Contacts of the helix formed by residues 364 - 371 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233I LEU* 3.3 6.8 - - - +
240I HIS* 2.6 28.0 + - - -
298I VAL* 3.5 25.8 - - + -
361I ARG 4.2 0.3 - - - +
362I TYR 3.3 2.0 + - - -
363I ARG* 1.3 79.6 - - + +
365I PRO* 1.4 76.6 - - - +
366I GLN* 2.9 42.0 + - - +
367I ALA* 2.9 4.1 + - - +
368I TYR* 2.9 21.7 + - - +
412I LEU* 4.3 5.6 - - - -
15J ARG* 3.0 19.2 + - - +
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Residues in contact with PRO 365 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240I HIS* 3.8 22.9 - - + -
241I THR* 4.1 12.6 - - + -
244I VAL* 3.3 26.3 - - + +
364I ASP* 1.4 93.5 - - - +
366I GLN* 1.3 62.0 + - - +
368I TYR* 4.1 8.3 - - + -
369I MET 3.2 19.6 + - - -
404I ILE* 3.5 16.8 - - + +
412I LEU* 4.3 5.6 - - + -
414I LEU* 3.9 22.2 - - + -
418I GLU* 4.7 0.9 - - - +
15J ARG* 3.7 12.8 - - - +
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Residues in contact with GLN 366 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227I MET* 3.3 35.1 + - - +
230I GLY* 5.9 0.2 - - - -
231I GLY 5.2 2.4 + - - -
240I HIS* 3.7 36.5 + - - +
243I ALA* 3.4 22.1 - - - +
244I VAL* 3.6 23.7 - - + +
247I ARG* 5.3 5.5 + - + +
298I VAL* 4.1 8.5 - - + +
299I MET* 3.4 23.2 - - + +
364I ASP* 2.9 28.1 + - - +
365I PRO* 1.3 78.7 - - - +
367I ALA* 1.3 59.6 + - - +
369I MET 4.2 0.2 + - - -
370I LEU* 3.6 18.2 + - - +
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Residues in contact with ALA 367 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298I VAL* 3.6 21.8 - - + +
299I MET* 3.8 19.4 - - + +
302I LEU* 3.7 9.2 - - + +
360I ASP* 3.2 27.6 - - + +
364I ASP* 2.9 10.5 + - - +
366I GLN* 1.3 77.7 - - - +
368I TYR* 1.3 68.3 + - - +
370I LEU* 2.8 16.6 + - - +
371I ALA 3.1 8.8 + - - -
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Residues in contact with TYR 368 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361I ARG* 3.1 60.0 + - + +
362I TYR* 3.8 19.8 + + - -
364I ASP 2.9 10.1 + - - +
365I PRO 3.5 8.7 + - - +
367I ALA* 1.3 77.2 - - - +
369I MET* 1.3 63.1 + - - +
370I LEU 3.2 0.2 + - - -
371I ALA* 3.4 9.0 + - - +
374I ASN* 2.9 39.5 + - - -
403I ILE* 3.5 25.3 + - + -
404I ILE* 3.7 15.3 - - + -
406I GLU* 4.6 1.9 - - - +
407I GLY* 3.3 24.9 + - - -
412I LEU* 3.8 21.3 - - + -
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Residues in contact with MET 369 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244I VAL* 3.3 48.7 - - + +
247I ARG* 3.9 14.6 - - + -
248I ALA* 3.4 26.7 - - + +
275I ILE* 4.0 13.7 - - + -
365I PRO 3.2 3.1 + - - +
366I GLN 4.5 0.7 - - - +
367I ALA 3.2 0.8 - - - -
368I TYR* 1.3 81.6 - - - +
370I LEU* 1.3 67.8 + - + +
374I ASN* 3.4 8.3 - - - +
375I ALA* 3.3 23.9 + - - -
378I VAL* 4.1 18.2 - - + -
400I CYS* 4.0 18.4 - - + -
403I ILE* 4.6 5.6 - - + -
404I ILE* 4.0 9.4 - - + -
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Residues in contact with LEU 370 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247I ARG* 3.7 27.6 - - + -
271I TYR* 4.0 26.9 - - + +
274I ILE* 3.7 31.4 - - + +
275I ILE* 4.3 7.4 - - + -
299I MET* 3.7 24.7 - - + -
302I LEU* 3.7 13.2 - - + -
303I VAL* 5.3 2.5 - - + -
305I GLN* 3.0 16.8 + - - -
366I GLN 3.6 15.7 - - - +
367I ALA 2.8 14.4 + - - +
369I MET* 1.3 87.6 - - + +
371I ALA* 1.3 67.9 + - - +
372I TYR 3.4 0.2 + - - -
375I ALA* 3.8 1.6 - - - +
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Residues in contact with ALA 371 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302I LEU* 3.8 11.1 - - + +
305I GLN* 3.6 7.6 - - - -
357I MET* 3.6 15.3 - - + -
361I ARG* 3.5 31.0 - - + +
367I ALA 3.1 6.1 + - - -
368I TYR 3.4 15.0 - - - +
370I LEU* 1.3 73.2 - - - +
372I TYR* 1.3 68.2 + - - +
373I ASP* 3.2 1.1 - - - +
374I ASN* 3.0 5.2 + - - +
375I ALA 2.8 20.4 + - - -
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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