Contacts of the helix formed by residues 326 - 335 (chain G) in PDB entry 2R9R
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 326 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68G MET* 3.9 19.1 - - + -
72G LEU* 3.6 10.0 - - - +
324G ALA* 3.5 3.0 - - - +
325G SER* 1.3 84.1 + - - +
327G ALA* 1.3 62.8 + - - +
328G GLU* 2.8 32.2 + - - +
329G GLN* 2.8 45.8 + - - +
330G LEU 3.3 8.8 + - - -
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Residues in contact with ALA 327 (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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68G MET* 4.1 5.3 - - + +
71G HIS* 3.7 34.3 - - + +
72G LEU* 3.6 11.1 - - + +
75G LEU* 3.8 11.0 - - + -
326G ASN* 1.3 71.8 - - - +
328G GLU* 1.3 75.6 + - - +
330G LEU* 3.9 2.3 - - - +
331G MET* 3.1 30.4 + - + +
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Residues in contact with GLU 328 (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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326G ASN* 2.8 24.2 + - - +
327G ALA* 1.3 84.7 + - - +
329G GLN* 1.3 63.6 + - + +
331G MET* 4.0 4.1 - - - +
332G GLU* 3.0 27.8 + - - +
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Residues in contact with GLN 329 (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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254G LYS* 3.8 4.4 - - - +
324G ALA* 3.5 4.1 - - + -
325G SER* 2.8 25.4 + - - -
326G ASN* 2.8 37.1 + - - +
328G GLU* 1.3 77.0 - - + +
330G LEU* 1.3 57.7 + - - +
332G GLU* 3.1 3.5 + - - +
333G ASN* 2.8 36.9 + - - -
1001G NAP 2.8 83.1 + - + +
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Residues in contact with LEU 330 (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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54G LEU* 4.3 19.7 - - + -
72G LEU* 3.4 41.5 - - + +
75G LEU* 3.9 6.1 - - + -
76G ALA* 4.0 8.5 - - + +
81G ILE* 4.9 4.9 - - + -
322G LEU* 4.2 19.7 - - + -
324G ALA* 4.0 16.9 - - + +
326G ASN 3.3 7.6 + - - +
327G ALA 4.0 5.8 - - - +
328G GLU 3.4 0.2 - - - -
329G GLN* 1.3 78.9 - - - +
331G MET* 1.3 77.5 + - + +
333G ASN* 3.1 4.6 + - - +
334G ILE* 2.9 40.4 + - + +
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Residues in contact with MET 331 (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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75G LEU* 3.4 43.1 - - + -
79G ASN* 4.0 19.7 - - - +
305G GLN* 5.1 0.2 + - - -
327G ALA* 3.1 18.4 + - + +
328G GLU* 4.1 4.0 - - - +
330G LEU* 1.3 79.7 - - + +
332G GLU* 1.3 65.3 + - - +
334G ILE* 3.6 29.4 + - + +
335G GLY* 3.5 13.9 + - - -
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Residues in contact with GLU 332 (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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302G THR* 2.8 40.3 + - + +
304G PRO* 3.3 10.6 - - - +
305G GLN* 3.0 31.3 + - + +
328G GLU* 3.0 21.2 + - - +
329G GLN* 3.4 5.3 - - - +
331G MET* 1.3 77.0 - - - +
333G ASN* 1.3 58.6 + - - +
335G GLY 2.9 16.1 + - - -
1001G NAP 3.2 26.1 + - - +
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Residues in contact with ASN 333 (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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52G LEU* 4.2 5.4 - - - +
246G LEU* 4.2 2.0 - - - +
304G PRO* 4.0 11.5 - - - +
305G GLN* 4.9 1.8 - - - -
308G ILE* 3.5 26.1 - - + +
322G LEU* 3.8 18.4 - - + +
323G GLY 3.7 9.7 - - - +
324G ALA* 5.1 0.2 - - - +
329G GLN 2.8 13.8 + - - +
330G LEU* 3.6 6.3 - - - +
332G GLU* 1.3 77.4 - - - +
334G ILE* 1.3 61.7 + - - +
335G GLY 3.0 0.2 - - - -
336G ALA* 2.9 23.7 + - - +
1001G NAP 2.9 52.2 + - - -
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Residues in contact with ILE 334 (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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38G PHE* 6.1 2.2 - - + -
52G LEU* 3.9 13.9 - - + -
76G ALA* 4.7 2.0 - - - -
79G ASN* 4.3 29.2 - - + +
81G ILE* 4.0 27.1 - - + -
322G LEU* 4.5 1.3 - - + -
330G LEU* 2.9 29.5 + - + +
331G MET* 3.6 38.1 - - + +
332G GLU 3.3 0.4 - - - -
333G ASN* 1.3 75.2 - - - +
335G GLY* 1.3 59.3 + - - +
336G ALA 3.1 1.4 + - - -
337G ILE* 3.5 25.6 + - + +
338G GLN* 5.4 0.3 - - - +
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Residues in contact with GLY 335 (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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305G GLN* 3.7 14.8 + - - -
331G MET 3.5 6.3 + - - -
332G GLU 2.9 12.1 + - - -
334G ILE* 1.3 75.6 - - - +
336G ALA* 1.3 64.3 + - - +
337G ILE 2.9 3.1 - - - -
338G GLN* 2.9 32.5 + - - +
339G VAL* 3.7 6.4 + - - +
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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