Contacts of the strand formed by residues 231 - 236 (chain K) 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 231 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106K LEU* 4.4 0.4 - - - +
107K GLY* 3.0 25.1 + - - -
108K ARG 4.5 0.3 + - - -
185K ILE* 4.8 7.3 - - - +
203K CYS* 3.1 23.3 - - - -
205K TYR* 5.8 1.6 - - - -
222K LEU* 4.6 6.1 - - - +
227K ALA 3.3 15.7 + - - -
228K MET* 3.6 11.1 + - - +
229K LYS 3.8 0.6 - - - -
230K TYR* 1.3 81.7 - - - +
232K ILE* 1.3 66.7 + - - +
233K ILE* 3.9 17.9 + - - +
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Residues in contact with ILE 232 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102K GLY 4.5 0.4 - - - +
105K LEU* 3.6 27.1 - - + +
106K LEU* 4.0 28.5 - - + -
108K ARG 4.3 9.9 - - - +
110K VAL* 5.0 6.5 - - + -
203K CYS 2.9 11.8 + - - +
204K VAL* 3.2 20.0 - - + +
205K TYR 3.1 20.4 + - - -
231K SER* 1.3 80.0 - - - +
233K ILE* 1.3 64.2 + - - +
234K VAL* 4.5 15.3 - - + -
255K ILE* 3.6 34.5 - - + -
259K PHE* 4.1 12.6 - - + -
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Residues in contact with ILE 233 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K ARG 3.6 6.0 + - - +
109K VAL* 3.4 22.4 - - + -
110K VAL* 3.1 24.3 + - - +
205K TYR* 3.3 31.2 - - + +
207K ALA* 5.3 0.2 - - + -
215K VAL* 4.3 24.9 - - + -
218K LEU* 4.9 1.8 - - + -
219K VAL* 4.9 6.7 - - + -
222K LEU* 4.0 17.0 - - + -
228K MET* 3.7 36.3 - - + -
231K SER* 3.9 13.7 - - - +
232K ILE* 1.3 76.5 - - - +
234K VAL* 1.3 69.0 + - - +
235K ALA* 4.6 0.9 - - + +
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Residues in contact with VAL 234 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K VAL* 3.3 16.6 - - + +
111K ASP 3.5 29.4 - - - +
112K ALA* 4.1 3.8 - - - +
204K VAL* 4.7 1.1 - - + -
205K TYR 2.9 7.9 + - - +
206K VAL* 3.3 8.1 - - + +
207K ALA 2.9 23.6 + - - -
232K ILE* 3.8 9.4 + - + +
233K ILE* 1.3 75.7 - - - +
235K ALA* 1.3 60.9 + - - +
236K ALA 4.1 0.2 + - - -
248K ALA* 4.3 10.3 - - + +
251K THR* 4.2 13.5 - - - +
252K ALA* 3.6 25.4 - - + -
255K ILE* 4.1 17.0 - - + -
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Residues in contact with ALA 235 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109K VAL* 4.7 2.0 - - + -
110K VAL 2.8 13.0 + - - +
111K ASP* 3.5 22.5 - - - +
112K ALA 4.9 0.4 - - - -
117K ILE* 4.3 19.1 - - + +
207K ALA* 3.7 17.0 - - + -
215K VAL* 4.2 16.2 - - + -
233K ILE* 4.0 6.2 + - + -
234K VAL* 1.3 73.4 - - - +
236K ALA* 1.3 59.7 + - - +
237K THR* 3.8 12.1 + - + +
240K GLU* 4.4 4.2 - - - +
124N PHE* 5.4 2.0 - - + -
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Residues in contact with ALA 236 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111K ASP* 5.7 0.4 - - + -
112K ALA* 4.6 6.1 - - + +
207K ALA 2.7 12.4 + - - +
208K VAL* 3.4 0.9 - - - -
209K GLY 2.9 22.9 + - - -
234K VAL 4.1 1.2 + - - -
235K ALA* 1.3 72.1 - - - +
237K THR* 1.3 64.3 + - - +
240K GLU* 3.9 11.0 - - + -
244K LEU* 3.4 28.5 - - + +
245K GLN* 3.7 11.5 - - + +
248K ALA* 3.5 18.5 - - + +
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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
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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