Contacts of the strand formed by residues 270 - 276 (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 MET 270 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194D GLU* 4.0 30.7 - - + +
195D ALA* 3.4 25.4 - - - +
196D THR* 3.4 22.9 - - + +
268D GLY 3.8 0.8 + - - +
269D LYS* 1.3 74.7 - - - +
271D VAL* 1.3 57.4 + - - +
292D ILE* 3.7 2.4 - - - +
293D ARG* 2.7 43.3 + - - +
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Residues in contact with VAL 271 (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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194D GLU* 3.4 4.9 - - - -
195D ALA* 3.1 34.3 + - + +
197D ILE* 3.5 37.2 - - + -
236D ILE* 4.6 7.2 - - + -
238D VAL* 4.5 13.2 - - + -
247D ILE* 5.5 3.8 - - + -
259D PHE* 4.9 2.0 - - + -
270D MET* 1.3 81.0 - - - +
272D LYS* 1.3 65.2 + - - +
273D PHE* 4.0 4.3 - - + -
289D PHE* 3.9 23.3 - - + -
291D GLY 3.5 7.0 - - - +
292D ILE* 4.1 15.3 - - + +
293D ARG 5.4 0.4 - - - -
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Residues in contact with LYS 272 (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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193D ALA 3.5 9.2 - - - +
194D GLU* 3.7 26.2 - - + +
271D VAL* 1.3 75.2 - - - +
273D PHE* 1.3 66.3 + - - +
289D PHE* 3.9 6.1 - - - -
290D ILE* 3.1 36.1 + - + -
291D GLY* 2.7 26.5 + - - +
292D ILE 3.7 17.8 + - - -
293D ARG 4.4 11.0 - - - +
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Residues in contact with PHE 273 (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* 3.7 1.6 - - - -
193D ALA* 3.1 41.8 + - + -
194D GLU 3.6 29.4 - - - -
195D ALA* 3.8 11.2 - - + -
240D TYR* 4.0 12.1 - + - -
245D PHE* 3.7 26.2 - + - -
247D ILE* 3.7 27.6 - - + -
271D VAL* 4.0 7.9 - - + -
272D LYS* 1.3 81.1 - - - +
274D LYS* 1.3 70.3 + - - +
275D TYR* 3.5 28.3 - + + -
284D PRO* 4.5 0.7 - - + -
287D PRO* 4.9 0.7 - - + -
288D VAL 3.1 17.0 - - - +
289D PHE* 4.1 1.6 - - - -
290D ILE* 3.7 10.6 - - - +
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Residues in contact with LYS 274 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D THR* 6.1 2.4 - - - +
13D GLU* 5.6 8.9 + - - +
190D PHE* 3.7 37.8 - - + +
191D LYS 3.2 11.0 - - - +
192D ASP* 4.2 6.1 - - - +
273D PHE* 1.3 76.0 - - - +
275D TYR* 1.3 64.2 + - - +
286D PHE 3.7 0.3 - - - +
287D PRO* 3.6 0.5 - - - +
288D VAL* 2.8 47.4 + - + +
290D ILE* 3.6 20.3 - - + +
33L A 4.0 7.6 + - - -
34L C 3.2 30.9 + - - -
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Residues in contact with TYR 275 (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* 3.5 11.7 - - - -
191D LYS* 2.8 79.0 + - + +
193D ALA* 4.2 10.5 - - + -
240D TYR* 4.0 18.9 + + - -
273D PHE* 3.5 21.1 - + + -
274D LYS* 1.3 76.7 - - - +
276D PHE* 1.3 70.5 + - - +
277D GLU* 3.2 32.4 + - + +
280D SER* 4.7 1.6 - - - -
284D PRO* 3.5 32.1 - - + -
285D ARG 3.6 11.2 - - - +
286D PHE 4.0 0.9 - - - -
287D PRO* 4.2 5.2 - - + -
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Residues in contact with PHE 276 (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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156D LEU* 6.2 0.9 - - + -
160D PHE 5.5 0.2 - - - -
161D GLU* 3.2 46.0 - - + -
188D LYS* 3.5 22.7 - - + -
189D GLN* 3.7 25.4 - - + -
190D PHE* 4.0 13.1 - + + -
275D TYR* 1.3 75.6 - - - +
277D GLU* 1.3 63.8 + - - +
278D MET* 3.2 43.5 - - + -
280D SER* 3.0 17.3 + - - -
285D ARG* 2.9 18.6 + - - +
286D PHE* 3.7 33.7 - + + -
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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