Contacts of the helix formed by residues 364 - 369 (chain A) in PDB entry 2I2X
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 ASP 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A LEU* 3.3 7.3 - - - +
240A HIS* 2.5 28.8 + - - +
298A VAL* 3.4 28.3 - - + -
360A ASP 4.3 0.6 + - - -
361A ARG 4.1 0.5 - - - +
362A TYR 3.3 3.0 + - - -
363A ARG* 1.3 78.7 - - + +
365A PRO* 1.4 74.2 - - - +
366A GLN* 3.0 39.0 + - - +
367A ALA* 3.0 3.8 + - + +
368A TYR* 3.0 21.5 + - - +
412A LEU* 4.2 5.6 - - - -
15B ARG* 3.0 20.3 + - - +
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Residues in contact with PRO 365 (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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240A HIS* 4.0 17.5 - - + -
241A THR* 4.0 17.0 - - + -
244A VAL* 3.4 17.5 - - + +
364A ASP* 1.4 95.7 - - - +
366A GLN* 1.3 61.7 + - - +
367A ALA 3.2 0.7 + - - -
368A TYR* 4.1 5.6 - - + -
369A MET 3.3 18.5 + - - -
404A ILE* 3.5 34.4 - - + +
412A LEU* 4.3 2.9 - - + -
414A LEU* 4.0 16.8 - - + -
418A GLU* 4.7 1.3 - - - +
15B ARG* 3.9 11.9 - - - +
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Residues in contact with GLN 366 (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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227A MET* 3.4 34.3 + - - +
230A GLY* 5.4 0.2 - - - -
231A GLY 4.9 2.8 + - - -
240A HIS* 3.5 41.8 + - - +
243A ALA* 3.4 24.5 - - + +
244A VAL* 3.9 18.4 - - + +
247A ARG* 5.2 2.6 + - + +
298A VAL* 4.2 14.4 - - + +
299A MET* 4.4 8.9 - - + +
364A ASP* 3.0 21.7 + - - +
365A PRO* 1.3 77.0 - - - +
367A ALA* 1.3 58.4 + - - +
369A MET 4.4 0.2 + - - -
370A LEU* 3.3 29.3 + - - +
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Residues in contact with ALA 367 (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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298A VAL 3.8 20.4 - - - +
299A MET* 3.8 19.1 - - + -
302A LEU* 3.5 10.6 - - + +
360A ASP* 3.4 25.4 - - + +
361A ARG 4.5 0.2 - - - -
364A ASP* 3.0 11.1 + - + +
366A GLN* 1.3 79.0 - - - +
368A TYR* 1.3 67.6 + - - +
369A MET 3.2 0.4 - - - -
370A LEU* 2.8 15.1 + - - +
371A ALA 3.1 9.5 + - - -
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Residues in contact with TYR 368 (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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361A ARG* 3.3 65.7 + - + +
362A TYR* 4.0 13.3 + + - -
364A ASP 3.0 12.8 + - - +
365A PRO* 3.4 11.0 + - + +
367A ALA* 1.3 78.1 - - - +
369A MET* 1.3 60.0 + - - +
371A ALA* 3.4 8.5 - - - +
374A ASN* 2.9 37.6 + - - -
403A ILE* 3.5 33.4 - - + -
404A ILE* 4.2 6.7 - - + -
406A GLU* 4.6 2.3 - - + +
407A GLY* 3.4 25.2 + - - -
412A LEU* 4.0 21.1 - - + -
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Residues in contact with MET 369 (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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244A VAL* 3.4 40.8 - - + +
247A ARG* 3.7 16.6 - - + -
248A ALA* 3.4 35.4 - - + +
275A ILE* 3.9 14.8 - - + -
365A PRO 3.3 3.1 + - - +
366A GLN 4.7 0.7 - - - +
367A ALA 3.2 1.0 - - - -
368A TYR* 1.3 80.1 - - - +
370A LEU* 1.3 71.8 + - + +
371A ALA 3.4 0.2 + - - -
374A ASN* 3.4 7.5 - - - +
375A ALA* 3.3 19.4 + - - -
378A VAL* 4.1 19.3 - - + -
400A CYS* 4.0 14.6 - - + -
403A ILE* 4.5 9.4 - - + -
404A ILE* 4.1 7.2 - - + +
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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