Contacts of the strand formed by residues 231 - 236 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106T LEU* 3.6 1.2 - - - +
107T GLY* 3.0 25.6 + - - -
185T ILE* 4.7 6.3 - - - -
203T CYS* 3.1 20.9 - - - -
205T TYR* 5.9 3.1 - - - -
222T LEU* 4.1 11.1 - - - +
227T ALA 2.9 19.7 + - - -
228T MET* 2.9 18.6 + - - +
229T LYS 3.5 1.0 + - - -
230T TYR* 1.3 78.4 - - - +
232T ILE* 1.3 66.5 + - - +
233T ILE* 4.3 10.6 - - - +
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Residues in contact with ILE 232 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102T GLY 4.2 3.4 - - - +
105T LEU* 3.4 48.2 - - + +
106T LEU* 3.7 22.4 - - + +
108T ARG 4.0 7.2 - - - +
110T VAL* 5.2 4.0 - - + -
202T TYR* 6.4 0.7 - - + -
203T CYS 2.9 13.2 + - - +
204T VAL* 3.4 16.8 - - + +
205T TYR 3.1 21.5 + - - +
231T SER* 1.3 79.5 - - - +
233T ILE* 1.3 65.1 + - - +
234T VAL* 3.8 5.1 + - + -
255T ILE* 3.6 36.6 - - + -
259T PHE* 4.4 8.5 - - + -
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Residues in contact with ILE 233 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108T ARG 3.6 4.7 + - - +
109T VAL* 3.3 27.4 - - + +
110T VAL* 3.0 26.0 + - - +
205T TYR* 3.3 32.8 - - + +
207T ALA* 5.0 1.3 - - + -
215T VAL* 4.5 17.0 - - + -
218T LEU* 5.3 0.9 - - + -
219T VAL* 4.6 5.2 - - + -
222T LEU* 3.7 31.2 - - + -
228T MET* 3.7 26.5 - - + -
231T SER* 4.3 5.2 - - - +
232T ILE* 1.3 84.2 - - - +
234T VAL* 1.3 68.2 + - - +
235T ALA* 4.5 1.6 - - + +
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Residues in contact with VAL 234 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110T VAL* 3.4 12.1 - - + -
111T ASP 3.2 25.4 - - - +
112T ALA* 4.3 2.7 - - - -
204T VAL* 5.0 1.8 - - + -
205T TYR 3.1 7.9 + - - +
206T VAL* 3.5 8.1 - - - +
207T ALA 3.0 20.8 + - - -
232T ILE* 3.8 6.9 + - + +
233T ILE* 1.3 75.4 - - - +
235T ALA* 1.3 59.3 + - - +
236T ALA 4.3 0.2 + - - -
248T ALA* 4.0 23.5 - - + +
251T THR* 4.1 8.1 - - - +
252T ALA* 4.0 18.2 - - + -
255T ILE* 3.8 29.6 - - + -
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Residues in contact with ALA 235 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109T VAL* 4.7 5.8 - - + -
110T VAL 3.0 9.8 + - - +
111T ASP* 3.5 24.5 - - - +
112T ALA 4.1 0.3 + - - -
117T ILE* 5.6 4.8 - - + +
207T ALA* 3.6 21.1 - - + +
215T VAL* 4.1 20.9 - - + -
233T ILE* 3.9 5.5 + - + -
234T VAL* 1.3 75.6 - - - +
236T ALA* 1.3 61.5 + - - +
237T THR* 4.0 7.4 - - + +
240T GLU* 4.4 3.5 - - - +
124W PHE* 5.7 2.5 - - + -
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Residues in contact with ALA 236 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112T ALA* 5.1 2.0 - - + -
207T ALA 2.7 13.4 + - - +
208T VAL* 4.8 1.6 - - - -
209T GLY 3.0 19.9 + - - -
235T ALA* 1.3 74.9 - - - +
237T THR* 1.3 69.5 + - - +
240T GLU* 3.7 10.5 - - + -
244T LEU* 3.5 28.0 - - + +
245T GLN* 3.4 17.9 - - + +
248T ALA* 3.8 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