Contacts of the helix formed by residues 323 - 332 (chain A) in PDB entry 3OM0
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 HIS 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A LEU* 4.4 3.5 - - + +
306A GLN* 2.9 28.7 + - - +
307A GLU* 3.3 22.2 - - + -
308A ILE* 4.0 6.5 - - + -
309A GLY* 3.1 43.1 + - - -
321A TRP* 3.0 29.6 + + + -
322A PRO* 1.3 92.5 - - + +
324A GLY* 1.3 59.4 + - - +
325A THR 3.3 1.8 - - - -
326A SER* 3.3 6.2 + - - -
327A LEU* 2.9 27.7 + - - +
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Residues in contact with GLY 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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95A GLU* 3.1 25.6 - - - -
97A PRO* 4.3 2.7 - - - +
114A PHE* 3.6 8.5 - - - -
321A TRP* 3.2 22.2 + - - -
322A PRO 3.4 0.2 - - - -
323A HIS* 1.3 78.5 - - - +
325A THR* 1.3 56.1 + - - +
327A LEU* 3.3 0.9 + - - +
328A MET* 2.9 34.0 + - - +
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Residues in contact with THR 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLU* 3.5 19.8 + - - -
114A PHE* 3.8 15.1 - - - -
322A PRO 4.7 5.3 + - - -
323A HIS 3.3 0.4 - - - -
324A GLY* 1.3 75.4 - - - +
326A SER* 1.3 65.7 + - - +
328A MET* 3.4 5.4 + - - +
329A ASN* 3.3 22.9 + - - +
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 3.9 12.1 - - - -
306A GLN* 3.3 30.0 + - - -
322A PRO 5.2 1.8 + - - -
323A HIS* 3.3 11.0 + - - -
324A GLY 3.3 0.4 - - - -
325A THR* 1.3 79.0 - - - +
327A LEU* 1.3 64.2 + - - +
329A ASN* 3.0 16.4 + - - +
330A TYR* 3.0 23.5 + - - -
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Residues in contact with LEU 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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72A VAL* 3.3 26.5 - - + +
73A SER* 4.2 5.6 - - - +
97A PRO* 3.9 11.7 - - + -
295A VAL* 5.4 0.7 - - + -
298A ALA* 3.8 37.7 - - + +
299A VAL* 3.8 24.7 - - + +
302A LEU* 3.9 15.5 - - + +
321A TRP* 3.8 18.4 - - + -
323A HIS 2.9 15.6 + - - +
324A GLY 3.3 3.6 + - - +
326A SER* 1.3 76.2 - - - +
328A MET* 1.3 58.8 + - - +
330A TYR* 3.1 2.5 + - + +
331A LEU* 2.8 33.4 + - + +
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Residues in contact with MET 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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97A PRO* 3.5 31.6 - - - -
98A HIS 5.7 0.2 - - - +
114A PHE* 3.4 31.4 - - + -
115A ALA* 3.3 26.9 - - + +
116A SER* 3.9 7.2 - - - -
117A VAL* 3.7 23.1 - - + +
324A GLY 2.9 7.2 + - - +
325A THR* 3.6 9.6 - - - +
326A SER 3.2 0.2 - - - -
327A LEU* 1.3 76.1 - - - +
329A ASN* 1.3 61.9 + - - +
331A LEU* 3.4 9.2 + - + +
332A ARG* 3.2 55.6 + - - +
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Residues in contact with ASN 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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325A THR* 3.3 10.8 + - - +
326A SER* 3.0 12.5 + - - +
328A MET* 1.3 79.3 - - - +
330A TYR* 1.3 69.4 + - + +
332A ARG* 3.1 23.5 + - - +
333A MET* 3.3 23.0 + - + +
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Residues in contact with TYR 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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298A ALA* 3.7 21.4 - - + +
301A GLU* 3.7 24.1 - - + +
302A LEU* 3.6 43.1 - - + -
305A SER* 3.3 24.2 + - - -
326A SER* 3.0 29.9 + - - +
327A LEU* 3.1 6.0 + - + +
329A ASN* 1.3 76.8 - - + +
331A LEU* 1.3 66.6 + - - +
333A MET* 3.0 50.0 + - + +
334A VAL* 3.5 10.0 + - - +
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Residues in contact with LEU 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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73A SER* 4.6 2.2 - - - +
97A PRO* 3.6 32.8 - - + -
99A ILE* 3.8 18.4 - - + -
117A VAL* 4.3 13.5 - - + -
294A VAL* 3.8 28.0 - - + +
295A VAL* 4.1 10.8 - - + -
298A ALA* 3.6 21.1 - - + +
327A LEU* 2.8 30.4 + - + +
328A MET* 3.6 17.3 - - + +
329A ASN 3.3 0.2 - - - -
330A TYR* 1.3 71.2 - - - +
332A ARG* 1.3 62.2 + - - +
334A VAL* 3.2 16.2 + - - +
345A PHE* 3.3 18.3 - - - -
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Residues in contact with ARG 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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115A ALA* 3.2 27.0 - - - +
116A SER 2.6 30.9 + - - +
117A VAL* 4.2 4.3 - - + -
328A MET* 3.2 38.4 + - - +
329A ASN* 3.1 20.5 + - - +
331A LEU* 1.3 78.8 - - - +
333A MET* 1.3 58.6 + - - +
334A VAL 3.4 0.8 - - - +
345A PHE* 3.9 31.6 + - + +
346A ASN 3.6 18.1 + - - +
347A SER* 3.7 14.7 + - - +
348A LYS 4.0 4.0 + - - -
349A GLY* 3.3 23.7 - - - +
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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