Contacts of the helix formed by residues 255 - 265 (chain S) in PDB entry 2C2V
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 255 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243S GLU* 3.0 53.2 + - + +
245S CYS* 3.3 45.3 - - - +
253S TYR 2.8 8.1 + - - -
254S ASP* 1.3 73.2 + - - +
256S LYS* 1.4 61.5 + - - +
257S ASP 2.9 0.2 + - - -
258S ILE* 2.9 6.3 - - + +
259S GLU* 2.9 47.8 + - + +
278S GLN* 4.8 6.7 + - - +
281S LEU* 3.8 26.5 + - + +
283S PRO* 4.0 23.0 - - - +
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Residues in contact with LYS 256 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242S ARG* 6.3 3.4 - - + -
243S GLU* 5.1 10.4 + - - -
254S ASP* 2.9 14.4 + - - +
255S ARG* 1.4 70.5 - - - +
257S ASP* 1.3 67.1 + - - +
259S GLU* 3.0 9.8 + - - +
260S GLU* 2.9 27.9 + - - +
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Residues in contact with ASP 257 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B MET* 6.1 0.2 - - - -
236S ILE* 3.8 28.3 - - + +
237S SER* 3.1 33.0 + - - +
253S TYR* 5.5 0.4 - - + -
254S ASP* 2.9 22.8 + - + +
255S ARG 2.9 0.2 + - - -
256S LYS* 1.3 88.8 + - - +
258S ILE* 1.3 69.5 + - - +
259S GLU 2.5 2.8 + - - -
260S GLU* 2.7 22.7 + - - +
261S HIS 2.7 10.6 + - - -
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Residues in contact with ILE 258 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236S ILE* 3.5 8.8 - - + +
245S CYS* 4.5 2.0 - - - -
253S TYR* 3.4 45.6 - - + +
254S ASP 3.7 3.3 + - - +
255S ARG* 2.9 25.6 - - - +
257S ASP* 1.3 77.4 - - - +
259S GLU* 1.3 77.1 + - + +
261S HIS* 4.2 4.7 - - + -
262S LEU* 3.2 26.6 + - + +
270S PRO* 3.9 24.9 - - + -
276S LEU* 4.5 5.4 - - + -
281S LEU* 4.0 29.6 - - + -
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Residues in contact with GLU 259 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255S ARG* 2.9 41.0 + - + +
256S LYS* 3.0 10.3 + - - +
257S ASP 2.5 11.1 + - - -
258S ILE* 1.3 90.6 - - + +
260S GLU* 1.4 56.7 - - - +
262S LEU* 3.0 13.1 + - - +
263S GLN* 2.0 37.0 + - - +
278S GLN* 2.9 39.3 + - + +
281S LEU* 4.3 2.9 - - + +
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Residues in contact with GLU 260 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B MET* 3.6 23.8 - - + +
256S LYS 2.9 12.3 + - - +
257S ASP* 2.7 13.6 + - - +
259S GLU* 1.4 70.2 - - - +
261S HIS* 1.3 68.7 - - - +
263S GLN* 2.8 15.6 + - - +
264S ARG* 2.8 62.6 + - - +
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Residues in contact with HIS 261 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B MET* 3.4 15.2 - - + +
101B PRO* 3.0 36.0 - - + +
236S ILE* 3.9 13.9 - - + -
257S ASP 2.7 11.5 + - - +
258S ILE* 3.8 4.9 - - + +
260S GLU* 1.3 80.5 - - - +
262S LEU* 1.3 71.5 + - + +
265S VAL* 2.8 33.4 + - + +
266S GLY 3.4 12.9 + - - -
268S PHE* 3.0 41.6 + + - -
270S PRO* 3.4 25.2 - - + +
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Residues in contact with LEU 262 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258S ILE* 3.2 18.3 + - + +
259S GLU* 3.0 10.4 + - - +
260S GLU 2.9 1.0 + - - -
261S HIS* 1.3 93.4 - - + +
263S GLN* 1.4 58.8 + - - +
264S ARG 3.0 0.6 + - - -
266S GLY* 3.5 10.2 - - - +
267S HIS* 3.2 30.0 + - + +
268S PHE 3.7 19.3 - - - +
276S LEU* 3.6 34.8 - - + +
277S THR* 3.8 4.0 - - - +
278S GLN* 3.7 41.7 - - + +
281S LEU* 4.4 9.9 - - + -
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Residues in contact with GLN 263 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259S GLU* 2.0 57.4 + - - +
260S GLU* 2.8 18.3 + - - +
262S LEU* 1.4 69.8 - - - +
264S ARG* 1.3 74.5 + - + +
266S GLY 4.4 1.1 - - - -
267S HIS* 5.1 3.4 - - - -
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Residues in contact with ARG 264 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLU* 4.4 16.2 + - - +
68B MET* 3.4 33.0 - - + +
260S GLU* 2.8 47.9 + - - +
262S LEU 3.0 0.6 - - - -
263S GLN* 1.3 94.5 - - + +
265S VAL* 1.3 66.2 + - + +
266S GLY 3.3 0.9 - - - -
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Residues in contact with VAL 265 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B MET* 3.1 53.8 - - + +
99B TRP* 4.0 22.2 - - + +
101B PRO* 4.5 3.4 - - + -
261S HIS* 2.8 31.0 + - + +
264S ARG* 1.3 81.1 - - + +
266S GLY* 1.3 58.4 + - - +
268S PHE* 3.8 12.9 - - + -
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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