Contacts of the strand formed by residues 182 - 187 (chain O) in PDB entry 3FKS
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 SER 182 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92O LEU* 4.1 2.9 - - - +
175O ALA* 4.8 13.3 + - - +
178O HIS* 4.8 2.9 - - - +
180O GLY 4.3 3.3 + - - -
181O PHE* 1.3 84.6 + - - +
183O VAL* 1.3 69.5 + - - +
214O LYS* 2.9 13.8 + - - +
215O VAL* 3.1 15.7 - - - -
216O ALA 2.9 21.8 + - - -
251O VAL* 4.9 2.0 - - - +
252O LEU* 3.4 28.0 - - - +
254O PHE* 5.5 6.3 - - - -
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Residues in contact with VAL 183 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181O PHE* 6.2 0.2 - - + -
182O SER* 1.3 81.4 - - - +
184O PHE* 1.3 63.1 + - - +
185O THR* 4.3 7.0 - - - +
215O VAL* 4.8 1.1 - - - -
216O ALA* 3.2 26.2 - - + +
218O VAL* 4.3 9.9 - - + -
236O GLY 3.7 22.4 - - - +
239O ILE* 4.3 13.9 - - + -
240O ALA* 4.5 16.2 - - + -
243O PHE* 4.8 9.4 - - + -
251O VAL* 5.2 3.1 - - + -
252O LEU 3.0 9.4 + - - +
253O LEU* 3.2 19.7 - - + +
254O PHE* 3.2 25.3 + - - -
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Residues in contact with PHE 184 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167O ILE* 4.4 9.4 - - + -
171O ILE* 3.7 25.1 - - + -
183O VAL* 1.3 72.8 - - - +
185O THR* 1.3 80.2 - - - +
186O GLY* 4.2 8.3 - - - -
197O LEU* 3.7 28.3 - - + -
215O VAL* 4.4 5.4 - - + +
216O ALA 3.0 7.3 + - - -
217O LEU* 3.6 18.2 - - + -
218O VAL 2.9 26.3 + - - +
219O PHE* 4.6 15.9 - + - -
221O GLN* 6.1 0.4 - - - -
254O PHE* 3.7 27.8 - + + -
256O ASP* 4.3 20.4 - - + -
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Residues in contact with THR 185 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183O VAL* 4.3 2.1 - - - +
184O PHE* 1.3 84.7 - - - +
186O GLY* 1.3 62.2 + - - +
187O VAL* 3.8 17.9 - - + -
218O VAL* 3.2 12.3 - - + +
232O VAL* 3.4 30.1 - - + +
233O ALA* 4.3 4.9 - - - -
236O GLY* 3.8 19.8 - - - -
237O LEU 4.6 0.2 + - - -
253O LEU* 4.1 4.7 - - - +
254O PHE 3.0 8.9 + - - +
255O ILE* 3.5 24.8 - - - +
256O ASP 3.3 20.5 + - - -
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Residues in contact with GLY 186 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184O PHE* 4.2 9.8 - - - -
185O THR* 1.3 73.9 - - - +
187O VAL* 1.3 61.0 + - - -
218O VAL 2.8 14.0 + - - -
219O PHE* 4.6 2.9 - - - -
220O GLY* 2.9 27.7 + - - +
221O GLN* 3.0 24.4 - - - +
232O VAL* 4.8 0.2 - - - -
256O ASP 3.2 8.5 - - - -
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Residues in contact with VAL 187 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185O THR* 3.8 17.9 - - + -
186O GLY* 1.3 71.1 - - - -
188O GLY* 1.3 65.7 + - - +
189O GLU 3.3 1.6 - - - -
220O GLY 3.6 2.7 - - - -
229O ARG* 3.4 26.5 - - + +
232O VAL* 3.5 17.5 - - + -
233O ALA* 4.0 15.9 - - + -
255O ILE* 4.3 11.9 - - + -
256O ASP 2.7 8.7 + - - -
257O ASN 2.8 34.4 + - - +
258O ILE* 5.2 0.7 - - - -
260O ARG* 3.1 24.1 - - + +
261O PHE* 4.0 11.0 - - + +
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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