Contacts of the strand formed by residues 187 - 194 (chain B) in PDB entry 4A69
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 VAL 187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ILE* 3.7 36.8 - - + -
158B LEU* 3.7 19.3 - - + -
164B VAL* 3.3 11.4 - - + +
166B TYR* 4.6 2.2 - - + -
181B PHE* 3.8 37.5 - - + -
184B THR* 3.7 7.4 + - + +
185B ASP 4.5 1.8 - - - -
186B ARG* 1.3 85.1 - - - +
188B MET* 1.3 60.8 + - - +
189B THR* 3.7 14.0 + - + +
217B TYR* 3.5 1.0 - - - +
247B TYR* 3.7 1.6 - - - -
504B K 2.6 29.6 - - - -
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Residues in contact with MET 188 (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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164B VAL 2.8 9.9 + - - -
165B LEU* 3.5 8.9 - - + +
166B TYR* 2.7 33.4 + - - +
187B VAL* 1.3 72.0 - - - +
189B THR* 1.3 63.7 + - - +
190B VAL* 4.3 5.6 - - + -
216B TYR 3.9 8.1 - - - +
217B TYR* 3.3 33.4 - - - +
218B CYS* 4.6 0.4 - - - -
219B LEU* 5.4 7.0 - - - -
243B VAL* 3.1 37.9 - - + -
247B TYR* 3.5 43.4 + - + -
366B LEU* 5.2 1.1 - - + -
369B LEU* 4.0 17.3 - - + -
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Residues in contact with THR 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B TYR* 3.6 24.0 - - + -
177B VAL* 4.2 22.7 - - + +
178B GLN* 4.1 15.3 + - - +
181B PHE* 4.7 5.6 - - + -
187B VAL* 4.1 19.7 - - + +
188B MET* 1.3 76.2 - - - +
190B VAL* 1.3 58.7 + - - +
191B SER* 5.7 1.1 - - - -
217B TYR 3.2 5.7 + - - -
218B CYS* 3.5 23.9 - - - +
219B LEU* 2.8 32.8 + - - +
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Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 3.9 22.4 - - + -
166B TYR* 2.8 13.0 + - - +
167B ILE* 3.4 5.9 - - + +
168B ASP* 2.9 27.2 + - - +
188B MET* 4.3 5.2 - - + -
189B THR* 1.3 78.1 - - - +
191B SER* 1.3 62.3 + - - +
192B PHE* 3.4 32.3 - - + -
219B LEU* 3.4 20.4 - - + +
239B VAL* 4.5 7.6 - - + -
240B ILE* 4.1 12.3 - - + -
243B VAL* 4.2 19.7 - - + -
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Residues in contact with SER 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B TYR* 5.9 1.3 - - - -
168B ASP* 3.6 10.3 - - - +
173B HIS* 4.1 4.0 - - - -
174B GLY* 3.3 17.4 + - - -
178B GLN* 5.6 0.2 - - - -
189B THR* 5.7 1.3 - - - -
190B VAL* 1.3 76.2 - - - +
192B PHE* 1.3 56.0 + - - +
193B HIS* 2.9 27.1 + - - -
219B LEU 3.1 7.3 + - - -
220B ASN* 3.6 15.6 - - - -
221B VAL* 2.8 32.1 + - - +
503B K 3.0 14.3 - - - -
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Residues in contact with PHE 192 (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 ILE* 4.6 1.3 - - + -
168B ASP 3.1 13.0 + - - +
169B ILE* 4.3 2.7 - - + -
170B ASP 3.0 7.8 - - - +
190B VAL* 3.4 25.6 - - + -
191B SER* 1.3 74.0 - - - +
193B HIS* 1.3 57.6 + - - +
221B VAL* 3.6 39.7 - - + +
223B LEU* 4.7 5.4 - - + -
232B TYR* 3.2 33.1 + + + +
235B LEU* 4.5 7.4 - - + -
236B PHE* 3.6 55.0 - + - -
239B VAL* 4.0 20.4 - - + -
240B ILE* 4.1 3.4 - - + -
269B PHE* 5.3 2.3 - - - -
503B K 2.6 22.7 - - - -
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Residues in contact with HIS 193 (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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171B ILE 3.2 17.3 - - - +
172B HIS 3.7 1.6 - - - -
173B HIS* 3.4 45.9 - + + +
191B SER* 2.9 27.5 + - - -
192B PHE* 1.3 71.8 - - - +
194B LYS* 1.3 65.9 + - - +
195B TYR* 4.0 9.4 - - + -
203B THR 4.2 2.2 - - - -
204B GLY* 2.6 31.8 + - - -
220B ASN* 3.5 14.6 - - + -
221B VAL 3.2 10.0 + - - +
222B PRO* 4.2 3.7 - - + +
223B LEU* 2.7 34.8 + - - +
269B PHE* 3.8 9.6 - - - -
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Residues in contact with LYS 194 (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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171B ILE* 3.0 13.2 + - + +
173B HIS* 5.1 2.3 + - - +
193B HIS* 1.3 81.5 - - - +
195B TYR* 1.3 64.4 + - - +
196B GLY* 3.1 30.5 + - - -
197B ASN* 4.9 7.6 - - - +
199B PHE* 3.4 48.7 - - + +
200B PHE 5.0 1.4 - - - +
201B PRO* 5.9 0.9 - - - +
203B THR 5.4 0.3 - - - +
223B LEU 3.4 17.7 - - - +
224B ARG* 3.9 3.4 - - - +
225B ASP* 2.8 42.0 - - - +
268B CYS* 3.9 10.5 - - - -
269B PHE* 3.4 19.7 - - + -
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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