Contacts of the helix formed by residues 513 - 524 (chain A) in PDB entry 1OMW
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 ILE 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A SER* 4.2 11.0 - - - +
247A SER* 4.0 18.4 - - - +
248A THR* 4.8 11.0 - - + -
257A MET* 3.7 37.7 - - + +
258A SER 3.1 19.3 + - - +
511A LEU* 4.2 16.4 - - + -
512A THR* 1.3 79.2 - - - +
514A SER* 1.3 69.2 + - - +
515A GLU* 4.4 8.1 - - + +
516A ARG* 2.8 37.4 + - + +
517A TRP 3.1 9.9 + - - -
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Residues in contact with SER 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLN* 4.7 4.9 + - - +
178A LYS* 4.1 4.6 + - - -
181A GLU* 2.6 28.3 + - - -
512A THR* 3.6 7.8 + - - +
513A ILE* 1.3 71.6 - - - +
515A GLU* 1.3 65.2 + - - +
516A ARG 3.2 0.2 + - - -
517A TRP* 3.3 4.4 + - - +
518A GLN* 2.9 40.5 + - - +
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Residues in contact with GLU 515 (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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62A LYS* 5.7 1.2 - - - +
247A SER 5.9 0.2 - - - +
248A THR* 3.2 19.2 - - + +
249A GLY* 3.1 33.5 + - - -
250A ASP 5.1 1.9 + - - +
513A ILE* 3.0 9.2 + - + +
514A SER* 1.3 81.2 - - - +
516A ARG* 1.3 58.6 - - + +
518A GLN* 4.0 4.8 - - - +
519A GLN* 3.1 25.5 + - - +
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Residues in contact with ARG 516 (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 TYR* 4.7 2.3 + - - -
247A SER 3.1 21.6 + - - +
249A GLY 4.4 1.0 + - - +
250A ASP* 3.6 38.5 + - - +
251A CYS 3.9 8.7 + - - +
256A CYS* 3.9 18.9 - - - +
257A MET 3.4 24.4 + - - +
258A SER* 3.5 29.0 + - - +
272A ASP* 3.4 33.5 + - - -
513A ILE* 2.8 22.8 + - + +
515A GLU* 1.3 77.2 - - + +
517A TRP* 1.3 58.8 + - - +
519A GLN* 3.2 8.5 + - - +
520A GLU* 3.0 26.5 + - - +
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Residues in contact with TRP 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 4.8 6.1 - - + +
63A LEU* 3.9 20.0 - - + -
177A TRP* 3.8 38.6 - + - -
180A VAL* 3.7 22.2 - - + -
181A GLU* 3.7 34.5 - - + -
184A ILE* 4.3 16.2 - - + +
210A LYS* 4.1 13.5 - - - +
212A ASP* 4.6 2.8 + - - -
258A SER* 5.2 1.6 + - - -
259A TYR* 3.3 34.8 - + + +
512A THR* 4.5 14.8 - - + -
513A ILE 3.1 8.0 + - - +
514A SER* 3.9 5.4 - - - +
516A ARG* 1.3 78.0 - - - +
518A GLN* 1.3 67.8 + - + +
520A GLU* 3.2 7.6 + - - +
521A VAL* 3.0 50.4 + - + +
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Residues in contact with GLN 518 (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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61A GLN* 3.0 28.7 + - - +
62A LYS* 3.3 18.1 + - + +
63A LEU* 2.9 56.8 + - + +
174A PHE* 5.2 0.4 - - - -
178A LYS* 3.5 2.6 - - - +
181A GLU* 3.0 22.2 + - - +
514A SER* 2.9 27.9 + - - +
515A GLU* 4.1 5.4 - - - +
517A TRP* 1.3 82.4 - - + +
519A GLN* 1.3 63.9 + - - +
521A VAL 4.6 0.2 - - - +
522A ALA* 3.1 25.8 + - - +
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Residues in contact with GLN 519 (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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62A LYS* 3.1 42.6 + - - +
215A LYS* 5.9 1.1 - - - +
250A ASP* 3.8 23.3 + - + +
515A GLU 3.1 16.1 + - - +
516A ARG* 3.2 12.1 + - - +
518A GLN* 1.3 76.2 - - - +
520A GLU* 1.3 62.8 + - - +
522A ALA* 3.5 0.7 - - - +
523A GLU* 3.2 56.2 + - - +
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Residues in contact with GLU 520 (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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210A LYS* 2.7 23.1 + - - +
213A THR* 2.6 35.3 + - + +
215A LYS* 4.0 11.9 - - + +
217A TYR* 2.5 38.9 + - - +
259A TYR* 2.8 22.2 + - - -
516A ARG 3.0 11.9 + - - +
517A TRP* 3.2 11.2 + - - +
519A GLN* 1.3 77.0 - - - +
521A VAL* 1.3 61.3 + - + +
523A GLU* 3.4 13.8 + - - +
524A THR* 2.9 29.3 + - - +
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Residues in contact with VAL 521 (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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32A ILE* 4.9 7.6 - - + -
63A LEU* 4.4 5.6 - - + -
177A TRP* 3.5 31.2 - - + -
213A THR* 4.7 2.5 - - + -
517A TRP* 3.0 52.8 + - + +
518A GLN 4.0 3.1 - - - +
520A GLU* 1.3 79.7 - - + +
522A ALA* 1.3 64.1 + - - +
524A THR* 3.1 11.9 + - - -
525A VAL* 3.2 6.6 + - + -
526A PHE* 3.1 45.2 + - + +
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Residues in contact with ALA 522 (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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62A LYS* 4.0 32.3 - - + +
63A LEU* 4.2 6.5 - - + -
66A LEU* 4.3 9.3 - - + +
518A GLN 3.1 18.3 + - - +
519A GLN 3.5 4.9 - - - +
521A VAL* 1.3 80.2 - - - +
523A GLU* 1.3 59.4 + - - +
524A THR 3.4 0.7 + - - -
526A PHE* 3.8 18.4 + - - +
527A ASP* 5.5 2.9 + - - +
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Residues in contact with GLU 523 (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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62A LYS* 6.0 0.2 - - - +
215A LYS* 2.5 41.8 + - + +
250A ASP* 5.6 0.2 - - - +
519A GLN* 3.2 40.3 + - - +
520A GLU* 3.5 12.2 - - - +
521A VAL 3.2 0.2 - - - -
522A ALA* 1.3 78.6 - - - +
524A THR* 1.3 67.5 + - + +
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Residues in contact with THR 524 (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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213A THR* 3.2 45.9 - - - +
214A GLY 5.2 0.7 - - - -
215A LYS* 4.6 17.3 - - + +
520A GLU* 2.9 20.7 + - + +
521A VAL 3.1 2.9 + - - -
522A ALA 3.4 0.6 - - - -
523A GLU* 1.3 91.0 - - + +
525A VAL* 1.3 70.3 + - - -
526A PHE 3.5 1.7 + - - -
527A ASP* 5.0 2.1 + - - +
528A THR* 4.7 4.9 + - - +
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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