Contacts of the strand formed by residues 285 - 292 (chain D) in PDB entry 2Q2U
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 ARG 285 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D ASP* 2.6 39.6 + - - -
75D PHE* 3.7 30.2 - - - -
161D GLU* 4.4 5.7 + - - -
275D TYR* 3.6 1.6 - - - +
276D PHE* 2.9 43.4 + - - +
278D MET 3.1 22.9 + - - +
279D GLY* 3.5 27.3 - - - +
280D SER* 3.0 11.5 + - - +
283D CYS 5.1 0.2 - - - +
284D PRO* 1.3 70.3 - - - +
286D PHE* 1.3 111.8 + - + +
287D PRO 3.3 2.1 - - - -
12K G 4.8 4.9 - - - +
13K G 5.5 7.2 - - - +
14K G 6.5 0.9 - - - -
31L C 4.6 7.2 + - - +
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Residues in contact with PHE 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D GLU* 4.6 4.3 - - - -
188D LYS* 4.0 17.7 - - - -
190D PHE* 3.6 26.4 - + + -
274D LYS 3.7 1.7 - - - +
276D PHE* 3.7 28.9 - + + -
285D ARG* 1.3 109.4 - - - +
287D PRO* 1.3 74.2 - - - +
288D VAL* 3.2 14.1 + - - +
11K G 6.2 1.1 - - - +
12K G 3.4 33.0 + + - +
13K G 5.4 0.6 + - - -
31L C 3.7 12.3 - - + -
32L C 3.7 32.8 - - + -
33L A 4.1 11.9 - - - -
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Residues in contact with PRO 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D PHE* 3.8 27.6 - - + -
246D SER 3.6 17.9 - - - +
247D ILE* 4.0 14.1 - - + +
249D THR* 3.4 18.0 - - - +
273D PHE* 4.9 1.3 - - + -
274D LYS 3.6 6.7 - - - +
275D TYR* 4.2 4.5 - - + -
284D PRO* 3.8 16.6 - - + +
285D ARG 3.3 3.3 - - - -
286D PHE* 1.3 90.3 - - - +
288D VAL* 1.3 58.1 + - - +
289D PHE 4.3 0.4 - - - -
12K G 4.3 25.2 - - - +
13K G 4.8 4.7 - - - -
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Residues in contact with VAL 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D PHE* 4.5 0.9 - - + -
247D ILE* 4.3 0.4 - - - -
249D THR* 4.0 7.2 - - + -
250D GLY* 4.3 5.8 - - - -
273D PHE* 3.1 7.2 - - - -
274D LYS* 2.8 57.3 + - + -
286D PHE 3.2 16.2 - - - +
287D PRO* 1.3 77.0 - - - +
289D PHE* 1.3 74.5 + - - +
290D ILE* 3.9 1.5 - - + +
33L A 3.4 32.3 - - - +
34L C 3.5 31.2 - - - +
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Residues in contact with PHE 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D ILE* 4.7 2.7 - - + -
247D ILE* 3.6 12.1 - - + +
249D THR 3.3 19.4 + - - +
250D GLY* 3.7 22.3 - - - +
251D PHE* 3.5 36.1 - + + -
255D GLN* 3.8 22.9 - - - -
259D PHE* 3.9 20.0 - + - -
271D VAL* 3.9 25.1 - - + -
272D LYS 3.9 9.4 - - - -
273D PHE* 4.1 2.7 - - + -
288D VAL* 1.3 85.4 - - - +
290D ILE* 1.3 66.0 + - - +
291D GLY* 3.4 39.9 - - - -
292D ILE* 3.9 3.6 - - + -
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Residues in contact with ILE 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D ASP* 3.5 25.1 - - - +
250D GLY 5.6 0.2 - - - +
255D GLN* 5.3 1.9 + - - -
272D LYS* 3.1 28.3 + - + +
273D PHE* 3.7 10.5 - - - +
274D LYS* 3.6 31.2 - - + +
288D VAL* 3.9 4.7 - - + +
289D PHE* 1.3 90.0 - - - +
291D GLY* 1.3 61.5 + - - +
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Residues in contact with GLY 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D GLN* 5.8 0.7 - - - -
271D VAL* 3.5 3.1 - - - +
272D LYS* 2.7 42.2 + - - +
289D PHE* 3.4 17.9 - - - -
290D ILE* 1.3 84.3 - - - +
292D ILE* 1.3 60.4 + - - -
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Residues in contact with ILE 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D GLN* 6.2 0.7 - - - +
259D PHE* 3.9 21.8 - - + -
266D TYR* 3.5 38.8 - - + +
269D LYS* 4.6 15.3 - - + +
270D MET 3.6 11.0 - - - +
271D VAL* 4.1 10.8 - - + -
272D LYS* 3.7 9.5 + - - -
289D PHE* 4.2 3.6 - - + -
291D GLY* 1.3 76.6 - - - -
293D ARG* 1.3 84.7 + - + +
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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