Contacts of the strand formed by residues 270 - 276 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194C GLU* 4.0 30.1 - - + +
195C ALA* 3.4 25.4 - - - +
196C THR* 3.5 23.1 - - + +
268C GLY 3.8 0.8 + - - +
269C LYS* 1.3 74.3 - - - +
271C VAL* 1.3 62.8 + - - +
292C ILE* 3.7 2.4 - - - +
293C ARG* 2.8 37.5 + - - +
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Residues in contact with VAL 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C GLU* 3.4 6.0 - - - -
195C ALA* 3.1 34.9 + - + +
197C ILE* 3.5 36.1 - - + -
236C ILE* 4.6 5.6 - - + -
238C VAL* 4.5 12.8 - - + -
247C ILE* 5.5 3.8 - - + -
259C PHE* 4.9 1.8 - - + -
270C MET* 1.3 80.6 - - - +
272C LYS* 1.3 65.7 + - - +
273C PHE* 4.0 4.1 - - + -
289C PHE* 3.9 25.4 - - + -
291C GLY 3.4 7.2 - - - +
292C ILE* 4.1 15.9 - - + +
293C ARG 5.4 0.2 - - - -
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Residues in contact with LYS 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C ALA 3.5 9.2 - - - +
194C GLU* 3.7 25.6 - - + +
271C VAL* 1.3 74.8 - - - +
273C PHE* 1.3 66.5 + - - +
289C PHE* 3.9 6.1 - - - -
290C ILE* 3.1 36.2 + - + -
291C GLY* 2.7 24.9 + - - +
292C ILE 3.7 17.8 + - - -
293C ARG 4.4 11.4 - - - +
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Residues in contact with PHE 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C LYS 3.9 0.3 - - - +
192C ASP* 3.7 1.0 - - - -
193C ALA* 3.1 42.3 + - + +
194C GLU 3.6 29.8 - - - -
195C ALA* 3.8 10.5 - - + -
240C TYR* 4.0 12.3 - + - -
245C PHE* 3.7 26.7 - + - -
247C ILE* 3.7 26.9 - - + -
271C VAL* 4.0 8.1 - - + -
272C LYS* 1.3 80.4 - - - +
274C LYS* 1.3 71.5 + - - +
275C TYR* 3.5 27.6 - + + -
284C PRO* 4.5 0.7 - - + -
287C PRO* 4.9 0.7 - - + -
288C VAL 3.2 17.3 - - - +
289C PHE* 4.1 1.3 - - + -
290C ILE* 3.7 11.0 - - - +
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Residues in contact with LYS 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C THR* 6.1 2.6 - - - +
13C GLU* 5.5 9.1 + - - +
190C PHE* 3.7 38.1 - - + +
191C LYS 3.2 11.4 - - - +
192C ASP* 4.3 5.8 - - - +
273C PHE* 1.3 77.2 - - - +
275C TYR* 1.3 64.3 + - - +
286C PHE 3.7 0.5 - - - +
287C PRO* 3.6 0.5 - - - +
288C VAL* 2.8 47.5 + - + +
290C ILE* 3.6 18.8 - - + +
33J A 4.0 7.9 + - - -
34J C 3.2 30.4 + - - -
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Residues in contact with TYR 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C PHE* 3.5 11.9 - - - -
191C LYS* 2.8 81.0 + - + +
193C ALA* 4.2 10.1 - - + -
240C TYR* 4.0 18.6 + + - -
273C PHE* 3.5 20.4 - + + -
274C LYS* 1.3 76.1 - - - +
276C PHE* 1.3 70.6 + - - +
277C GLU* 3.2 32.2 + - + -
280C SER* 4.7 1.6 - - - -
284C PRO* 3.5 33.2 - - + -
285C ARG 3.6 11.2 - - - +
286C PHE 4.0 0.7 - - - -
287C PRO* 4.2 4.7 - - + -
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Residues in contact with PHE 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C LEU* 6.2 0.7 - - + -
160C PHE 5.5 0.2 - - - -
161C GLU* 3.2 46.7 - - + -
188C LYS* 3.5 21.5 - - + -
189C GLN* 3.7 25.1 - - + -
190C PHE* 4.0 13.4 - + + +
275C TYR* 1.3 76.6 - - - +
277C GLU* 1.3 64.2 + - - +
278C MET* 3.2 42.6 - - + -
280C SER* 3.0 17.5 + - - -
285C ARG* 2.9 17.6 + - - +
286C 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