Contacts of the helix formed by residues 323 - 328 (chain A) in PDB entry 2OF2
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 SER 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A 547 4.2 16.9 - - - -
321A ASN 4.1 0.3 - - - +
322A GLY* 1.3 74.0 - - - -
324A LEU* 1.3 61.1 + - - +
325A VAL* 3.4 8.5 - - - +
326A ASP* 3.1 23.9 + - - +
327A PHE* 2.8 27.3 + - - +
367A ALA 3.3 0.3 + - - -
368A ALA* 3.0 39.4 + - - +
370A ILE 3.3 6.5 - - - -
371A LEU* 3.7 5.1 - - - +
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Residues in contact with LEU 324 (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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322A GLY 3.8 0.8 + - - -
323A SER* 1.3 71.3 + - - +
325A VAL* 1.3 65.7 + - - +
326A ASP 3.1 0.2 + - - -
327A PHE* 4.3 2.7 - - + -
328A LEU* 3.0 56.8 + - + +
344A MET* 4.2 19.1 - - + -
348A ILE* 3.8 28.5 - - + -
367A ALA* 3.5 19.5 - - + +
370A ILE* 2.8 27.6 + - + +
372A VAL* 3.8 22.0 - - + +
378A CYS* 4.5 2.9 - - - -
429A LEU* 4.7 0.7 - - + -
433A ILE* 4.1 20.2 - - + -
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Residues in contact with VAL 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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323A SER* 3.4 15.3 - - - +
324A LEU* 1.3 79.4 - - - +
326A ASP* 1.3 75.1 + - - +
328A LEU* 4.2 3.3 + - - +
329A LYS* 3.5 29.3 - - - +
367A ALA* 3.4 18.0 + - + -
368A ALA* 3.8 17.7 - - + +
432A GLU* 4.1 15.3 - - - +
437A GLY* 4.0 32.1 - - - +
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Residues in contact with ASP 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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201A 547 5.1 7.1 - - - -
321A ASN 5.8 0.7 - - - +
323A SER* 3.1 21.5 + - - +
324A LEU 3.1 0.4 - - - -
325A VAL* 1.3 93.0 - - - +
327A PHE* 1.3 65.4 + - - +
329A LYS* 3.0 29.8 + - - +
330A THR* 3.6 11.0 + - + +
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Residues in contact with PHE 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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321A ASN* 3.7 44.4 + - + +
323A SER 2.8 19.7 + - - +
324A LEU* 3.8 3.8 - - + +
326A ASP* 1.3 73.0 - - - +
328A LEU* 1.3 67.1 + - + +
329A LYS 3.0 0.6 + - - -
330A THR* 2.7 43.3 + - + -
332A SER* 4.1 15.7 - - - -
333A GLY* 3.3 17.2 - - - -
336A LEU* 3.9 24.0 - - + -
344A MET* 4.3 14.4 - - + -
372A VAL* 4.2 19.5 - - + -
376A LEU* 4.0 25.4 - - + -
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Residues in contact with LEU 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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324A LEU* 3.0 46.9 + - + +
325A VAL* 4.4 3.4 - - - +
326A ASP 3.3 0.2 - - - -
327A PHE* 1.3 76.9 - - + +
329A LYS* 1.3 58.6 + - - +
330A THR 3.5 0.2 - - - -
333A GLY* 3.9 5.2 - - - -
334A ILE* 3.6 10.7 + - - +
336A LEU* 4.0 15.7 - - + -
341A LEU* 3.7 27.1 - - + -
344A MET* 4.9 0.7 - - - -
367A ALA* 5.7 1.6 - - + -
432A GLU 3.7 24.0 - - - +
433A ILE* 3.8 18.4 - - + +
436A HIS* 3.1 42.4 + - - +
437A GLY* 4.0 4.3 - - - +
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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