Contacts of the helix formed by residues 326 - 335 (chain A) in PDB entry 2A79
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A MET* 3.8 10.5 - - + +
72A LEU* 3.4 12.2 - - - +
324A ALA* 4.0 1.4 - - - +
325A SER* 1.3 97.7 + - - +
327A ALA* 1.3 64.6 + - - +
328A GLU* 3.7 21.7 - - + +
329A GLN* 3.3 32.3 + - + +
330A LEU* 3.2 16.8 + - - +
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Residues in contact with ALA 327 (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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68A MET* 4.2 7.1 - - + +
71A HIS* 3.2 39.7 - - + +
72A LEU* 3.7 11.3 - - - +
75A LEU* 4.1 8.2 - - + +
326A ASN* 1.3 72.4 - - - +
328A GLU* 1.3 78.4 + - - +
330A LEU* 3.5 2.0 + - - +
331A MET* 3.1 29.4 + - - +
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Residues in contact with GLU 328 (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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68A MET* 5.7 1.4 - - - +
326A ASN* 3.0 17.5 - - + +
327A ALA* 1.3 89.5 + - - +
329A GLN* 1.3 67.0 + - + +
330A LEU 3.1 0.5 + - - -
331A MET* 3.1 6.3 + - - +
332A GLU* 2.9 26.4 + - - +
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Residues in contact with GLN 329 (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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254A LYS* 3.5 7.5 - - - +
324A ALA* 4.2 2.9 - - + -
325A SER* 2.7 36.9 + - - -
326A ASN* 3.3 29.9 + - - +
328A GLU* 1.3 78.1 - - - +
330A LEU* 1.3 60.8 + - - +
332A GLU* 3.5 3.4 + - - +
333A ASN* 3.0 34.3 + - - -
1001A NAP 3.1 75.6 + - + +
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Residues in contact with LEU 330 (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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54A LEU* 4.4 15.7 - - + -
72A LEU* 3.3 44.0 - - + +
75A LEU* 4.1 15.0 - - + -
76A ALA* 4.2 13.2 - - + +
81A ILE* 5.4 1.8 - - + -
322A LEU* 4.2 23.8 - - + -
324A ALA* 4.1 15.9 - - + +
326A ASN 3.2 10.4 + - - +
327A ALA* 3.7 7.9 - - - +
328A GLU 3.1 0.8 - - - -
329A GLN* 1.3 77.3 - - - +
331A MET* 1.3 65.9 + - + +
333A ASN* 3.1 5.3 + - + +
334A ILE* 2.9 38.1 + - + +
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Residues in contact with MET 331 (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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75A LEU* 3.7 26.5 - - + -
79A ASN* 4.0 29.4 - - - +
305A GLN* 4.9 0.2 + - - -
327A ALA* 3.1 16.1 + - + +
328A GLU* 3.1 6.1 + - - +
330A LEU* 1.3 76.4 - - - +
332A GLU* 1.3 64.2 + - - +
334A ILE* 3.6 22.0 + - + +
335A GLY* 3.5 13.0 + - - -
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Residues in contact with GLU 332 (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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302A THR* 2.6 42.2 + - + +
304A PRO* 3.1 18.1 - - - +
305A GLN* 2.6 36.9 + - + +
328A GLU 2.9 16.3 + - - +
329A GLN* 3.7 6.9 - - - +
331A MET* 1.3 77.8 - - - +
333A ASN* 1.3 58.1 + - - +
335A GLY 2.9 10.7 + - - -
1001A NAP 3.2 20.3 + - - +
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Residues in contact with ASN 333 (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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52A LEU* 4.5 2.1 - - - +
246A LEU* 4.0 2.6 - - - +
304A PRO* 3.7 11.3 - - - +
305A GLN* 4.8 2.2 - - - -
308A ILE* 3.4 32.6 - - + +
322A LEU* 3.9 20.1 - - + +
323A GLY 3.8 8.7 - - - +
324A ALA* 5.0 0.3 - - - +
329A GLN 3.0 14.1 + - - +
330A LEU* 3.1 5.7 + - + +
332A GLU* 1.3 72.2 - - - +
334A ILE* 1.3 56.2 + - - +
335A GLY 3.0 4.9 - - - -
336A ALA* 2.9 29.8 + - - +
1001A NAP 2.9 48.6 + - - -
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Residues in contact with ILE 334 (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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38A PHE* 6.1 1.6 - - + -
52A LEU* 4.2 12.6 - - + -
76A ALA* 4.8 3.6 - - - -
79A ASN* 4.3 32.3 - - + +
81A ILE* 4.7 16.4 - - + -
322A LEU* 4.7 5.6 - - + -
330A LEU* 2.9 46.2 + - + +
331A MET* 3.8 28.7 - - + +
332A GLU 3.3 0.2 - - - -
333A ASN* 1.3 75.7 - - - +
335A GLY* 1.3 60.2 + - - +
336A ALA 3.1 1.4 + - - -
337A ILE* 3.4 26.2 + - + +
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Residues in contact with GLY 335 (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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305A GLN* 3.7 13.9 + - - -
331A MET 3.5 5.4 + - - -
332A GLU 2.9 15.1 + - - -
334A ILE* 1.3 75.1 - - - +
336A ALA* 1.3 65.8 + - - +
337A ILE 2.8 5.1 + - - -
338A GLN* 3.0 28.1 + - - +
339A VAL* 3.7 5.4 + - - +
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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