Contacts of the strand formed by residues 266 - 271 (chain B) in PDB entry 4QGC
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 LYS 266 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B ASP 3.3 6.6 + - - +
239B MET* 3.3 8.2 - - + +
240B VAL 2.8 28.1 + - - +
264B ASN 4.5 5.2 - - - +
265B ILE* 1.3 73.9 - - - +
267B ILE* 1.3 60.4 + - - +
268B ILE* 3.9 16.8 - - + -
288B ASP* 3.3 23.8 - - + +
434B SER 5.7 1.5 + - - -
439B HIS* 3.8 26.7 - - - -
462B GLN* 3.5 40.6 + - + +
465B LEU* 4.3 12.4 - - + +
466B TYR* 4.0 15.0 + - - +
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Residues in contact with ILE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B VAL* 3.7 8.1 - - + +
242B ALA* 4.6 7.9 - - + -
251B VAL* 4.2 20.4 - - + +
254B VAL* 3.9 15.9 - - + -
255B ARG* 3.5 65.7 - - + +
258B LEU* 3.8 22.2 - - + -
265B ILE 4.0 0.7 - - - +
266B LYS* 1.3 75.1 - - - +
268B ILE* 1.3 64.1 + - - +
269B SER* 4.5 7.0 - - - +
287B SER* 3.8 1.6 - - - -
288B ASP* 2.7 38.5 + - - +
289B GLY 3.3 3.8 + - - +
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Residues in contact with ILE 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B MET* 4.0 10.1 - - + -
240B VAL 2.8 9.1 + - - +
241B PHE* 3.4 27.3 - - + -
242B ALA 2.9 26.7 + - - -
266B LYS* 3.9 17.9 - - + +
267B ILE* 1.3 77.2 - - - +
269B SER* 1.3 61.9 + - - +
270B LYS 3.6 0.3 + - - -
288B ASP* 5.3 0.7 - - + -
289B GLY* 3.4 18.6 - - - +
290B ILE 3.7 6.5 - - - +
291B MET* 3.6 35.0 - - + +
323B PRO* 5.6 2.0 - - + +
325B ILE* 4.2 12.8 - - + -
465B LEU* 3.8 28.3 - - + -
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Residues in contact with SER 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B ALA* 3.9 5.4 - - - -
245B ILE* 3.9 12.7 - - - +
251B VAL* 3.4 18.2 - - - +
267B ILE* 3.8 4.4 + - - +
268B ILE* 1.3 70.9 - - - +
270B LYS* 1.3 63.0 + - - +
271B ILE* 3.6 2.2 + - - -
283B ILE* 3.7 19.5 - - - -
287B SER* 2.5 28.2 + - - -
289B GLY 3.0 7.5 + - - -
290B ILE* 3.5 10.9 - - - +
291B MET 2.8 22.7 + - - +
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Residues in contact with LYS 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ARG* 4.8 2.8 - - - +
113B ASP* 3.0 18.0 + - - +
241B PHE* 3.8 26.0 - - + +
242B ALA 2.8 16.6 + - - +
243B SER* 2.8 33.9 + - - +
244B PHE* 3.7 3.1 + - - -
245B ILE* 3.4 24.1 + - - +
268B ILE 4.3 0.7 - - - +
269B SER* 1.3 71.1 - - - +
271B ILE* 1.3 63.4 + - - +
272B GLU* 3.5 27.7 + - + +
291B MET* 3.5 38.4 - - + +
293B ALA* 5.4 4.5 - - + -
360B MET* 6.4 0.4 - - - -
1001B K 4.1 4.8 - - - -
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Residues in contact with ILE 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B ILE 4.1 7.4 - - - +
269B SER* 4.3 3.1 - - - +
270B LYS* 1.3 73.8 - - - +
272B GLU* 1.3 60.7 + - - +
273B ASN 4.1 3.1 - - - +
276B GLY* 3.8 34.5 - - - +
277B VAL* 3.9 12.1 - - + +
280B PHE* 4.2 6.1 - - + -
283B ILE* 3.9 32.3 - - + -
290B ILE* 4.0 22.9 - - + -
291B MET 2.9 10.5 + - - +
293B ALA 3.4 21.7 + - - -
297B LEU* 3.6 11.0 - - + +
313B MET* 3.9 27.8 - - + -
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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