Contacts of the strand formed by residues 258 - 262 (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 HIS 258 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206F HIS 3.6 6.9 + - - +
207F ILE* 4.0 15.3 - - + -
208F THR* 3.0 25.7 + - - -
253F VAL* 4.4 2.4 + - - +
256F THR* 2.8 28.8 + - - -
257F ASN* 1.3 83.3 - - + +
259F LEU* 1.3 62.4 + - - +
288F LEU* 4.2 3.1 - - - -
289F ASP* 3.6 27.3 + - + +
290F ALA* 3.9 10.6 - - + +
326F THR* 3.6 40.3 + - + -
327F LEU* 3.9 19.9 - - + +
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Residues in contact with LEU 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208F THR* 3.5 19.3 - - + +
210F VAL* 3.7 27.1 - - + -
249F ILE* 4.4 2.7 - - + -
253F VAL* 3.8 14.1 - - + -
258F HIS* 1.3 75.5 - - - +
260F VAL* 1.3 86.8 + - - +
261F THR* 4.4 4.3 - - + -
275F ILE* 4.2 20.4 - - + +
276F CYS* 5.3 0.7 - - - -
279F ILE* 4.0 27.6 - - + -
288F LEU* 4.2 10.6 - - + +
290F ALA 4.7 2.6 + - - -
291F PRO 4.2 1.9 - - - +
292F ALA* 3.3 23.5 - - + +
293F VAL 3.2 17.0 + - - -
326F THR* 4.7 3.0 + - - +
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Residues in contact with VAL 260 (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 18.4 - - + -
208F THR 2.8 12.6 + - - +
209F VAL* 3.2 9.3 - - + +
210F VAL 3.1 21.8 + - - -
259F LEU* 1.3 83.1 - - - +
261F THR* 1.3 72.2 + - - +
262F VAL* 4.8 6.5 - - + -
293F VAL* 3.4 33.0 - - + +
295F VAL* 4.4 5.8 - - + -
319F ILE* 5.7 0.4 - - + -
322F ALA* 4.3 19.1 - - + +
323F ILE* 4.7 11.7 - - + -
326F THR* 3.7 11.2 - - - +
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Residues in contact with THR 261 (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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210F VAL* 3.4 12.3 - - + +
259F LEU* 4.4 10.5 - - + -
260F VAL* 1.3 75.3 - - - +
262F VAL* 1.3 62.4 + - - +
263F GLU* 5.3 1.9 + - - +
272F GLY* 3.6 17.3 - - - +
275F ILE* 3.9 39.5 - - + -
276F CYS* 4.6 7.0 - - - -
292F ALA* 6.0 0.2 - - + -
293F VAL 3.1 6.1 + - - +
294F ARG* 3.6 24.1 - - - +
295F VAL* 2.9 26.6 + - - +
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Residues in contact with VAL 262 (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* 3.7 15.3 - - + -
210F VAL 2.8 6.5 + - - +
211F SER* 2.6 42.0 + - - +
212F HIS 4.1 0.2 + - - -
215F PRO* 4.0 14.6 - - + -
219F CYS* 3.5 21.1 - - - -
238F MET* 5.4 0.5 - - - +
260F VAL* 4.8 2.9 - - + -
261F THR* 1.3 79.2 - - - +
263F GLU* 1.3 63.0 + - - +
295F VAL* 3.2 19.1 - - + -
314F PRO* 4.5 6.1 - - + -
319F ILE* 3.8 35.9 - - + -
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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