET* 4.1 5.2 - - + +
226B ALA* 1.3 74.9 - - - +
228B GLN* 1.3 70.8 + - - +
235B PHE* 3.1 4.8 - - - +
236B ASP* 2.6 67.7 + - - +
237B TYR* 3.3 25.3 + - + +
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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