Contacts of the helix formed by residues 236 - 246 (chain A) in PDB entry 1XPM
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 PHE 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A GLY 5.5 0.2 - - - -
37A ILE* 3.5 39.0 - - + -
39A GLN* 3.1 17.3 - - + +
152A THR* 4.1 8.7 - - + -
202A LYS* 4.0 9.4 - - + -
234A VAL* 3.1 8.4 - - - +
235A PRO* 1.3 87.9 - - + +
237A THR* 1.3 67.7 + - - +
238A LYS* 3.9 7.0 - - + -
239A MET* 3.0 72.1 + - + +
240A GLY 3.6 2.3 + - - -
1402A CAA 3.4 52.0 - - + -
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Residues in contact with THR 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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38A GLY* 2.5 39.3 + - - +
39A GLN* 3.0 7.7 + - - +
234A VAL* 3.8 7.3 - - + +
236A PHE* 1.3 70.2 - - - +
238A LYS* 1.3 69.9 + - - +
239A MET 3.2 0.3 + - - -
240A GLY 3.2 0.2 + - - -
241A LYS* 3.2 5.5 + - - +
263A TYR* 2.5 31.8 + - - -
267A VAL* 3.8 28.3 - - + +
271A ARG* 3.4 35.6 + - + +
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Residues in contact with LYS 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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35A ILE* 3.3 19.8 + - + +
36A GLY* 2.9 43.8 + - - +
37A ILE 3.1 22.1 + - - +
38A GLY* 3.7 3.6 - - - +
236A PHE* 3.9 8.7 - - + -
237A THR* 1.3 81.6 + - - +
239A MET* 1.3 63.5 + - - +
241A LYS* 3.0 25.0 + - + +
242A LYS* 3.0 25.4 + - + +
1402A CAA 4.1 25.3 + - - +
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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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202A LYS* 3.3 37.5 - - + +
205A TYR* 3.8 31.2 - - + -
206A ILE* 3.9 24.2 - - + -
235A PRO* 3.5 23.8 - - + -
236A PHE* 3.0 37.2 + - + +
238A LYS* 1.3 77.6 - - - +
240A GLY* 1.3 64.1 + - - +
242A LYS* 3.1 7.9 + - + +
243A ALA* 3.1 12.6 + - - +
1402A CAA 3.9 13.0 - - - -
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Residues in contact with GLY 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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205A TYR* 4.5 10.3 - - - -
232A PHE* 4.9 6.1 - - - -
233A HIS 5.0 5.6 + - - -
234A VAL* 6.0 0.6 - - - +
236A PHE 3.6 2.0 + - - -
237A THR 3.2 4.0 + - - -
239A MET* 1.3 80.6 - - - +
241A LYS* 1.3 56.5 + - - +
243A ALA* 3.8 7.6 - - - +
244A LEU* 2.9 29.1 + - - +
263A TYR* 3.0 26.9 + - - -
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Residues in contact with LYS 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 THR 3.2 11.4 + - - +
238A LYS* 3.0 26.1 + - + +
240A GLY* 1.3 76.2 - - - +
242A LYS* 1.3 61.3 + - + +
244A LEU* 3.2 12.8 + - + +
245A GLU* 2.9 68.2 + - + +
260A ARG* 3.8 23.4 + - - +
263A TYR* 3.3 15.6 + - + -
264A GLU* 5.0 9.8 + - - +
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Residues in contact with LYS 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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206A ILE* 4.3 16.4 - - + +
238A LYS* 3.0 27.8 + - + +
239A MET* 3.6 11.2 - - + +
241A LYS* 1.3 76.8 - - + +
243A ALA* 1.3 65.6 + - - +
245A GLU* 3.4 6.6 + - - +
246A SER* 3.2 21.1 + - - -
1402A CAA 5.0 11.0 - - - +
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Residues in contact with ALA 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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205A TYR* 3.6 35.2 - - + -
206A ILE* 4.1 12.9 - - + +
209A PHE* 3.7 22.7 - - + -
232A PHE* 4.7 5.4 - - + -
239A MET 3.1 11.4 + - - +
240A GLY* 3.8 4.9 - - - +
242A LYS* 1.3 75.8 - - - +
244A LEU* 1.3 65.1 + - - +
246A SER* 2.5 27.8 + - - -
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Residues in contact with LEU 244 (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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209A PHE* 4.9 1.3 - - - -
230A LEU* 4.5 8.1 - - + -
232A PHE* 4.0 31.3 - - + -
240A GLY 2.9 19.3 + - - +
241A LYS* 3.3 13.7 - - + +
243A ALA* 1.3 77.9 - - - +
245A GLU* 1.3 75.7 + - - +
246A SER 3.1 1.4 + - - -
247A ILE* 3.3 11.4 + - + +
248A ILE* 3.3 41.8 + - + +
259A LEU* 4.4 13.7 - - + +
260A ARG* 4.2 17.3 - - + -
263A TYR* 4.0 27.1 - - + -
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Residues in contact with GLU 245 (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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241A LYS* 2.9 47.3 + - + +
242A LYS* 3.9 6.5 - - - +
244A LEU* 1.3 78.6 - - - +
246A SER* 1.3 62.2 + - - +
247A ILE 3.2 1.1 + - - -
248A ILE* 3.0 20.0 - - - +
249A ASP* 3.5 15.9 - - - +
260A ARG* 2.8 45.1 + - - +
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Residues in contact with SER 246 (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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206A ILE* 3.8 16.0 - - - +
209A PHE* 4.3 0.9 - - - -
210A GLN* 3.3 30.1 + - - +
242A LYS 3.2 11.6 + - - -
243A ALA* 2.5 22.3 + - - -
245A GLU* 1.3 77.6 - - - +
247A ILE* 1.3 65.3 + - - +
249A ASP* 3.6 10.1 - - - -
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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