Contacts of the helix formed by residues 371 - 384 (chain G) 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 ALA 371 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302G LEU* 4.0 10.3 - - + -
305G GLN* 3.7 7.0 - - - -
357G MET* 3.5 24.5 - - + -
361G ARG* 3.9 8.7 - - + +
367G ALA 3.2 4.8 + - - -
368G TYR 3.4 14.1 - - - +
369G MET 3.2 0.8 - - - -
370G LEU* 1.3 74.9 - - - +
372G TYR* 1.3 57.7 + - - +
373G ASP* 3.2 15.0 - - - +
374G ASN* 2.7 29.2 + - - +
375G ALA 2.8 9.7 + - - -
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Residues in contact with TYR 372 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ALA* 3.4 39.5 - - + +
15G ASP* 4.0 4.6 + - - -
17G MET* 4.9 6.6 - - + +
274G ILE* 4.0 8.5 - - + -
305G GLN* 3.0 37.6 + - + +
306G CYS* 4.0 16.8 - - - -
353G ARG* 2.9 39.6 + - + -
354G ASP* 2.5 24.7 + - - -
357G MET* 4.1 15.3 - - + -
370G LEU 3.4 2.1 + - - -
371G ALA* 1.3 70.6 - - - +
373G ASP* 1.3 57.4 + - - +
375G ALA* 3.6 8.3 - - - +
376G TYR* 2.9 30.7 + - - +
1H MET* 3.4 34.2 - - + +
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Residues in contact with ASP 373 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ALA* 3.6 17.6 - - + +
357G MET* 4.8 0.2 - - - +
361G ARG* 2.5 42.1 + - - -
371G ALA* 3.4 11.4 - - - +
372G TYR* 1.3 78.7 + - - +
374G ASN* 1.3 72.5 + - - +
376G TYR* 3.5 4.0 + - - +
377G ARG* 3.1 24.9 + - - +
1H MET* 3.5 23.1 - - + +
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Residues in contact with ASN 374 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361G ARG* 3.4 26.5 + - - +
368G TYR* 2.9 34.0 + - - +
369G MET 3.3 16.4 - - - +
371G ALA* 2.7 6.6 + - - +
373G ASP* 1.3 83.3 + - - +
375G ALA* 1.3 59.8 + - - +
377G ARG* 3.5 12.6 + - - -
378G VAL* 3.0 31.7 + - - +
403G ILE* 3.5 31.2 - - + +
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Residues in contact with ALA 375 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G ILE* 3.7 28.5 - - + +
275G ILE* 3.8 31.1 - - + +
278G ALA* 4.8 0.7 - - + -
369G MET 3.4 7.1 + - - +
370G LEU* 4.0 6.3 - - - +
371G ALA 2.8 13.0 + - - +
372G TYR 3.6 5.4 - - - +
374G ASN* 1.3 76.8 - - - +
376G TYR* 1.3 58.9 + - - +
378G VAL* 3.2 6.2 + - - +
379G GLY* 2.9 24.1 + - - -
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Residues in contact with TYR 376 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G MET* 3.3 35.5 - - + +
11G TYR* 2.6 36.0 + - + -
12G ALA* 3.0 14.1 + - - -
13G ASN* 3.7 21.1 - - + -
14G ALA* 3.7 25.1 - - + -
17G MET* 4.5 4.7 - - - -
278G ALA* 4.0 20.6 - - + +
372G TYR 2.9 17.5 + - - +
373G ASP 3.6 5.8 - - - +
375G ALA* 1.3 75.6 - - - +
377G ARG* 1.3 57.2 + - - +
379G GLY* 2.8 17.5 + - - -
380G GLN* 2.9 42.6 + - + -
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Residues in contact with ARG 377 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373G ASP 3.1 12.2 + - - +
374G ASN* 3.6 16.6 + - - +
375G ALA 3.3 0.2 - - - -
376G TYR* 1.3 79.5 - - + +
378G VAL* 1.3 61.2 + - - +
380G GLN* 3.1 29.6 + - + +
381G SER* 3.2 12.0 + - - -
399G GLU* 2.6 30.6 + - - +
402G ASN* 4.1 15.2 - - - +
403G ILE* 3.7 23.8 - - + +
406G GLU* 2.9 42.0 + - - -
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Residues in contact with VAL 378 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248G ALA* 4.6 5.4 - - + +
275G ILE* 3.9 17.9 - - + -
369G MET* 4.2 22.0 - - + -
374G ASN 3.0 20.3 + - - +
375G ALA 3.2 8.0 + - - +
377G ARG* 1.3 74.4 - - - +
379G GLY* 1.3 63.1 + - - +
381G SER* 2.8 22.9 + - - -
382G ILE* 3.1 25.7 + - + +
396G ALA* 4.2 20.6 - - + +
399G GLU* 4.3 5.4 - - + -
400G CYS* 4.7 8.5 - - + +
403G ILE* 3.7 16.2 - - + -
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Residues in contact with GLY 379 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G MET* 3.6 11.0 - - - +
275G ILE* 4.0 3.3 - - - +
279G ILE* 3.7 25.4 - - - -
375G ALA 2.9 9.8 + - - -
376G TYR 2.8 9.8 + - - -
378G VAL* 1.3 77.3 - - - +
380G GLN* 1.3 61.7 + - - +
382G ILE* 3.0 14.8 + - - +
383G VAL* 3.0 17.7 + - - +
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Residues in contact with GLN 380 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G MET* 3.7 10.7 - - + +
376G TYR* 2.9 38.2 + - + +
377G ARG* 3.1 28.7 + - + +
379G GLY* 1.3 75.5 - - - +
381G SER* 1.3 61.9 + - - +
383G VAL* 3.4 9.9 + - + +
384G LYS* 3.1 27.3 + - - +
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Residues in contact with SER 381 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377G ARG 3.2 1.8 + - - -
378G VAL* 2.8 18.6 + - - -
380G GLN* 1.3 79.3 - - - +
382G ILE* 1.3 60.1 + - - +
384G LYS* 3.7 23.4 - - - +
395G ASN* 3.1 42.0 + - - +
396G ALA* 3.9 1.7 - - - -
399G GLU* 3.2 46.0 - - - +
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Residues in contact with ILE 382 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251G ALA* 4.2 1.3 - - + -
252G PRO* 4.0 32.3 - - + -
255G LEU* 4.1 20.2 - - + -
275G ILE* 3.7 27.4 - - + -
279G ILE* 3.7 11.0 - - + -
378G VAL* 3.1 21.7 + - + +
379G GLY 3.0 4.6 + - - +
381G SER* 1.3 78.4 - - - +
383G VAL* 1.3 67.3 + - - +
385G ASP 3.1 12.5 + - - -
386G GLY* 3.1 8.8 + - - -
392G ARG* 3.4 33.9 - - + +
396G ALA* 4.1 17.0 - - + -
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Residues in contact with VAL 383 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G TYR* 3.4 20.6 - - + +
7G THR* 3.4 31.0 - - - +
8G SER* 3.7 28.3 - - - +
9G MET* 3.8 16.4 - - + -
279G ILE* 3.9 26.9 - - + -
379G GLY 3.0 14.2 + - - +
380G GLN* 3.4 15.0 - - - +
382G ILE* 1.3 78.2 - - + +
384G LYS* 1.3 58.1 + - - +
385G ASP 3.1 0.7 - - - -
386G GLY 3.0 13.6 + - - -
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Residues in contact with LYS 384 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G THR 5.3 1.1 - - - -
380G GLN 3.1 12.3 + - - +
381G SER* 3.7 32.6 - - - +
382G ILE 3.2 0.8 + - - -
383G VAL* 1.3 77.0 - - + +
385G ASP* 1.3 71.2 + - - +
395G ASN* 3.7 22.8 - - - +
399G GLU* 4.4 7.7 + - - -
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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