Contacts of the helix formed by residues 231 - 243 (chain A) in PDB entry 2XCW
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 LYS 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ALA 3.2 22.5 + - - -
13A ALA 3.3 2.4 + - - -
15A MET* 2.6 33.6 + - - +
16A PRO* 4.3 1.8 - - + +
17A ALA* 3.8 35.2 - - + +
27A TYR* 6.1 0.4 - - - -
229A ASP* 2.7 34.0 + - - +
230A GLY* 1.3 78.4 - - - +
232A LEU* 1.3 63.5 + - - +
233A PRO 3.5 0.2 - - - -
234A LEU* 3.2 9.9 + - + +
235A LEU* 3.1 18.7 + - - +
466A ILE* 3.4 21.6 - - + +
469A LEU* 3.8 9.0 - - + +
470A TYR* 3.4 26.2 - - + +
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Residues in contact with LEU 232 (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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57A LEU* 3.6 22.7 - - + +
229A ASP* 3.0 18.2 + - + +
231A LYS* 1.3 75.8 - - - +
233A PRO* 1.4 70.2 - - + +
234A LEU 3.2 0.3 + - - -
235A LEU* 3.2 2.6 + - - +
236A LEU* 3.1 33.3 + - + +
263A LEU* 4.1 27.8 - - + +
264A PHE* 3.6 32.1 - - + -
465A PHE* 3.4 34.5 - - + -
466A ILE* 3.7 10.2 - - + +
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Residues in contact with PRO 233 (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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229A ASP 3.9 2.7 - - - +
230A GLY* 3.3 18.6 - - - +
232A LEU* 1.4 97.1 - - + +
234A LEU* 1.3 54.4 + - - +
236A LEU* 4.6 0.2 - - + -
237A SER* 2.9 31.4 + - - -
263A LEU 4.8 0.2 - - - +
264A PHE* 3.9 20.6 - - + +
266A PHE* 4.6 16.8 - - + -
268A HIS 5.7 0.7 - - - +
269A GLY 4.2 8.7 - - - +
270A PRO* 3.8 11.5 - - + +
282A TYR* 3.6 34.1 - - + +
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Residues in contact with LEU 234 (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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17A ALA* 3.5 33.0 - - + -
19A MET* 4.1 14.1 - - + -
230A GLY 4.7 0.2 - - - +
231A LYS* 3.2 15.0 + - + +
232A LEU 3.1 0.6 - - - -
233A PRO* 1.3 79.2 - - - +
235A LEU* 1.3 63.5 + - - +
237A SER* 2.6 23.6 + - - +
238A ARG* 3.0 26.1 + - + +
270A PRO* 3.4 26.8 + - + +
271A LYS* 4.9 14.1 - - + -
469A LEU* 4.0 19.7 - - + -
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Residues in contact with LEU 235 (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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231A LYS 3.1 12.4 + - - +
232A LEU 3.2 6.0 + - - +
234A LEU* 1.3 76.5 - - - +
236A LEU* 1.3 58.4 + - + +
238A ARG* 3.1 10.6 + - + +
239A MET* 2.9 54.6 + - + +
465A PHE* 3.6 47.1 - - + +
466A ILE* 3.9 17.9 - - + +
468A LEU* 4.1 7.2 - - + +
469A LEU* 3.7 36.1 - - + +
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Residues in contact with LEU 236 (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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51A PHE* 3.3 43.5 - - + -
57A LEU* 5.0 2.5 - - + -
232A LEU* 3.1 31.0 + - + +
235A LEU* 1.3 78.6 - - + +
237A SER* 1.3 63.4 + - - +
239A MET* 3.3 9.6 + - - +
240A LYS* 3.0 24.3 + - - +
245A VAL* 4.2 8.1 - - + +
264A PHE* 3.8 23.6 - - + -
282A TYR* 4.0 23.6 - - + +
283A PHE* 3.7 29.8 - - + -
465A PHE* 5.3 0.2 - - + -
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Residues in contact with SER 237 (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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233A PRO 2.9 17.1 + - - -
234A LEU* 2.6 26.2 + - - +
236A LEU* 1.3 77.8 - - - +
238A ARG* 1.3 62.0 + - - +
240A LYS* 3.4 8.0 + - - +
241A GLU* 3.2 30.4 + - - +
270A PRO* 3.5 25.6 - - - +
277A ARG* 3.8 15.0 - - - +
282A TYR* 4.3 2.4 - - - -
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Residues in contact with ARG 238 (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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19A MET* 3.4 37.5 - - - +
24A LEU* 5.8 2.0 - - - +
234A LEU* 3.0 24.9 + - + +
235A LEU* 3.1 11.3 + - + +
237A SER* 1.3 82.2 + - - +
239A MET* 1.3 64.8 + - - +
241A GLU* 3.2 34.6 + - - +
242A VAL* 3.6 2.6 + - - +
469A LEU* 3.8 16.0 + - - +
471A TYR 5.1 8.5 + - - -
472A PRO* 5.4 2.8 - - - +
473A PHE* 3.5 56.4 - - + +
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Residues in contact with MET 239 (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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43A MET* 5.9 0.9 - - + -
49A PHE* 3.7 45.1 - - + -
51A PHE* 3.6 38.6 - - + -
235A LEU* 2.9 35.4 + - + +
236A LEU* 3.6 15.5 - - - +
238A ARG* 1.3 76.7 - - - +
240A LYS* 1.3 58.1 + - - +
242A VAL* 3.2 7.8 + - - +
243A GLY* 2.9 28.9 + - - +
245A VAL* 3.9 7.4 - - + -
349A ILE* 4.4 1.1 - - + -
468A LEU* 3.9 29.2 - - + -
473A PHE* 5.4 0.2 - - - -
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Residues in contact with LYS 240 (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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236A LEU 3.0 16.6 + - - +
237A SER* 3.8 7.6 - - - +
238A ARG 3.2 0.4 - - - -
239A MET* 1.3 75.6 - - - +
241A GLU* 1.3 61.1 + - - +
243A GLY 3.1 17.0 + - - +
245A VAL* 3.9 5.8 - - + +
277A ARG* 5.7 1.3 - - - +
281A SER 3.5 24.5 - - - -
282A TYR* 3.2 26.5 - - + +
283A PHE 4.1 3.6 - - - +
284A ASP* 3.0 40.6 + - - +
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Residues in contact with GLU 241 (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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237A SER* 3.2 21.9 + - - +
238A ARG* 3.3 23.8 + - - +
239A MET 3.1 0.4 - - - -
240A LYS* 1.3 79.4 - - - +
242A VAL* 1.3 63.4 + - + +
473A PHE* 3.9 17.7 - - + -
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Residues in contact with VAL 242 (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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46A ILE 4.6 8.8 - - - +
47A LYS* 4.8 5.0 - - - +
49A PHE* 4.0 21.1 - - + -
238A ARG 4.1 5.6 - - - +
239A MET* 3.5 11.7 - - - +
241A GLU* 1.3 82.6 - - + +
243A GLY* 1.3 58.9 + - - +
473A PHE* 3.6 47.3 - - + +
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Residues in contact with GLY 243 (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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47A LYS* 3.2 15.3 - - - -
49A PHE* 4.6 3.4 - - - -
239A MET 2.9 9.3 + - - -
240A LYS* 3.1 28.6 + - - +
241A GLU 3.6 1.0 - - - -
242A VAL* 1.3 79.4 - - - +
244A LYS* 1.3 66.5 + - - +
284A ASP* 4.3 0.2 - - - +
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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