Contacts of the strand formed by residues 207 - 211 (chain V) 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 V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206V HIS* 1.3 81.9 - - + +
208V THR* 1.3 72.9 + - - +
209V VAL* 3.9 3.5 + - + -
231V VAL* 4.6 0.7 - - + -
232V GLU 3.7 0.6 + - - -
233V CYS* 3.7 29.6 - - + -
234V GLU* 2.8 28.8 + - - +
256V THR* 3.5 9.0 - - - +
258V HIS* 4.1 19.5 - - + +
259V LEU 4.9 0.2 - - - -
260V VAL* 3.7 26.2 - - + -
323V ILE* 3.5 39.9 - - + +
326V THR* 4.5 4.0 - - - -
327V LEU* 4.1 16.6 - - + -
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Residues in contact with THR 208 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207V ILE* 1.3 76.1 - - - +
209V VAL* 1.3 64.1 + - - +
210V VAL* 4.1 4.9 - - + -
234V GLU* 4.0 3.1 - - - +
236V ILE* 3.6 20.2 - - + -
249V ILE* 4.7 2.0 - - + -
252V SER* 2.9 40.3 + - - +
253V VAL* 3.5 8.0 + - + -
256V THR* 2.8 21.7 + - - +
258V HIS 3.1 8.5 + - - -
259V LEU* 3.5 18.0 - - + +
260V VAL 2.8 27.5 + - - +
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Residues in contact with VAL 209 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207V ILE* 4.3 13.2 - - + -
208V THR* 1.3 79.9 - - - +
210V VAL* 1.3 60.2 + - - +
219V CYS* 3.7 32.1 - - + -
233V CYS* 4.4 12.1 - - + -
234V GLU 3.3 7.2 + - - +
235V VAL* 3.4 11.0 - - + +
236V ILE* 2.7 33.1 + - - +
260V VAL* 3.3 7.9 - - + +
262V VAL* 4.1 13.0 - - + -
319V ILE* 4.7 2.9 - - + -
323V ILE* 3.7 33.7 - - + -
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Residues in contact with VAL 210 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208V THR* 4.1 6.5 - - + -
209V VAL* 1.3 77.7 - - - +
211V SER* 1.3 66.5 + - - +
236V ILE* 3.8 11.0 - - + +
238V MET* 3.5 28.6 - - + +
249V ILE* 3.8 37.5 - - + -
259V LEU* 3.8 13.2 - - + -
260V VAL 2.9 7.9 + - - -
261V THR* 3.4 11.6 - - + -
262V VAL* 2.7 28.1 + - - +
275V ILE* 3.8 19.5 - - + -
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Residues in contact with SER 211 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209V VAL 5.4 0.4 - - - -
210V VAL* 1.3 82.0 - - - +
212V HIS* 1.3 69.6 + - - +
215V PRO* 3.7 8.1 - - - +
216V VAL* 3.5 30.0 + - - +
219V CYS* 3.8 20.9 - - - -
235V VAL* 5.8 0.7 - - - -
236V ILE 3.2 9.2 + - - +
238V MET* 2.9 33.2 + - - +
262V VAL* 2.7 22.4 + - - +
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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