Contacts of the helix formed by residues 265 - 274 (chain F) in PDB entry 2CNW
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 265 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43F ASP* 3.1 15.8 + - - +
228F LEU* 3.8 26.2 - - + -
229F ASP 5.5 1.3 - - - +
230F ALA 5.8 0.2 - - - +
232F THR* 4.4 12.6 - - - +
233F GLY 3.2 32.1 - - - +
234F GLN* 4.1 10.1 - - - +
236F GLY* 4.3 4.7 - - - -
237F LEU* 3.9 18.8 - - + +
263F GLY* 3.1 6.1 - - - +
264F GLY* 1.3 77.0 - - - +
266F LEU* 1.3 62.5 + - - +
267F ILE 3.3 0.2 - - - -
268F PRO* 3.2 26.8 - - + +
269F ILE* 3.3 16.2 + - + +
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Residues in contact with LEU 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F LEU* 4.5 5.8 - - + -
228F LEU* 3.6 28.3 - - + -
252F VAL* 3.8 13.5 - - + -
254F VAL* 3.8 32.8 - - + -
263F GLY 3.0 18.8 + - - +
265F VAL* 1.3 75.9 - - - +
267F ILE* 1.3 67.3 + - - +
269F ILE* 3.2 6.6 + - + +
270F VAL* 2.9 27.9 + - - +
277F ILE* 3.6 36.1 - - + -
292F PHE* 4.8 2.5 - - + -
297F PHE* 3.9 20.6 - - + -
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Residues in contact with ILE 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F VAL* 4.1 20.2 - - + -
48F ALA* 4.1 15.3 - - + -
52F ILE* 4.6 3.6 - - + -
72F LEU* 4.7 15.0 - - + +
75F MET* 3.8 32.3 - - + +
76F LEU* 3.7 32.5 - - + -
264F GLY* 3.3 16.6 - - - +
266F LEU* 1.3 81.4 - - - +
268F PRO* 1.4 66.7 - - + +
270F VAL* 3.9 1.7 - - - +
271F ARG* 2.9 26.1 + - - +
297F PHE* 4.6 9.4 - - + -
301F LEU* 4.6 12.1 - - + -
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Residues in contact with PRO 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F VAL 3.5 20.4 - - - +
47F SER* 5.8 0.4 - - - +
48F ALA* 4.3 3.4 - - + -
234F GLN* 5.0 3.8 - - - +
237F LEU* 3.6 19.2 - - + +
264F GLY 3.4 8.1 - - - +
265F VAL* 3.2 31.9 - - + +
267F ILE* 1.4 91.4 - - + +
269F ILE* 1.3 54.8 + - - -
271F ARG* 3.8 29.4 - - + +
272F THR* 2.8 36.0 + - - -
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Residues in contact with ILE 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226F LEU* 5.5 0.7 - - + -
228F LEU* 3.6 31.4 - - + -
236F GLY 3.7 21.3 - - - +
237F LEU* 3.8 25.1 - - + -
240F ALA* 3.8 20.9 - - + -
252F VAL* 4.4 21.3 - - + -
265F VAL* 3.3 19.2 + - + +
266F LEU* 3.2 12.3 + - + +
267F ILE 3.1 1.0 + - - -
268F PRO* 1.3 74.5 - - - +
270F VAL* 1.3 60.1 + - + +
272F THR 3.2 0.2 + - - -
273F LEU* 2.6 46.9 + - + +
275F VAL* 5.6 2.2 - - + +
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Residues in contact with VAL 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F MET 3.5 18.8 - - - +
76F LEU* 3.7 29.4 - - + +
77F GLU 3.9 13.7 - - - +
78F PRO 4.1 2.7 - - - -
266F LEU 2.9 19.6 + - - +
267F ILE 4.0 0.7 - - - +
269F ILE* 1.3 71.3 - - + +
271F ARG* 1.3 63.0 + - - +
274F LYS* 2.6 38.4 + - - +
275F VAL 3.9 18.4 - - - +
277F ILE* 3.5 33.9 - - + -
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Residues in contact with ARG 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F SER* 3.4 35.8 + - - -
48F ALA* 4.0 16.4 - - - +
51F GLU* 5.1 10.1 - - - +
75F MET* 3.6 42.9 + - + +
237F LEU* 5.8 2.2 - - - +
267F ILE* 2.9 16.7 + - - +
268F PRO* 3.7 25.0 - - - +
270F VAL* 1.3 77.9 - - - +
272F THR* 1.3 70.1 + - - +
274F LYS* 4.2 10.8 + - - +
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Residues in contact with THR 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237F LEU* 3.9 23.1 - - + +
241F LYS* 4.5 21.1 - - + +
268F PRO 2.8 22.2 + - - -
271F ARG* 1.3 92.0 + - - +
273F LEU* 1.3 71.8 + - + +
274F LYS* 3.7 6.0 - - - +
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Residues in contact with LEU 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237F LEU* 5.6 0.9 - - + -
240F ALA* 3.4 43.5 - - + +
241F LYS* 4.7 13.0 - - + +
244F HIS* 3.4 40.3 + - + +
249F LEU* 4.3 8.3 - - + -
269F ILE* 2.6 26.3 + - + +
272F THR* 1.3 89.9 - - + +
274F LYS* 1.3 71.7 + - - +
275F VAL* 3.5 20.1 + - + +
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Residues in contact with LYS 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F GLU 5.4 0.4 - - - +
78F PRO* 3.4 47.6 + - + +
270F VAL* 2.6 28.0 + - - +
271F ARG* 4.2 10.9 + - - +
272F THR 4.6 5.4 - - - +
273F LEU* 1.3 77.7 - - - +
275F VAL* 1.3 61.1 + - - +
276F PRO* 4.4 1.2 - - - +
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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