Contacts of the strand formed by residues 238 - 243 (chain F) in PDB entry 6FF7
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 238 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197F LEU* 3.4 21.5 - - - +
198F ALA* 4.9 1.9 + - + -
211F GLY* 4.1 20.9 - - - +
212F GLY 3.0 17.1 + - - +
215F ASN* 5.2 5.1 - - - +
216F ASP 5.9 1.6 - - - +
217F ILE* 6.2 3.4 - - + +
236F ASP 3.6 1.9 + - - +
237F SER* 1.3 74.0 - - - +
239F THR* 1.3 60.9 + - - +
240F GLY 4.9 2.5 - - - +
252F SER* 5.7 6.5 - - - -
253F ASN 3.4 10.5 - - - +
254F ALA* 4.2 3.8 - - + +
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Residues in contact with THR 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197F LEU* 4.5 10.6 - - - +
198F ALA* 3.9 11.4 - - - +
237F SER* 3.8 4.2 + - - -
238F VAL* 1.3 75.0 - - - +
240F GLY* 1.3 57.6 + - - +
253F ASN 3.0 11.6 + - - -
254F ALA* 5.3 2.5 - - - -
255F MET 5.8 0.2 - - - -
287F ASN 4.9 2.0 - - - -
288F LEU* 4.3 14.8 - - - +
289F LEU* 3.2 38.7 + - - +
290F ARG* 5.2 0.5 - - - +
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Residues in contact with GLY 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F ALA* 3.8 6.1 - - - +
238F VAL* 3.7 3.1 - - - +
239F THR* 1.3 81.0 - - - +
241F LEU* 1.3 60.5 - - - -
251F LEU 3.5 1.0 - - - +
252F SER* 3.3 7.3 - - - -
253F ASN* 3.0 27.2 + - - +
289F LEU 3.4 13.4 + - - -
290F ARG* 4.5 10.3 - - - -
291F CYS* 5.2 4.9 + - - +
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Residues in contact with LEU 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F ALA* 3.8 23.8 - - + +
199F VAL 5.0 1.8 + - - +
200F THR* 4.6 19.5 - - - +
209F ILE* 5.2 6.5 - - + +
210F SER 6.3 0.2 - - - -
211F GLY* 5.7 3.6 - - - +
240F GLY* 1.3 74.5 - - - -
242F SER* 1.3 66.1 + - - +
250F LEU* 6.0 3.6 - - + -
251F LEU 3.3 5.8 - - - +
252F SER* 4.8 3.1 - - - +
291F CYS 5.1 0.8 - - - +
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Residues in contact with SER 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200F THR* 5.0 5.4 - - - -
241F LEU* 1.3 79.2 - - - +
243F LEU* 1.3 65.3 + - - +
244F SER 3.9 0.3 + - - -
249F TYR 3.8 0.5 - - - +
250F LEU* 3.4 4.3 - - - +
251F LEU* 2.8 44.0 + - - +
291F CYS 3.5 25.6 - - - -
292F SER* 4.8 5.2 - - - -
293F TRP* 5.2 3.6 - - - -
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Residues in contact with LEU 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200F THR* 4.9 9.6 - - - -
201F PHE 4.4 17.0 - - - +
202F ASN* 5.7 2.5 - - - -
203F ASP 6.2 0.2 - - - +
242F SER* 1.3 76.5 - - - +
244F SER* 1.3 70.8 + - - +
245F SER 3.9 0.2 + - - -
247F GLY* 5.1 8.7 - - - +
249F TYR 3.4 6.5 - - - +
250F LEU* 4.3 6.5 - - + +
293F TRP* 4.5 9.5 - - - +
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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