Contacts of the strand formed by residues 270 - 276 (chain A) 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 MET 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A GLU* 4.0 31.6 - - + +
195A ALA* 3.4 26.0 - - - +
196A THR* 3.4 23.1 - - + +
268A GLY 3.8 1.2 + - - +
269A LYS* 1.3 75.0 - - - +
271A VAL* 1.3 63.3 + - - +
292A ILE* 3.7 2.1 - - - +
293A ARG* 2.8 37.2 + - - +
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A GLU* 3.4 5.2 - - - -
195A ALA* 3.1 33.5 + - + +
197A ILE* 3.5 37.0 - - + -
236A ILE* 4.6 7.0 - - + -
238A VAL* 4.5 13.0 - - + -
247A ILE* 5.5 4.0 - - + -
259A PHE* 4.9 1.3 - - + -
270A MET* 1.3 79.7 - - - +
272A LYS* 1.3 67.2 + - - +
273A PHE* 4.0 4.5 - - + -
289A PHE* 3.9 22.9 - - + -
291A GLY 3.4 8.3 - - - +
292A ILE* 4.1 16.2 - - + -
293A ARG 4.4 0.4 - - - +
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Residues in contact with LYS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ALA 3.5 8.5 - - - +
194A GLU* 3.7 25.6 - - + +
271A VAL* 1.3 75.0 - - - +
273A PHE* 1.3 65.5 + - - +
289A PHE* 4.0 6.1 - - - -
290A ILE* 3.1 37.4 + - + +
291A GLY* 2.7 26.6 + - - +
292A ILE 3.7 18.0 + - - -
293A ARG 4.4 11.4 - - - +
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Residues in contact with PHE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ASP* 3.7 1.7 - - - -
193A ALA* 3.1 40.5 + - + -
194A GLU 3.6 29.2 - - - -
195A ALA* 3.8 11.7 - - + -
240A TYR* 4.0 11.9 - + - -
245A PHE* 3.7 24.7 - + - -
247A ILE* 3.7 26.9 - - + -
271A VAL* 4.0 9.2 - - + -
272A LYS* 1.3 80.2 - - - +
274A LYS* 1.3 70.8 + - - +
275A TYR* 3.5 28.5 - + + -
284A PRO* 4.5 0.9 - - + -
287A PRO* 4.9 0.7 - - + -
288A VAL 3.1 17.5 - - - +
289A PHE* 4.1 0.9 - - - -
290A ILE* 3.7 11.0 - - - +
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Residues in contact with LYS 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A THR* 6.1 2.2 - - - +
13A GLU* 5.5 9.1 + - - +
190A PHE* 3.7 37.7 - - + +
191A LYS 3.2 11.0 - - - +
192A ASP* 4.3 5.6 - - - +
273A PHE* 1.3 77.7 - - - +
275A TYR* 1.3 64.3 + - - +
286A PHE 3.7 0.5 - - - +
287A PRO* 3.6 0.5 - - - +
288A VAL* 2.8 48.0 + - + +
290A ILE* 3.6 19.4 - - + +
33F A 4.1 7.2 + - - -
34F C 3.2 31.1 + - - -
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Residues in contact with TYR 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PHE* 3.5 12.0 - - - -
191A LYS* 2.8 79.0 + - + +
193A ALA* 4.2 10.5 - - + -
240A TYR* 3.9 18.3 + + - -
273A PHE* 3.5 22.2 - + + -
274A LYS* 1.3 78.0 - - - +
276A PHE* 1.3 69.7 + - - +
277A GLU* 3.3 33.0 + - + +
280A SER* 4.8 1.3 - - - -
284A PRO* 3.5 31.4 - - + -
285A ARG 3.6 11.7 - - - +
286A PHE 4.0 1.1 - - - -
287A PRO* 4.2 3.8 - - + -
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Residues in contact with PHE 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LEU* 6.2 1.3 - - + -
160A PHE 5.4 0.4 - - - -
161A GLU* 3.2 46.0 - - + -
188A LYS* 3.5 23.1 - - + -
189A GLN* 3.8 26.5 - - + -
190A PHE* 4.0 12.3 - + + -
275A TYR* 1.3 74.7 - - - +
277A GLU* 1.3 63.0 + - - +
278A MET* 3.2 42.4 - - + -
280A SER* 3.1 16.8 + - - -
285A ARG* 2.9 19.4 + - + +
286A PHE* 3.7 34.5 - + + -
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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