Contacts of the helix formed by residues 371 - 384 (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 ALA 371 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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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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Residues in contact with TYR 372 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ALA* 3.5 32.3 - - + +
15I ASP* 4.3 3.8 + - - -
17I MET* 4.9 6.6 - - + +
274I ILE* 4.1 5.8 - - + +
305I GLN* 2.9 39.4 + - + +
306I CYS* 3.9 15.9 - - - -
353I ARG* 3.1 44.9 + - + -
354I ASP* 2.5 24.6 + - - -
357I MET* 3.9 22.9 - - + -
370I LEU 4.0 1.3 - - - -
371I ALA* 1.3 70.8 - - - +
373I ASP* 1.3 65.1 + - - +
375I ALA* 3.6 6.2 - - - +
376I TYR* 3.0 23.6 + - - +
1J MET* 3.5 27.4 - - + +
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Residues in contact with ASP 373 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ALA* 3.6 17.7 - - + +
357I MET* 4.8 0.9 - - - +
361I ARG* 2.2 44.1 + - - -
371I ALA* 3.5 5.9 - - - +
372I TYR* 1.3 78.4 + - - +
374I ASN* 1.3 68.2 + - - +
376I TYR* 3.4 5.5 + - - +
377I ARG* 3.2 19.8 + - - +
1J MET* 3.4 30.2 - - + +
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Residues in contact with ASN 374 (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* 3.6 19.5 + - - +
368I TYR* 2.9 44.3 + - - +
369I MET 3.4 15.5 - - - +
371I ALA 3.0 2.5 + - - +
373I ASP* 1.3 86.7 + - - +
375I ALA* 1.3 60.4 + - - +
377I ARG* 3.2 15.9 + - - +
378I VAL* 2.9 31.1 + - - +
403I ILE* 3.6 26.1 - - + +
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Residues in contact with ALA 375 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274I ILE* 3.8 28.0 - - + +
275I ILE* 3.6 30.0 - - + +
278I ALA* 4.8 1.0 - - + +
369I MET 3.3 7.9 + - - +
370I LEU* 3.8 6.3 - - - +
371I ALA 2.8 15.4 + - - +
372I TYR 3.6 5.2 - - - +
374I ASN* 1.3 77.5 - - - +
376I TYR* 1.3 61.7 + - - +
378I VAL* 3.2 6.3 + - - +
379I GLY* 3.0 17.5 + - - -
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Residues in contact with TYR 376 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I MET* 3.5 31.2 - - + +
11I TYR* 2.4 37.3 + - + -
12I ALA 3.2 11.6 + - - -
13I ASN* 3.5 22.4 - - + -
14I ALA* 3.7 24.9 - - + -
17I MET* 4.1 5.2 - - - -
278I ALA* 3.9 18.1 - - + +
372I TYR 3.0 14.3 + - - +
373I ASP 3.4 10.3 - - - +
374I ASN 3.2 0.2 - - - -
375I ALA* 1.3 75.3 - - - +
377I ARG* 1.3 57.9 + - - +
379I GLY* 2.9 17.5 + - - -
380I GLN* 3.0 43.3 + - + +
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Residues in contact with ARG 377 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373I ASP 3.2 9.0 + - - +
374I ASN* 3.2 17.0 + - - +
376I TYR* 1.3 79.6 - - - +
378I VAL* 1.3 61.5 + - - +
380I GLN* 3.3 22.5 + - - +
381I SER* 3.2 20.4 + - - -
399I GLU* 2.7 28.3 + - - +
402I ASN* 4.1 14.8 - - - +
403I ILE* 3.5 24.5 - - + +
406I GLU* 2.5 45.2 + - - -
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Residues in contact with VAL 378 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248I ALA* 4.7 6.7 - - + +
275I ILE* 4.1 17.9 - - + -
369I MET* 4.1 22.4 - - + -
374I ASN 2.9 19.9 + - - +
375I ALA* 3.2 7.4 + - - +
377I ARG* 1.3 75.1 - - - +
379I GLY* 1.3 60.8 + - - +
381I SER* 2.7 24.9 + - - +
382I ILE* 3.2 22.3 + - + +
396I ALA* 4.0 22.0 - - + +
399I GLU* 4.3 4.3 - - + -
400I CYS* 4.8 5.2 - - - +
403I ILE* 3.4 20.2 - - + -
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Residues in contact with GLY 379 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I MET* 3.6 16.2 - - - -
275I ILE* 4.2 4.4 - - - +
279I ILE* 4.0 18.4 - - - -
375I ALA 3.0 9.2 + - - -
376I TYR 2.9 9.5 + - - -
378I VAL* 1.3 74.5 - - - +
380I GLN* 1.3 65.2 + - - +
382I ILE* 3.1 6.9 + - - +
383I VAL* 3.1 26.2 + - - +
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Residues in contact with GLN 380 (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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9I MET* 3.7 9.5 - - + +
376I TYR* 3.0 36.2 + - + +
377I ARG* 3.5 26.5 - - + +
379I GLY* 1.3 75.7 - - - +
381I SER* 1.3 63.4 + - - +
383I VAL* 3.3 10.6 + - - +
384I LYS* 3.2 26.8 + - - +
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Residues in contact with SER 381 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377I ARG 3.2 2.8 + - - -
378I VAL 2.7 18.3 + - - -
380I GLN* 1.3 78.9 - - - +
382I ILE* 1.3 60.6 + - - +
384I LYS* 3.4 16.7 - - - +
395I ASN* 3.1 36.0 + - - +
396I ALA* 3.5 20.1 - - - -
399I GLU* 3.5 35.8 - - - +
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Residues in contact with ILE 382 (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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6I TYR 5.7 0.2 - - - +
251I ALA* 4.1 1.1 - - + -
252I PRO* 4.0 24.0 - - + -
255I LEU* 3.9 27.1 - - + -
275I ILE* 3.8 25.6 - - + -
279I ILE* 4.1 7.6 - - + -
378I VAL* 3.2 21.7 + - + +
379I GLY* 3.1 8.5 + - - +
381I SER* 1.3 81.4 + - - +
383I VAL* 1.3 62.9 + - + +
385I ASP 3.2 5.2 + - - -
386I GLY* 3.1 19.7 + - - -
392I ARG* 3.3 35.6 - - + +
396I ALA* 3.8 24.5 - - + -
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Residues in contact with VAL 383 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I TYR* 3.9 14.4 - - + +
7I THR* 3.5 30.6 - - - +
8I SER* 3.8 30.1 - - - +
9I MET* 4.0 10.5 - - + -
279I ILE* 3.8 28.5 - - + -
379I GLY 3.1 12.0 + - - +
380I GLN* 3.3 19.7 - - - +
382I ILE* 1.3 73.7 - - + +
384I LYS* 1.3 61.6 + - - +
385I ASP 3.1 5.4 - - - -
386I GLY 3.1 10.9 + - - +
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Residues in contact with LYS 384 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I THR 5.5 0.2 - - - -
380I GLN 3.2 11.1 + - - +
381I SER* 3.4 23.8 - - - +
383I VAL* 1.3 78.9 - - + +
385I ASP* 1.3 69.7 + - - +
386I GLY 3.6 0.2 - - - -
395I ASN* 3.4 26.6 - - - +
399I GLU* 4.6 13.7 + - - -
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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