Contacts of the helix formed by residues 125 - 137 (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 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A PHE* 1.3 80.5 - - - +
126A LYS* 1.3 63.8 + - - +
127A SER* 3.5 9.1 + - - -
128A ALA* 3.0 26.3 + - - +
129A ILE* 3.4 16.1 + - - +
152A GLU* 2.4 30.4 + - - -
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Residues in contact with LYS 126 (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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124A PHE 4.1 0.2 + - - -
125A SER* 1.3 72.9 - - - +
127A SER* 1.3 60.6 + - - +
129A ILE* 3.9 11.2 + - + +
130A GLU* 3.3 43.7 + - - +
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Residues in contact with SER 127 (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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125A SER* 3.1 10.0 + - - -
126A LYS* 1.3 79.0 - - - +
128A ALA* 1.3 66.6 + - - +
130A GLU* 3.2 12.1 + - - +
131A HIS* 3.1 21.8 + - - +
152A GLU* 5.0 0.5 + - - -
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Residues in contact with ALA 128 (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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125A SER* 3.0 33.0 + - - +
127A SER* 1.3 80.7 + - - +
129A ILE* 1.3 62.4 + - - +
131A HIS* 3.2 15.0 + - - +
132A VAL* 3.6 5.5 + - - +
148A PRO* 5.3 9.1 - - + +
149A TYR* 3.3 38.3 - - + -
152A GLU* 3.7 14.8 - - + +
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Residues in contact with ILE 129 (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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109A PHE* 4.4 3.6 - - + -
113A ILE* 4.3 15.7 - - + -
114A MET* 5.7 1.1 - - + -
117A LEU* 3.5 35.2 - - + -
122A HIS* 4.0 12.1 - - + +
124A PHE 4.2 5.2 - - - +
125A SER 3.4 20.2 + - - +
126A LYS* 4.1 11.0 - - + +
127A SER 3.3 0.4 - - - -
128A ALA* 1.3 76.3 - - + +
130A GLU* 1.3 60.2 + - + +
132A VAL* 3.8 2.8 + - - +
133A GLN* 3.2 37.4 + - - +
149A TYR* 3.0 22.4 - - - +
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Residues in contact with GLU 130 (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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126A LYS* 3.3 37.1 + - - +
127A SER* 3.2 12.2 + - - +
128A ALA 3.2 0.8 - - - -
129A ILE* 1.3 79.0 - - + +
131A HIS* 1.3 65.6 + - - +
132A VAL 3.2 2.0 - - - -
133A GLN* 4.0 9.6 - - + +
134A GLY* 3.1 18.7 + - - -
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Residues in contact with HIS 131 (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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127A SER 3.1 11.9 + - - +
128A ALA* 3.2 11.3 + - - +
130A GLU* 1.3 77.9 - - - +
132A VAL* 1.3 67.4 + - + +
134A GLY* 4.0 0.3 - - - -
135A HIS* 3.5 51.6 + + - -
144A ASP 4.9 2.9 - - - -
145A LEU* 3.6 27.0 + - + +
148A PRO* 3.6 33.9 - - + +
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Residues in contact with VAL 132 (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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109A PHE* 3.5 12.1 - - + -
113A ILE* 4.1 7.6 - - + -
128A ALA 3.6 2.1 + - - +
129A ILE 4.1 5.6 - - - +
130A GLU 3.2 0.2 - - - -
131A HIS* 1.3 79.2 - - - +
133A GLN* 1.3 67.1 + - - +
134A GLY 2.9 2.7 + - - -
135A HIS* 2.9 4.7 + - - +
136A LEU* 2.9 51.3 + - + +
145A LEU* 3.8 24.6 - - + +
146A PHE* 4.3 18.8 - - + -
149A TYR* 3.4 37.7 - - + -
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Residues in contact with GLN 133 (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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109A PHE* 3.9 28.8 - - + -
129A ILE* 3.2 25.5 + - - +
130A GLU* 4.4 9.0 - - + +
132A VAL* 1.3 79.4 - - - +
134A GLY* 1.3 55.3 + - - +
136A LEU* 4.0 5.2 - - - -
137A VAL* 3.2 44.1 + - + +
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Residues in contact with GLY 134 (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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130A GLU 3.1 17.1 + - - -
131A HIS 4.0 1.1 - - - -
132A VAL 2.9 1.8 + - - -
133A GLN* 1.3 76.2 - - - +
135A HIS* 1.3 65.2 + - - +
137A VAL* 4.7 2.3 - - - +
138A LYS* 3.4 31.5 + - - +
140A GLN* 4.1 0.2 + - - -
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Residues in contact with HIS 135 (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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131A HIS* 3.5 38.9 + + - -
132A VAL 2.9 6.2 + - - +
134A GLY* 1.3 78.3 - - - +
136A LEU* 1.3 62.0 + - - +
138A LYS 3.0 15.4 + - - -
139A LYS 3.1 9.5 + - - -
140A GLN* 3.1 53.0 + - + +
142A PRO* 4.7 16.8 - - + -
145A LEU* 4.0 17.5 - - + -
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Residues in contact with LEU 136 (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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102A LEU* 4.9 1.3 - - + +
105A SER* 3.1 36.6 - - - +
106A ARG* 4.3 16.5 + - + +
109A PHE* 3.3 33.9 - - + -
132A VAL* 2.9 40.9 + - + +
133A GLN* 4.1 4.5 - - - +
135A HIS* 1.3 78.8 - - - +
137A VAL* 1.3 61.4 + - + +
139A LYS* 3.2 19.8 + - - +
140A GLN 4.6 2.2 - - - -
141A VAL* 4.4 8.5 - - + -
145A LEU* 4.4 6.5 - - + -
146A PHE* 5.4 0.2 - - + -
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Residues in contact with VAL 137 (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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133A GLN* 3.2 34.8 + - + +
134A GLY* 4.7 3.1 - - - +
135A HIS 3.4 0.2 - - - -
136A LEU* 1.3 78.7 - - + +
138A LYS* 1.3 64.3 + - + +
139A LYS* 3.4 4.1 + - - +
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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