Contacts of the helix formed by residues 373 - 385 (chain A) in PDB entry 2G1X
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 ASN 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A LYS* 4.9 2.8 - - - +
242A GLN 5.9 0.6 - - - +
307A ALA* 2.7 39.9 + - - +
308A ARG* 3.8 3.6 - - - +
309A GLU 5.1 0.2 - - - +
310A ARG* 5.5 2.0 - - - +
311A LYS* 2.8 34.4 - - - +
369A TYR* 3.1 15.7 + - + +
370A THR 4.1 0.8 - - - +
371A MET 3.6 1.3 - - - -
372A SER* 1.3 75.5 - - - +
374A GLU* 1.3 64.7 + - - +
375A ASP* 3.7 10.3 - - - +
376A PHE* 2.6 28.2 + - + +
377A LYS* 3.0 22.5 + - - +
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Residues in contact with GLU 374 (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 LEU* 4.5 5.1 - - - +
241A LYS* 2.9 66.5 + - + +
242A GLN* 5.4 1.2 - - + +
371A MET 5.8 0.4 - - - -
372A SER 3.5 5.3 + - - -
373A ASN* 1.3 75.6 - - - +
375A ASP* 1.3 68.4 + - - +
377A LYS* 3.4 9.1 + - + +
378A GLN* 3.3 36.6 + - + +
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Residues in contact with ASP 375 (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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80A LEU* 4.4 15.5 - - - +
242A GLN* 2.9 49.0 + - + +
307A ALA* 4.0 10.5 - - + -
373A ASN* 3.2 14.4 - - - +
374A GLU* 1.3 87.5 - - - +
376A PHE* 1.3 62.3 + - - +
378A GLN* 3.5 8.8 + - - +
379A ALA* 3.3 15.8 + - - +
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Residues in contact with PHE 376 (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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69A PHE* 4.9 1.6 - + - -
70A VAL* 4.6 8.1 - - + -
73A THR* 2.9 43.1 - - + -
74A VAL* 4.6 0.2 - - + -
80A LEU* 4.0 10.3 - - + -
307A ALA* 4.3 2.7 - - + -
369A TYR* 2.8 51.8 - + + +
370A THR* 3.2 40.6 - - + -
373A ASN* 2.6 23.3 + - + +
374A GLU 3.3 0.2 - - - -
375A ASP* 1.3 71.5 - - - +
377A LYS* 1.3 64.2 + - - +
379A ALA* 2.8 26.8 + - + +
380A PHE* 2.9 24.0 + + + -
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Residues in contact with LYS 377 (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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370A THR 3.7 14.1 - - - +
371A MET* 5.2 12.1 - - + +
373A ASN 3.0 16.8 + - - +
374A GLU* 3.7 10.3 - - - +
375A ASP 3.3 0.2 - - - -
376A PHE* 1.3 75.3 - - - +
378A GLN* 1.3 73.5 + - + +
380A PHE* 2.7 53.5 + - + -
381A HIS* 2.9 29.6 + - + -
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Residues in contact with GLN 378 (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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374A GLU* 3.3 29.1 + - + +
375A ASP* 3.9 8.0 - - - +
377A LYS* 1.3 84.0 - - + +
379A ALA* 1.3 53.3 + - - +
381A HIS* 3.0 16.0 + - + +
382A LYS* 2.7 34.1 + - - +
389A THR* 6.0 1.2 - - - +
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Residues in contact with ALA 379 (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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73A THR* 4.0 11.2 - - - +
77A THR* 4.5 13.7 - - + +
80A LEU* 4.5 10.8 - - + -
375A ASP* 3.3 8.7 + - - +
376A PHE* 2.8 25.5 + - + +
378A GLN* 1.3 79.5 - - - +
380A PHE* 1.3 58.8 + - - +
382A LYS* 3.1 8.4 + - - +
383A LEU* 2.7 30.9 + - - +
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Residues in contact with PHE 380 (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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64A THR* 5.1 10.3 - - + -
65A LEU* 6.1 4.0 - - + -
69A PHE* 3.0 38.6 - + + -
73A THR* 4.1 5.8 + - - -
370A THR* 4.4 16.2 - - + -
371A MET* 5.9 2.0 - - + -
376A PHE* 2.9 28.6 + + + -
377A LYS* 2.7 46.6 + - + -
379A ALA* 1.3 76.8 - - - +
381A HIS* 1.3 113.9 + + - +
383A LEU* 3.0 5.3 + - - +
384A ILE* 2.8 28.3 + - + +
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Residues in contact with HIS 381 (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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377A LYS* 2.9 49.0 + - - -
378A GLN* 3.0 14.2 + - + +
380A PHE* 1.3 114.5 - + - +
382A LYS* 1.3 59.7 + - - +
384A ILE* 2.7 33.3 - - + +
385A ARG* 3.3 5.7 + - - +
388A CYS 4.2 4.4 - - - +
389A THR* 4.9 12.7 - - - +
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Residues in contact with LYS 382 (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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77A THR* 5.7 4.3 - - - +
378A GLN 2.7 17.4 + - - +
379A ALA* 3.1 13.2 + - - +
381A HIS* 1.3 73.0 - - - +
383A LEU* 1.3 55.6 + - + +
385A ARG* 2.5 32.7 + - - +
387A LYS* 3.3 45.5 + - + +
388A CYS* 3.9 11.4 + - - +
389A THR* 5.4 6.0 - - - +
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Residues in contact with LEU 383 (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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69A PHE* 4.4 13.7 - - + +
72A ALA* 3.7 13.2 - - + +
73A THR* 2.9 55.2 - - - +
76A ARG* 3.9 37.9 + - + +
77A THR* 4.3 9.6 - - - +
379A ALA 2.7 32.7 + - - +
380A PHE* 3.0 6.7 + - - +
382A LYS* 1.3 78.9 - - + +
384A ILE* 1.3 59.9 + - - +
385A ARG 2.5 15.8 - - - +
387A LYS 5.2 0.7 - - - +
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Residues in contact with ILE 384 (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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64A THR* 5.8 9.6 - - + +
69A PHE* 4.8 12.1 - - + -
380A PHE* 2.8 13.2 + - + +
381A HIS* 2.7 36.6 - - + +
383A LEU* 1.3 78.5 - - - +
385A ARG* 1.3 72.5 + - + +
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Residues in contact with ARG 385 (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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76A ARG* 5.2 0.9 + - - -
381A HIS* 4.2 4.4 + - - +
382A LYS 2.5 20.2 + - - +
383A LEU* 2.5 16.1 - - - +
384A ILE* 1.3 93.2 - - + +
386A PHE* 1.3 62.3 + - - +
387A LYS 2.9 1.4 + - - -
388A CYS* 2.7 39.9 - - + +
389A THR* 4.3 5.8 + - - +
390A SER* 2.7 38.7 + - - +
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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