Contacts of the helix formed by residues 168 - 183 (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 SER 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ARG* 3.3 4.8 + - - +
71A PHE* 3.8 20.8 - - - -
164A LYS 3.4 11.2 - - - -
165A PHE 3.1 16.2 + - - -
166A ILE 2.8 7.1 + - - -
167A GLU* 1.3 79.8 - - - +
169A ASP* 1.3 64.5 + - - +
170A LYS* 3.0 21.1 + - - +
171A PHE 3.1 10.9 + - - -
172A THR* 3.1 15.3 + - - -
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Residues in contact with ASP 169 (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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168A SER* 1.3 74.3 + - - +
170A LYS* 1.3 69.6 + - + +
172A THR* 3.2 13.5 + - - +
173A ARG* 3.0 25.1 + - - +
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Residues in contact with LYS 170 (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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67A LEU* 3.9 31.0 - - + +
70A ASP* 4.5 18.5 + - + +
71A PHE* 3.7 22.4 - - + -
74A LYS* 5.9 3.3 - - - +
75A HIS* 3.7 29.2 + - + -
165A PHE* 3.6 20.6 - - + -
168A SER* 3.0 7.3 + - - +
169A ASP* 1.3 86.0 - - + +
171A PHE* 1.3 67.1 + - - +
173A ARG* 3.2 9.7 + - + +
174A PHE* 3.1 19.1 + - - +
534A ASP* 5.1 11.5 + - - -
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Residues in contact with PHE 171 (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* 3.6 18.2 - - - -
44A GLN* 4.0 25.4 - - + -
47A LEU* 4.4 12.3 - - + -
53A VAL* 3.9 16.8 - - + -
58A ILE* 3.8 17.3 - - + -
165A PHE* 3.5 35.4 + + + +
166A ILE* 3.5 26.7 - - + +
168A SER* 3.1 5.8 + - - +
170A LYS* 1.3 75.4 - - - +
172A THR* 1.3 66.9 + - - +
174A PHE* 2.8 39.3 + + - +
175A CYS* 3.0 33.0 + - - -
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Residues in contact with THR 172 (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* 3.7 38.6 - - + +
40A ARG* 3.3 28.7 + - + +
168A SER 3.1 14.1 + - - -
169A ASP* 3.2 17.9 + - - -
171A PHE* 1.3 78.4 - - - +
173A ARG* 1.3 62.0 + - - +
175A CYS* 3.1 9.6 + - - +
176A GLN* 3.0 25.9 + - + +
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Residues in contact with ARG 173 (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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34A LEU* 3.7 19.1 - - - +
67A LEU* 3.9 17.5 - - + -
169A ASP 3.0 12.9 + - - +
170A LYS* 3.6 14.0 - - + +
171A PHE 3.1 0.4 - - - -
172A THR* 1.3 76.5 - - - +
174A PHE* 1.3 63.9 + - - +
176A GLN* 2.9 36.9 + - - +
177A TRP* 3.1 18.2 + - + +
530A ASN* 3.4 44.8 + - - +
533A THR* 4.0 6.9 - - - -
534A ASP* 2.8 34.9 + - - +
537A GLU* 3.5 27.5 + - - -
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Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.6 10.1 - - + -
52A GLU* 5.4 1.6 - - - -
58A ILE* 3.9 20.2 - - + -
61A GLN* 3.5 29.2 - - - -
63A LEU* 4.4 5.8 - - + -
64A GLY* 3.8 35.2 - - - -
67A LEU* 3.7 17.7 - - + +
165A PHE* 5.1 2.7 - - + -
170A LYS 3.1 11.5 + - - +
171A PHE* 2.8 37.6 + + + +
173A ARG* 1.3 76.5 - - - +
175A CYS* 1.3 58.3 + - - +
177A TRP* 3.1 7.7 + - + +
178A LYS* 2.9 62.4 + - + +
518A GLN* 5.2 0.2 - - - -
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Residues in contact with CYS 175 (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* 4.6 3.8 - - + +
40A ARG* 4.3 22.7 - - - -
43A MET* 4.0 27.9 - - + +
44A GLN 4.4 2.0 - - - -
47A LEU* 4.3 7.0 - - - -
171A PHE* 3.0 47.8 + - - -
172A THR 3.2 8.5 - - - +
174A PHE* 1.3 77.2 - - - +
176A GLN* 1.3 62.1 + - - +
178A LYS* 3.8 6.9 - - - +
179A ASN* 3.0 26.0 + - - +
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Residues in contact with GLN 176 (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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34A LEU* 4.0 20.2 - - + +
35A PRO* 3.3 43.9 + - - +
36A GLU 4.1 0.2 - - - +
37A PRO* 3.6 18.4 - - - +
39A ILE* 3.9 17.7 - - + -
172A THR* 3.0 15.8 + - - +
173A ARG* 2.9 45.9 + - - +
175A CYS* 1.3 77.4 - - - +
177A TRP* 1.3 62.1 + - - +
179A ASN* 3.5 1.0 - - - +
180A VAL* 3.4 14.6 + - - +
537A GLU* 2.9 30.6 + - - +
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Residues in contact with TRP 177 (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* 4.5 15.0 - - + -
34A LEU* 3.7 20.0 - - + +
63A LEU* 4.6 13.5 - - + -
67A LEU* 4.7 4.0 - - + -
173A ARG* 3.1 32.8 + - + -
174A PHE* 3.6 8.5 - - + +
176A GLN* 1.3 75.0 - - - +
178A LYS* 1.3 59.8 + - - +
180A VAL* 2.9 9.7 + - + +
181A GLU* 2.9 22.6 + - - +
517A TRP* 3.8 32.2 - + - -
521A VAL* 3.5 29.2 - - + -
525A VAL* 4.7 2.2 - - + -
526A PHE* 3.5 34.2 - + - -
529A ILE* 3.7 37.7 - - + -
530A ASN* 2.9 23.3 + - - -
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Residues in contact with LYS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A MET* 4.3 10.3 - - + -
47A LEU* 4.4 5.4 - - + -
52A GLU* 3.5 24.5 + - - -
61A GLN* 2.8 24.4 + - - +
174A PHE* 2.9 46.9 + - + +
175A CYS* 3.8 7.4 - - - +
177A TRP* 1.3 73.7 - - - +
179A ASN* 1.3 66.0 + - - +
181A GLU* 2.5 36.9 + - - +
182A LEU* 3.0 44.1 + - + +
514A SER* 4.1 3.6 + - - -
518A GLN* 3.5 2.8 - - - +
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Residues in contact with ASN 179 (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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35A PRO* 3.2 21.7 - - + +
39A ILE* 3.6 23.9 - - + +
43A MET* 3.3 28.8 - - + +
175A CYS 3.0 17.8 + - - +
176A GLN 3.5 6.5 - - - +
178A LYS* 1.3 76.4 - - - +
180A VAL* 1.3 64.4 + - - +
182A LEU* 3.1 5.0 + - - +
183A ASN* 3.0 26.5 + - - +
636A SER* 3.3 30.2 + - - -
638A PRO* 4.3 3.9 - - - +
639A GLU* 3.8 3.4 + - - +
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Residues in contact with VAL 180 (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* 5.0 14.1 - - + -
33A LEU 3.8 14.4 - - - +
34A LEU* 4.0 11.2 - - + -
35A PRO* 3.7 19.3 - - + -
176A GLN 3.4 12.7 + - - +
177A TRP* 2.9 13.9 + - + +
179A ASN* 1.3 78.4 - - - +
181A GLU* 1.3 63.8 + - - +
183A ASN* 3.3 19.8 + - - +
184A ILE* 3.7 12.2 - - + +
517A TRP* 3.7 23.3 - - + -
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Residues in contact with GLU 181 (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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177A TRP 2.9 8.4 + - - +
178A LYS* 2.5 41.8 + - - +
179A ASN 3.2 0.4 - - - -
180A VAL* 1.3 78.5 - - - +
182A LEU* 1.3 65.6 + - + +
183A ASN 3.2 3.6 + - - -
184A ILE* 3.4 22.1 + - - +
512A THR* 5.1 9.3 - - + +
514A SER* 2.6 41.7 + - - -
517A TRP* 3.7 35.2 - - + -
518A GLN* 3.0 14.4 + - - +
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Residues in contact with LEU 182 (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* 4.3 13.0 - - + -
46A TYR* 3.8 33.4 - - + +
47A LEU* 4.7 3.8 - - + -
52A GLU* 5.3 6.7 - - - +
178A LYS* 3.0 33.5 + - + +
179A ASN 3.1 0.9 + - - +
181A GLU* 1.3 85.7 - - + +
183A ASN* 1.3 57.5 + - - +
184A ILE 3.5 1.9 + - - -
185A HIS* 5.8 0.2 - - - -
637A ASP* 4.4 7.4 - - - +
638A PRO* 3.7 25.6 - - + +
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Residues in contact with ASN 183 (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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179A ASN* 3.0 17.0 + - - +
180A VAL* 3.6 9.6 - - - +
181A GLU 3.1 0.4 - - - -
182A LEU* 1.3 79.6 - - - +
184A ILE* 1.3 58.8 + - - +
185A HIS* 3.6 27.2 + - - -
635A ASP 3.6 11.5 + - - -
636A SER* 3.4 28.1 - - - -
637A ASP* 3.2 20.4 + - - +
638A PRO* 4.4 0.9 - - + -
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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