Contacts of the strand formed by residues 264 - 271 (chain I) in PDB entry 3Q3G
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 VAL 264 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219I VAL* 4.3 15.3 - - + -
223I PHE* 3.6 42.6 - - + -
235I LYS* 3.4 19.1 - - + +
237I LEU* 3.8 24.0 - - + -
259I ALA* 2.9 25.3 + - + +
260I ASP* 4.9 1.3 - - - +
262I GLU* 4.1 9.2 - - + +
263I GLY* 1.3 71.9 - - - +
265I ILE* 1.4 60.5 + - - +
266I ARG* 3.2 34.9 + - + +
289I SER* 3.7 0.9 + - - -
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Residues in contact with ILE 265 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234I PHE* 4.1 24.0 - - + -
235I LYS 2.7 27.3 + - - +
236I ILE* 3.3 20.1 - - + +
237I LEU* 2.7 32.7 + - - +
263I GLY 4.4 7.9 - - - +
264I VAL* 1.4 68.5 - - - +
266I ARG* 1.3 55.8 + - - +
267I TYR* 3.7 25.6 - - + +
289I SER* 3.7 5.8 - - - +
295I HIS* 3.9 19.3 - - - +
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Residues in contact with ARG 266 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215I ILE* 4.8 9.2 - - - -
237I LEU* 3.5 15.7 - - + +
239I VAL* 5.6 0.7 - - + -
256I ILE* 3.9 27.6 - - - +
259I ALA* 3.9 24.3 - - - +
260I ASP* 2.8 31.7 + - - +
264I VAL* 3.2 36.9 + - + +
265I ILE* 1.3 73.6 - - - +
267I TYR* 1.3 61.8 + - - +
286I THR 4.4 1.2 + - - -
287I ILE* 2.6 32.3 + - + +
288I ALA* 3.5 8.4 + - - -
289I SER* 2.9 63.7 + - - +
290I LYS* 4.9 3.2 - - - +
295I HIS* 3.3 13.9 - - - +
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Residues in contact with TYR 267 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236I ILE* 3.8 22.7 - - + -
237I LEU 2.7 11.8 + - - +
238I VAL* 4.4 9.6 - - + -
239I VAL* 2.8 35.6 + - - +
265I ILE* 3.7 22.0 - - + +
266I ARG* 1.3 75.5 - - - +
268I VAL* 1.3 55.6 + - - +
269I ILE* 6.2 0.2 - - + -
287I ILE* 5.7 0.2 - - - -
288I ALA* 4.8 0.4 - - - -
294I ASP 3.3 21.8 + - - -
295I HIS* 3.4 28.9 + + - +
297I PHE* 4.2 14.6 - + + -
312I LEU* 4.4 13.7 - - + -
315I LYS* 3.1 39.2 + - + +
316I ILE* 3.7 20.7 - - + -
318I ALA 4.8 1.7 + - - -
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Residues in contact with VAL 268 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239I VAL* 3.3 15.3 - - + +
241I THR* 4.7 4.3 - - + -
267I TYR* 1.3 73.2 - - - +
269I ILE* 1.4 64.5 + - - +
284I LEU* 3.3 53.6 - - + +
287I ILE* 3.8 34.3 - - + -
288I ALA* 3.7 11.6 - - + +
295I HIS 3.0 8.3 + - - +
296I VAL* 3.7 8.5 - - + -
297I PHE* 2.8 35.2 + - - +
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Residues in contact with ILE 269 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156I PHE* 3.6 36.3 - - + -
238I VAL* 4.0 14.4 - - + -
239I VAL 2.8 12.4 + - - +
240I ILE* 3.7 19.0 - - + -
241I THR* 3.2 28.8 + - - +
267I TYR 5.7 0.2 - - - -
268I VAL* 1.4 79.1 - - - +
270I GLY* 1.3 58.7 + - - +
271I VAL* 3.6 5.3 + - + +
297I PHE* 3.7 15.7 - - + +
299I VAL* 4.1 14.6 - - + -
305I LEU* 3.7 22.0 - - + -
308I ILE* 3.8 21.5 - - + -
312I LEU* 4.5 6.1 - - + -
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Residues in contact with GLY 270 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241I THR 3.6 0.2 - - - -
269I ILE* 1.3 69.3 - - - +
271I VAL* 1.3 61.2 + - - -
272I GLY 3.8 1.4 + - - +
275I PHE* 3.6 27.9 - - - -
284I LEU* 3.7 15.9 - - - +
297I PHE 3.1 13.4 + - - -
298I GLN* 3.6 10.7 + - - +
299I VAL 3.2 23.5 + - - +
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Residues in contact with VAL 271 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240I ILE* 3.9 12.8 - - + -
241I THR 3.0 17.1 + - - +
242I ASP* 3.4 26.2 - - - +
269I ILE* 3.8 11.0 - - + +
270I GLY* 1.3 71.4 - - - -
272I GLY* 1.3 63.9 + - - +
275I PHE* 3.9 2.2 - - - -
299I VAL* 3.6 14.8 - - + -
301I ASN* 3.4 37.5 - - - +
302I PHE* 3.6 44.8 - - + +
305I LEU* 4.5 2.0 - - + -
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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