Contacts of the helix formed by residues 324 - 332 (chain A) in PDB entry 2G9Y
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 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ASP* 3.8 2.8 - - - +
147A SER* 3.9 0.2 - - - +
148A THR* 3.0 13.2 + - - +
149A ALA* 3.3 36.1 - - + +
322A GLU* 3.3 27.6 - - + +
323A GLY* 1.3 75.1 - - - +
325A SER* 1.3 62.0 + - - +
326A ILE 3.3 1.6 + - - -
327A ASP* 3.5 15.1 + - - +
328A LYS* 3.6 16.4 + - - +
452A MG 4.3 2.2 - - - -
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Residues in contact with SER 325 (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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148A THR* 3.7 9.7 + - - -
263A ASN* 4.9 5.7 - - - +
264A MET 4.6 7.3 + - - -
266A VAL* 3.9 16.8 - - - +
323A GLY 3.5 1.0 - - - -
324A ALA* 1.3 75.1 - - - +
326A ILE* 1.3 64.7 + - - +
327A ASP 3.1 1.6 - - - -
328A LYS* 3.7 22.4 - - - +
329A GLN* 3.0 26.4 + - - +
341A GLU* 3.4 33.8 + - - +
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Residues in contact with ILE 326 (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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50A GLY* 4.1 10.1 - - - -
51A ASP 3.4 12.3 - - - +
52A GLY 4.5 0.9 - - - -
53A MET* 4.0 34.3 - - - +
57A GLU* 4.4 10.1 - - + -
323A GLY 3.9 14.4 - - - +
324A ALA 3.3 1.0 - - - -
325A SER* 1.3 77.3 - - - +
327A ASP* 1.3 58.7 + - - +
330A ASP* 3.1 27.1 + - - +
338A GLN* 3.7 19.4 - - + +
341A GLU* 3.6 30.9 - - + +
342A THR* 3.7 31.6 - - - +
345A LEU* 4.3 5.4 - - + -
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Residues in contact with ASP 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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51A ASP* 2.9 50.4 + - + +
52A GLY* 4.0 0.4 - - - +
324A ALA 3.5 2.8 + - - +
326A ILE* 1.3 75.1 - - - +
328A LYS* 1.3 69.8 + - - +
330A ASP* 2.9 5.1 + - - +
331A HIS* 2.9 41.2 + - - -
370A HIS* 3.2 1.0 - - - -
372A HIS* 2.9 23.7 + - - -
412A HIS* 3.2 2.1 + - - -
450A ZN 2.1 36.9 - - - -
656A PO4 3.4 5.3 + - - -
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Residues in contact with LYS 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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149A ALA* 3.9 8.1 - - - -
150A GLU* 5.2 2.8 + - - -
153A ASP* 3.1 33.4 + - - -
263A ASN* 3.4 42.0 + - + +
324A ALA* 3.6 15.3 - - - +
325A SER* 3.5 19.5 + - - +
326A ILE 3.5 0.2 - - - -
327A ASP* 1.3 85.0 + - - +
329A GLN* 1.3 61.2 + - + +
331A HIS* 3.2 12.2 + - + +
332A ALA* 3.1 24.6 + - - +
656A PO4 5.2 5.7 + - - -
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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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266A VAL* 3.6 26.5 - - + +
325A SER* 3.0 21.9 + - - +
328A LYS* 1.3 76.6 - - - +
330A ASP* 1.3 62.9 + - - +
331A HIS 3.2 0.2 - - - -
332A ALA* 3.3 8.7 + - - +
333A ALA 3.2 3.3 + - - -
334A ASN* 3.0 63.6 + - - +
337A GLY* 3.4 20.6 - - - +
338A GLN* 3.3 23.3 - - - +
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Residues in contact with ASP 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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52A GLY 4.3 0.3 - - - +
57A GLU* 2.7 31.9 - - - +
326A ILE 3.1 14.3 + - - +
327A ASP 2.9 10.2 + - - +
329A GLN* 1.3 75.6 - - - +
331A HIS* 1.3 65.0 + - - +
333A ALA 3.1 9.4 + - - -
338A GLN* 3.0 23.5 - - - +
372A HIS* 3.2 32.3 + - + +
373A ALA* 3.6 0.3 + - - +
374A SER 3.1 22.3 + - - -
402A TYR* 3.3 11.6 - - - -
410A GLN* 3.6 7.3 - - - +
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Residues in contact with HIS 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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327A ASP* 2.9 28.7 + - - -
328A LYS* 3.2 11.7 - - + +
330A ASP* 1.3 80.0 - - - +
332A ALA* 1.3 56.6 + - - +
333A ALA* 3.2 3.7 + - - +
372A HIS* 3.5 3.4 - - - -
408A ASP 4.0 1.7 - - - +
409A SER* 3.0 22.6 + - - +
410A GLN* 2.6 51.9 + - - +
411A GLU* 3.5 11.4 - - - -
412A HIS* 3.5 14.8 - + - -
450A ZN 2.0 38.3 - - - -
656A PO4 2.8 12.3 + - - -
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Residues in contact with ALA 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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272A LYS* 3.4 25.6 - - + +
328A LYS 3.1 14.7 + - - +
329A GLN* 3.3 17.0 + - - +
330A ASP 3.2 0.4 - - - -
331A HIS* 1.3 76.5 - - - +
333A ALA* 1.3 70.4 + - - +
334A ASN* 3.1 5.6 + - + +
408A ASP 5.2 2.2 - - - -
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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