Contacts of the helix formed by residues 371 - 384 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302K LEU* 3.9 11.0 - - + +
305K GLN* 3.6 7.6 - - - -
357K MET* 3.7 15.5 - - + -
361K ARG* 3.7 17.7 - - + +
367K ALA 3.2 6.2 + - - +
368K TYR 3.5 14.1 - - - +
369K MET 3.3 0.2 - - - -
370K LEU* 1.3 73.3 - - - +
372K TYR* 1.3 56.0 + - - +
373K ASP* 3.2 14.8 - - - +
374K ASN* 2.9 6.6 + - - +
375K ALA 2.7 30.8 + - - -
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Residues in contact with TYR 372 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K ALA* 3.5 36.6 - - + -
15K ASP* 4.2 3.7 + - - +
17K MET* 4.8 6.8 - - + +
274K ILE* 3.9 5.2 - - + -
305K GLN* 2.9 32.3 + - + +
306K CYS* 3.9 19.7 - - - -
353K ARG* 2.9 40.6 + - + -
354K ASP* 2.6 23.8 + - - -
357K MET* 4.1 17.5 - - + -
370K LEU 3.3 1.5 + - - -
371K ALA* 1.3 71.0 - - - +
373K ASP* 1.3 57.1 + - - +
375K ALA* 3.5 9.4 - - - +
376K TYR* 2.9 30.5 + - - +
1L MET* 3.2 33.8 - - + +
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Residues in contact with ASP 373 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K ALA* 3.7 18.1 - - + +
361K ARG* 2.5 40.2 + - - -
371K ALA* 3.5 7.4 - - - +
372K TYR* 1.3 79.1 + - - +
374K ASN* 1.3 68.5 + - - +
376K TYR* 3.7 3.8 - - - +
377K ARG* 3.2 23.4 + - - +
1L MET* 3.4 28.5 - - + +
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Residues in contact with ASN 374 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361K ARG* 3.7 20.9 + - - +
368K TYR* 2.8 42.0 + - - +
369K MET 3.3 15.9 - - - +
371K ALA 2.9 2.2 + - - +
373K ASP* 1.3 88.1 + - - +
375K ALA* 1.3 65.7 + - - +
377K ARG* 3.2 15.2 + - - +
378K VAL* 3.0 26.7 + - - +
403K ILE* 3.6 26.9 - - + +
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Residues in contact with ALA 375 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274K ILE* 3.6 33.7 - - + +
275K ILE* 3.8 31.7 - - + +
278K ALA* 4.9 0.7 - - + -
369K MET 3.3 7.3 + - - +
370K LEU 4.0 1.3 - - - +
371K ALA 2.7 19.7 + - - +
372K TYR 3.3 5.1 + - - +
374K ASN* 1.3 71.5 - - - +
376K TYR* 1.3 63.1 + - - +
378K VAL* 3.1 7.1 + - - +
379K GLY* 2.9 17.8 + - - -
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Residues in contact with TYR 376 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K MET* 3.6 22.4 - - + +
11K TYR* 2.7 35.0 + - + -
12K ALA 2.9 16.4 + - - -
13K ASN* 3.6 21.5 - - + -
14K ALA* 3.7 24.7 - - + -
17K MET* 4.2 4.7 - - - -
278K ALA* 3.9 25.9 - - + +
372K TYR 2.9 18.1 + - - +
373K ASP 3.7 6.3 - - - +
375K ALA* 1.3 76.3 - - - +
377K ARG* 1.3 58.0 + - - +
379K GLY* 2.9 17.0 + - - -
380K GLN* 2.9 44.4 + - + +
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Residues in contact with ARG 377 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373K ASP 3.2 13.1 + - - +
374K ASN* 3.2 18.2 + - - +
376K TYR* 1.3 80.7 - - - +
378K VAL* 1.3 61.6 + - - +
380K GLN* 3.3 20.9 + - - +
381K SER* 3.3 15.1 + - - -
399K GLU* 2.6 33.2 + - - +
402K ASN* 4.0 9.3 - - - +
403K ILE* 3.6 25.6 - - + +
406K GLU* 2.6 45.9 + - - -
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Residues in contact with VAL 378 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248K ALA* 4.5 5.6 - - + +
275K ILE* 4.1 17.3 - - + -
369K MET* 4.1 22.7 - - + -
374K ASN 3.0 18.5 + - - +
375K ALA 3.1 7.2 + - - +
377K ARG* 1.3 73.8 - - - +
379K GLY* 1.3 63.0 - - - +
381K SER* 2.6 25.0 + - - -
382K ILE* 3.1 16.2 + - + +
396K ALA* 3.7 30.1 - - + +
399K GLU* 4.2 6.1 - - + -
400K CYS* 4.7 7.2 - - - +
403K ILE* 3.6 18.2 - - + -
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Residues in contact with GLY 379 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K MET* 3.5 17.9 - - - -
275K ILE* 3.9 6.1 - - - -
279K ILE* 3.8 17.0 - - - -
375K ALA 2.9 10.2 + - - -
376K TYR 2.9 8.9 + - - -
378K VAL* 1.3 77.1 - - - +
380K GLN* 1.3 61.1 + - - +
382K ILE* 3.2 3.0 + - - +
383K VAL* 3.1 29.1 + - - +
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Residues in contact with GLN 380 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K MET* 3.6 10.6 - - + +
376K TYR* 2.9 44.4 + - + +
377K ARG* 3.3 25.4 + - - +
379K GLY* 1.3 75.0 - - - +
381K SER* 1.3 62.5 + - - +
383K VAL* 3.3 11.1 + - + +
384K LYS* 3.1 28.4 + - - +
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Residues in contact with SER 381 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377K ARG 3.3 2.0 + - - -
378K VAL 2.6 20.4 + - - -
380K GLN* 1.3 78.9 - - - +
382K ILE* 1.3 59.7 + - - +
384K LYS* 3.5 22.1 - - - +
395K ASN* 2.8 37.8 + - - +
396K ALA* 3.5 20.6 - - - -
399K GLU* 3.6 34.1 - - - +
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Residues in contact with ILE 382 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251K ALA* 3.9 3.1 - - + -
252K PRO* 3.7 31.2 - - + -
255K LEU* 4.1 25.4 - - + -
275K ILE* 3.8 25.4 - - + -
279K ILE* 4.0 10.1 - - + -
378K VAL* 3.1 20.7 + - + +
379K GLY 3.5 6.3 - - - +
381K SER* 1.3 83.4 + - - +
383K VAL* 1.3 64.5 + - + +
385K ASP 3.3 4.3 + - - -
386K GLY* 3.3 15.7 + - - -
392K ARG* 3.5 31.2 - - + +
396K ALA* 3.7 16.4 - - + -
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Residues in contact with VAL 383 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K TYR* 4.1 12.1 - - + +
7K THR* 3.6 19.9 - - - +
8K SER* 3.7 31.4 - - - +
9K MET* 3.7 26.2 - - + -
279K ILE* 3.8 26.7 - - + -
379K GLY 3.1 15.2 + - - +
380K GLN* 3.5 13.0 - - + +
382K ILE* 1.3 74.1 - - + +
384K LYS* 1.3 68.3 + - - +
385K ASP 3.1 2.5 - - - -
386K GLY* 3.0 10.3 + - - -
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Residues in contact with LYS 384 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K THR 5.3 0.9 - - - -
380K GLN 3.1 17.8 + - - +
381K SER* 3.5 29.4 - - - +
383K VAL* 1.3 77.2 - - + +
385K ASP* 1.3 69.7 + - - +
386K GLY 3.7 0.2 - - - -
395K ASN* 3.7 22.3 - - - +
399K GLU* 4.3 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