Contacts of the strand formed by residues 264 - 271 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E VAL* 4.2 16.4 - - + -
223E PHE* 4.0 26.7 - - + -
235E LYS* 3.5 22.4 - - + +
237E LEU* 3.8 31.6 - - + -
259E ALA* 2.8 26.1 + - + +
260E ASP 4.4 0.2 + - - -
262E GLU* 4.3 9.0 - - + +
263E GLY* 1.3 72.3 - - - +
265E ILE* 1.3 64.2 + - - +
266E ARG* 3.4 33.4 + - + -
902E CL 3.6 8.0 - - - +
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Residues in contact with ILE 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E PHE* 4.1 24.2 - - + -
235E LYS 2.7 27.6 + - - +
236E ILE* 3.3 19.2 - - + +
237E LEU 2.7 32.4 + - - +
263E GLY 4.4 6.7 - - - +
264E VAL* 1.3 69.0 - - - +
266E ARG* 1.3 57.0 + - - +
267E TYR* 3.7 26.0 - - + +
289E SER* 3.7 5.2 - - - +
295E HIS* 3.9 18.8 - - + +
319E ILE* 5.4 4.0 - - + +
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Residues in contact with ARG 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E ILE* 4.8 9.4 - - - -
237E LEU* 3.5 14.8 - - + +
239E VAL* 5.7 0.4 - - + -
256E ILE* 3.7 30.9 - - - +
259E ALA* 3.8 25.4 - - - +
260E ASP* 2.7 33.5 + - - +
264E VAL* 3.4 32.8 + - + +
265E ILE* 1.3 72.3 - - - +
267E TYR* 1.3 63.3 + - - +
286E THR 4.3 1.0 + - - -
287E ILE* 2.6 33.0 + - + +
288E ALA* 3.4 20.0 + - - -
289E SER* 2.9 47.1 + - - +
290E LYS* 5.1 1.4 - - - +
295E HIS* 3.3 13.0 - - - +
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Residues in contact with TYR 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E ILE* 3.8 22.2 - - + -
237E LEU 2.7 13.9 + - - +
238E VAL* 4.3 13.9 - - + -
239E VAL* 2.8 29.4 + - - +
265E ILE* 3.7 22.4 - - + +
266E ARG* 1.3 76.7 - - - +
268E VAL* 1.3 61.5 + - - +
269E ILE* 6.2 0.2 - - + -
294E ASP 3.3 22.6 + - - -
295E HIS* 3.4 29.0 + + - -
297E PHE* 4.2 14.6 - + + -
312E LEU* 4.2 9.2 - - + -
315E LYS* 3.1 37.8 + - + +
316E ILE* 3.7 23.9 - - + -
318E ALA 4.8 1.7 + - - -
319E ILE* 6.0 1.0 - - - +
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Residues in contact with VAL 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E VAL* 3.5 14.8 - - + +
241E THR* 4.5 4.5 - - + -
267E TYR* 1.3 73.1 - - - +
269E ILE* 1.4 62.6 + - - +
284E LEU* 3.2 54.7 - - + +
287E ILE* 3.8 33.2 - - + -
288E ALA* 3.7 10.9 - - + +
295E HIS 3.0 8.9 + - - +
296E VAL* 4.0 8.1 - - + -
297E PHE* 2.8 36.1 + - - +
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Residues in contact with ILE 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E PHE* 3.7 36.1 - - + -
238E VAL* 3.8 15.5 - - + -
239E VAL 2.8 12.4 + - - +
240E ILE* 3.6 16.7 - - + -
241E THR* 2.9 29.8 + - - +
267E TYR* 5.7 0.4 - - + -
268E VAL* 1.4 77.9 - - - +
270E GLY* 1.3 60.5 + - - +
271E VAL* 3.6 9.9 + - + +
297E PHE* 3.6 15.5 - - + +
299E VAL* 4.2 8.7 - - + -
305E LEU* 3.8 21.5 - - + -
308E ILE* 3.8 22.9 - - + -
312E LEU* 4.2 5.8 - - + -
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Residues in contact with GLY 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E THR* 3.5 5.2 - - - -
269E ILE* 1.3 69.6 - - - +
271E VAL* 1.3 61.8 - - - -
272E GLY 4.0 0.9 + - - +
275E PHE* 3.7 22.3 - - - -
284E LEU* 3.8 16.4 - - - +
297E PHE 3.1 12.0 + - - -
298E GLN* 3.4 9.7 + - - +
299E VAL 3.1 25.5 + - - +
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Residues in contact with VAL 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E ILE* 3.7 29.8 - - + -
241E THR 2.7 16.6 + - - +
242E ASP* 3.3 27.7 - - - +
269E ILE* 3.9 5.6 - - + +
270E GLY* 1.3 74.2 - - - -
272E GLY* 1.3 60.6 + - - +
275E PHE* 3.8 2.7 - - - -
299E VAL* 3.6 15.5 - - + -
301E ASN* 3.4 36.1 - - - +
302E PHE* 3.5 35.7 - - + +
305E LEU* 4.4 3.1 - - + -
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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