Contacts of the helix formed by residues 39 - 50 (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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A PRO* 3.9 15.0 - - + -
36A GLU 3.1 18.9 + - - +
37A PRO 3.0 2.9 - - - +
38A SER* 1.3 78.8 + - - +
40A ARG* 1.3 62.0 + - + +
41A SER 3.2 0.2 - - - -
42A VAL* 3.2 10.0 + - + -
43A MET* 2.9 29.3 + - + +
172A THR 5.3 0.4 - - - +
175A CYS* 4.6 2.7 - - + +
176A GLN* 3.9 30.1 - - + +
179A ASN* 3.6 29.6 - - - +
639A GLU* 3.6 38.4 - - + +
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Residues in contact with ARG 40 (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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37A PRO 3.2 15.6 + - - +
38A SER* 4.7 0.4 - - - -
39A ILE* 1.3 79.8 - - - +
41A SER* 1.3 58.5 - - - +
43A MET 4.3 1.1 - - - +
44A GLN* 2.7 58.0 + - + +
166A ILE* 2.7 40.3 + - - +
167A GLU* 4.4 5.8 - - - +
168A SER 3.3 20.2 + - - +
171A PHE* 3.6 12.7 - - - -
172A THR* 3.3 25.1 + - + +
175A CYS* 4.3 23.8 - - + -
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Residues in contact with SER 41 (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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38A SER 3.5 4.1 + - - -
39A ILE 3.2 0.4 - - - -
40A ARG* 1.3 81.3 - - - +
42A VAL* 1.3 62.3 + - - +
44A GLN* 4.8 1.9 - - - +
45A LYS* 3.5 23.4 + - - +
560A ILE 4.7 2.3 + - - -
561A MET* 4.0 9.2 - - - +
562A HIS* 3.3 61.1 + - - -
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Residues in contact with VAL 42 (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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38A SER 5.1 1.6 - - - +
39A ILE* 3.2 10.9 + - + +
40A ARG 3.1 0.2 - - - -
41A SER* 1.3 78.4 - - - +
43A MET* 1.3 61.3 + - + +
45A LYS* 3.5 4.7 + - - +
46A TYR* 3.1 23.8 + - + +
561A MET* 4.0 18.2 - - + -
562A HIS 3.6 20.4 - - - +
563A GLY* 4.9 3.8 - - - -
638A PRO 4.6 2.0 - - - +
639A GLU* 3.8 42.6 - - + +
642A GLN* 3.8 17.3 - - + +
643A TRP* 4.1 16.2 - - + +
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Residues in contact with MET 43 (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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39A ILE* 2.9 25.7 + - + +
40A ARG 4.1 0.2 - - - +
42A VAL* 1.3 75.6 - - + +
44A GLN* 1.3 67.1 + - - +
45A LYS 3.0 1.6 - - - -
46A TYR* 3.0 8.3 + - + +
47A LEU* 2.9 62.2 + - + +
175A CYS* 4.0 21.8 - - + +
178A LYS* 4.3 7.6 - - + -
179A ASN* 3.3 51.6 - - + +
182A LEU* 4.3 10.5 - - + -
638A PRO* 3.9 17.3 - - - -
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Residues in contact with GLN 44 (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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40A ARG* 2.7 56.9 + - + +
41A SER* 4.8 2.5 - - - +
43A MET* 1.3 72.6 - - - +
45A LYS* 1.3 57.8 + - + +
47A LEU* 3.9 9.7 - - - +
48A GLU* 3.0 46.4 + - - +
53A VAL* 4.5 4.4 - - + +
166A ILE* 3.8 24.4 - - - +
171A PHE* 4.0 14.5 - - + -
175A CYS* 4.4 3.4 - - - -
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Residues in contact with LYS 45 (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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41A SER 3.5 16.2 - - - +
42A VAL 3.5 9.5 + - - +
43A MET 3.0 0.2 - - - -
44A GLN* 1.3 78.5 - - + +
46A TYR* 1.3 64.9 + - - +
48A GLU* 3.6 5.3 - - - +
49A ASP* 3.0 30.5 + - - -
560A ILE* 3.3 39.6 + - - +
561A MET* 4.5 5.6 - - - -
642A GLN* 3.8 14.1 - - + +
646A GLU* 3.6 26.4 + - - +
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Residues in contact with TYR 46 (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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42A VAL* 3.1 14.3 + - + +
43A MET* 3.0 16.2 + - + +
45A LYS* 1.3 78.0 - - - +
47A LEU* 1.3 76.4 + - + +
49A ASP* 3.5 0.7 + - - +
50A ARG* 3.3 74.8 + - - +
52A GLU* 5.5 1.3 - - - -
182A LEU* 3.8 30.6 - - + +
638A PRO* 3.6 41.5 - - + +
641A VAL* 4.2 13.4 - - + +
642A GLN* 3.4 19.2 + - + +
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Residues in contact with LEU 47 (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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43A MET* 2.9 47.6 + - + +
44A GLN* 3.9 1.8 - - - +
46A TYR* 1.3 84.8 - - + +
48A GLU* 1.3 63.0 + - - +
50A ARG* 3.0 13.2 + - - -
51A GLY 3.1 10.2 + - - -
52A GLU* 3.1 36.6 + - + +
53A VAL* 3.4 18.2 - - + -
171A PHE* 4.4 12.3 - - + -
174A PHE* 4.6 14.1 - - + -
175A CYS* 4.3 17.0 - - - -
178A LYS* 4.4 13.5 - - + -
182A LEU* 4.7 2.7 - - + -
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Residues in contact with GLU 48 (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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44A GLN* 3.0 45.4 + - - +
45A LYS* 3.6 7.1 - - - +
47A LEU* 1.3 77.3 - - - +
49A ASP* 1.3 64.6 + - - +
50A ARG 3.4 0.2 + - - -
51A GLY* 3.5 10.4 + - - +
52A GLU 4.9 0.2 - - - +
53A VAL* 3.7 25.5 - - - +
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Residues in contact with ASP 49 (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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45A LYS* 3.0 15.5 + - - +
46A TYR 3.7 6.3 - - - +
47A LEU 3.2 0.2 - - - -
48A GLU* 1.3 80.3 - - - +
50A ARG* 1.3 67.9 + - - +
51A GLY 3.4 1.5 + - - -
642A GLN* 2.6 34.8 + - - +
645A LYS* 2.8 30.3 + - - -
646A GLU* 4.7 1.2 - - - +
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Residues in contact with ARG 50 (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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46A TYR* 3.3 68.2 + - - +
47A LEU* 3.0 6.5 + - - +
49A ASP* 1.3 85.9 + - - +
51A GLY* 1.3 62.8 + - - +
52A GLU* 3.4 22.3 + - + +
57A LYS* 5.0 4.3 + - - -
641A VAL* 4.0 17.2 - - - +
642A GLN* 4.4 4.6 + - - -
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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