Contacts of the strand formed by residues 262 - 267 (chain F) in PDB entry 3GHG
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 TYR 262 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245F ALA* 3.5 6.3 - - - +
246F LEU* 3.1 48.9 + - + +
248F VAL* 5.1 1.1 - - + -
260F ALA 3.9 12.6 - - - -
261F ASP* 1.3 91.1 - - - +
263F ALA* 1.3 61.8 + - - +
265F PHE* 4.5 2.2 - - + +
278F TYR* 3.2 50.3 - + + -
280F TYR 3.9 3.4 - - - -
281F PHE* 3.6 20.9 - + + -
282F ALA* 5.0 1.8 - - - -
288F ASP* 2.2 40.4 + - - -
289F ALA 3.6 1.4 + - - -
290F PHE* 3.1 45.6 + + + -
369F TRP* 3.9 11.0 - + - -
392F LEU* 6.2 0.2 - - - -
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Residues in contact with ALA 263 (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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245F ALA* 4.6 6.3 - - + -
262F TYR* 1.3 71.3 - - - +
264F MET* 1.3 76.3 + - - +
265F PHE 3.1 4.0 + - - -
278F TYR* 3.3 5.4 - - - +
279F ALA 2.9 19.7 + - - -
280F TYR* 3.1 53.2 + - + +
282F ALA* 4.6 4.9 - - + +
389F PHE* 4.6 10.3 - - + -
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Residues in contact with MET 264 (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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243F PRO* 3.7 33.0 - - + -
244F TYR 3.2 13.3 + - - +
245F ALA* 4.6 0.6 - - - +
263F ALA* 1.3 80.1 - - - +
265F PHE* 1.3 64.1 + - - +
266F LYS* 3.5 13.7 + - + +
277F THR* 3.2 10.9 - - - +
278F TYR* 3.6 4.2 - - - -
279F ALA* 4.0 17.4 + - + -
280F TYR* 5.7 4.5 - - + -
389F PHE* 4.2 34.3 - - + -
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Residues in contact with PHE 265 (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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194F PHE* 4.1 19.3 - + - -
233F ILE* 4.3 4.5 - - + -
237F SER* 3.8 12.6 - - - +
244F TYR* 2.6 32.8 + - + +
245F ALA* 4.3 0.2 - - - -
246F LEU* 3.4 42.8 - - + +
262F TYR 4.5 3.8 - - - +
263F ALA 3.1 3.2 + - - +
264F MET* 1.3 73.8 - - - +
266F LYS* 1.3 67.1 + - - +
267F VAL* 3.3 30.1 - - + -
276F LEU* 3.3 32.3 - - + -
277F THR 3.5 5.6 - - - -
278F TYR* 4.5 5.4 - + + +
335F TRP* 5.2 3.4 - + - -
384F MET* 6.4 0.2 - - + -
386F ILE* 3.8 33.0 - - + -
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Residues in contact with LYS 266 (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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237F SER* 3.4 28.5 + - - +
238F THR* 4.2 19.4 - - + +
241F ALA* 4.6 14.8 + - - +
242F ILE 4.3 12.1 + - - -
243F PRO* 4.4 10.3 - - - +
244F TYR 5.7 0.2 - - - +
264F MET* 3.6 16.2 - - + +
265F PHE* 1.3 84.8 + - - +
267F VAL* 1.3 66.2 + - - +
276F LEU* 3.8 0.7 - - - -
277F THR* 2.8 48.2 + - - +
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Residues in contact with VAL 267 (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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230F ASN* 5.2 3.4 - - + +
233F ILE* 3.2 32.8 - - + -
234F HIS* 2.1 47.4 + - + +
237F SER* 2.9 9.1 + - - +
238F THR* 3.2 6.9 - - - +
265F PHE* 3.3 26.9 - - + -
266F LYS* 1.3 75.2 - - - +
268F GLY* 1.3 61.2 - - - +
274F TYR* 3.6 18.8 - - + +
275F ARG 3.2 10.1 - - - +
276F LEU* 4.7 0.7 - - + -
335F TRP* 4.2 17.3 - - + -
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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