Contacts of the strand formed by residues 251 - 256 (chain X) 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 VAL 251 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178X HIS* 4.1 4.1 + - - -
181X PHE* 3.4 9.2 - - + +
183X VAL* 4.5 7.6 - - + -
240X ALA* 3.7 30.7 - - + +
243X PHE* 3.6 41.3 - - + +
244X ARG* 4.0 3.6 - - - +
249X GLN* 3.9 5.6 - - + +
250X ASP* 1.3 77.2 - - - +
252X LEU* 1.3 71.8 + - - +
303X SER 3.1 6.5 + - - +
304X VAL* 3.6 24.6 - - + -
305X THR* 2.9 27.8 + - - -
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Residues in contact with LEU 252 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174X ILE* 3.7 29.4 - - + -
175X ALA* 3.7 25.8 - - + +
178X HIS* 4.0 20.9 - - + +
181X PHE 3.1 7.7 + - - +
182X SER* 3.2 17.4 - - - +
183X VAL 2.7 32.9 + - - +
251X VAL* 1.3 78.1 - - - +
253X LEU* 1.3 59.0 + - - +
254X PHE* 3.3 31.3 - - + -
305X THR* 3.3 26.2 - - + +
307X VAL* 4.7 7.0 - - + -
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Residues in contact with LEU 253 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183X VAL* 3.0 35.0 - - + +
185X THR* 3.5 22.7 - - - +
236X GLY 4.7 3.8 - - - +
237X LEU* 4.0 22.2 - - + -
240X ALA* 4.6 13.2 - - + -
251X VAL 4.3 0.2 - - - -
252X LEU* 1.3 75.0 - - - +
254X PHE* 1.3 64.9 + - - +
255X ILE* 4.0 19.2 - - + +
296X ILE* 3.9 25.4 - - + -
304X VAL* 4.6 9.6 - - + -
305X THR 3.0 8.6 + - - +
306X SER* 3.3 8.4 - - - -
307X VAL 2.8 31.7 + - - +
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Residues in contact with PHE 254 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167X ILE* 4.1 14.8 - - + -
170X LEU* 3.9 29.8 - - + -
171X ILE* 4.0 20.4 - - + -
174X ILE* 5.5 1.8 - - + -
175X ALA* 4.1 18.6 - - + -
182X SER* 5.6 2.9 - - - -
183X VAL 3.1 9.7 + - - -
184X PHE* 3.3 28.8 - + + -
185X THR* 2.9 30.5 + - - +
252X LEU* 3.3 32.5 - - + -
253X LEU* 1.3 75.2 - - - +
255X ILE* 1.3 63.1 + - - +
256X ASP 4.0 0.2 - - - -
307X VAL* 3.3 40.8 - - + -
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Residues in contact with ILE 255 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185X THR* 3.8 7.4 - - - +
187X VAL* 4.4 15.3 - - + -
233X ALA* 5.3 5.8 - - + -
237X LEU* 6.0 0.2 - - + -
253X LEU* 4.0 22.7 - - + +
254X PHE* 1.3 76.3 - - - +
256X ASP* 1.3 59.5 + - - +
258X ILE* 3.5 32.2 + - + -
296X ILE* 3.5 33.2 - - + -
306X SER* 5.4 0.4 - - - -
307X VAL 3.0 8.3 + - - +
308X GLN* 3.6 28.3 - - + +
309X ALA* 2.6 35.2 + - - +
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Residues in contact with ASP 256 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163X LYS* 4.9 2.6 - - - +
164X THR* 4.3 16.9 + - - +
167X ILE* 3.4 26.4 - - + +
184X PHE* 4.7 20.1 - - + -
185X THR 3.3 7.5 + - - -
186X GLY* 3.4 8.7 - - - -
187X VAL 2.8 24.3 + - - +
189X GLU* 3.4 26.3 - - - +
254X PHE 4.0 0.4 + - - -
255X ILE* 1.3 76.4 - - - +
257X ASN* 1.3 63.9 + - - +
309X ALA* 3.3 17.5 - - + +
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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