Contacts of the helix formed by residues 244 - 247 (chain A) in PDB entry 1OVM
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 LEU 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A MET* 1.3 75.6 - - - +
245A MET* 1.3 62.9 + - - +
247A LYS* 3.3 15.8 + - + +
260A THR* 3.8 11.0 - - - +
261A TYR 4.4 1.6 + - - -
262A SER* 6.0 0.4 - - - -
290A THR 5.8 0.7 - - - +
291A LEU* 4.0 16.0 - - + +
383A GLN* 5.7 0.4 - - - +
387A ALA* 4.4 9.0 - - + +
388A PHE* 3.9 29.6 - - + -
391A ILE* 3.7 33.4 - - + +
401A PHE* 3.9 15.7 - - + -
403A VAL* 3.5 26.8 - - + +
405A PRO* 3.5 24.5 - - + -
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Residues in contact with MET 245 (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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64A ARG* 5.7 1.7 + - - -
92A GLU* 3.5 35.2 - - + +
217A ASP* 2.9 16.2 - - - +
218A PHE* 3.6 58.6 - - + +
221A LEU* 4.1 7.8 - - - +
222A ARG* 4.8 2.8 + - - +
243A MET 3.2 1.2 - - - -
244A LEU* 1.3 78.4 - - - +
246A GLY* 1.3 57.3 + - - +
247A LYS 3.3 2.5 + - - +
286A ARG* 5.5 0.4 - - - -
288A THR* 5.1 4.7 - - - -
291A LEU* 3.9 20.0 - - + +
401A PHE 5.0 3.3 - - - +
403A VAL* 4.1 13.3 - - - +
405A PRO* 3.4 23.1 - - + -
406A LEU* 4.2 20.0 - - + -
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Residues in contact with GLY 246 (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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217A ASP* 2.8 26.1 + - - -
218A PHE* 3.3 22.4 - - - -
221A LEU* 4.2 4.3 - - - -
242A THR* 3.5 9.6 + - - -
243A MET 3.1 0.2 + - - -
245A MET* 1.3 71.1 - - - +
247A LYS* 1.3 69.5 + - - +
248A GLY 3.1 0.9 + - - -
249A ILE* 2.8 25.4 + - - +
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Residues in contact with LYS 247 (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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221A LEU* 4.6 4.3 - - - +
242A THR* 3.4 9.6 - - - +
243A MET 3.2 8.0 + - - +
244A LEU* 3.3 18.9 + - + +
245A MET 3.3 1.4 - - - +
246A GLY* 1.3 77.2 - - - +
248A GLY* 1.3 59.3 + - - +
252A GLU* 3.0 32.3 + - - +
260A THR* 2.9 26.5 + - + +
390A ALA 3.5 11.9 - - - -
391A ILE* 3.3 24.5 + - + +
392A ASP 4.9 0.2 - - - -
393A LEU 3.0 17.0 + - - -
395A LEU* 3.9 13.9 - - + -
401A PHE* 3.3 49.3 + - + +
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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