Contacts of the strand formed by residues 207 - 211 (chain F) in PDB entry 3EXG
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 ILE 207 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206F HIS* 1.3 80.7 - - + +
208F THR* 1.3 73.5 + - - +
209F VAL* 3.9 3.8 + - + -
231F VAL* 4.6 0.4 - - + -
232F GLU 3.7 1.7 + - - +
233F CYS* 3.7 31.2 - - + -
234F GLU* 2.9 28.1 + - - +
256F THR* 3.6 10.7 - - - +
258F HIS* 3.9 21.3 - - + +
260F VAL* 3.9 24.9 - - + -
323F ILE* 3.6 38.6 - - + +
326F THR* 4.4 3.1 - - - -
327F LEU* 4.2 13.5 - - + -
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Residues in contact with THR 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F ILE* 1.3 76.4 - - - +
209F VAL* 1.3 63.3 + - - +
210F VAL* 4.0 12.1 - - + -
234F GLU* 3.9 5.2 - - - +
236F ILE* 3.7 22.2 - - + -
249F ILE* 4.7 1.1 - - + -
252F SER* 2.9 30.7 + - - +
253F VAL* 3.4 12.6 + - + -
256F THR* 2.6 22.7 + - - +
258F HIS 3.0 13.8 + - - -
259F LEU* 3.5 9.5 - - + +
260F VAL 2.8 28.2 + - - +
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Residues in contact with VAL 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F ILE* 3.9 6.9 + - + -
208F THR* 1.3 78.8 - - - +
210F VAL* 1.3 57.2 + - - +
219F CYS* 3.8 17.9 - - + -
233F CYS* 4.4 18.6 - - + -
234F GLU 3.3 7.0 + - - +
235F VAL* 3.4 12.8 - - + +
236F ILE* 2.7 34.3 + - - +
260F VAL* 3.2 11.7 - - + +
262F VAL* 3.7 24.9 - - + -
319F ILE* 4.8 0.2 - - + -
323F ILE* 3.8 33.7 - - + -
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Residues in contact with VAL 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208F THR* 4.0 7.9 - - + -
209F VAL* 1.3 76.4 - - - +
211F SER* 1.3 68.3 + - - +
236F ILE* 3.9 10.1 - - + -
238F MET* 3.6 26.2 - - + -
249F ILE* 3.8 35.9 - - + -
259F LEU* 3.7 25.4 - - + -
260F VAL 3.1 8.1 + - - +
261F THR* 3.4 6.9 - - + -
262F VAL* 2.8 25.5 + - - +
275F ILE* 3.8 15.0 - - + -
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Residues in contact with SER 211 (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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209F VAL 5.3 0.4 - - - -
210F VAL* 1.3 84.5 - - - +
212F HIS* 1.3 67.6 + - - +
215F PRO* 3.8 15.9 - - - +
216F VAL* 3.5 16.9 - - - +
219F CYS* 4.1 11.4 - - - -
235F VAL* 5.9 0.9 - - - -
236F ILE 3.2 9.2 + - - +
238F MET* 2.9 33.4 + - - +
262F VAL* 2.6 33.3 + - - +
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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