Contacts of the helix formed by residues 134 - 140 (chain B) in PDB entry 4OMC
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 VAL 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LEU* 3.4 31.7 + - + +
132B LEU* 3.9 24.2 - - + +
133B ASN* 1.3 73.0 - - - +
135B LYS* 1.3 66.5 + - - +
136B ALA 3.1 2.0 - - - -
137B ALA* 2.9 14.0 + - - +
138B TRP* 3.0 49.3 + - + +
215B VAL* 4.1 23.6 - - + +
377B ILE* 4.4 3.6 - - + -
380B LEU* 4.4 3.6 - - + -
431B ALA* 3.7 13.5 - - + -
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Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B TYR* 4.2 22.9 - - + -
112B GLU* 2.6 40.3 + - + +
118B PHE* 5.5 0.4 - - + -
124B LEU 3.9 3.4 + - - -
125B SER* 3.6 31.1 + - - +
133B ASN* 3.5 0.8 - - - +
134B VAL* 1.3 78.4 - - - +
136B ALA* 1.3 57.1 + - - +
138B TRP* 3.0 20.1 + - + +
139B ALA* 2.8 30.5 + - + +
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ASN* 3.2 38.3 + - - +
134B VAL 3.1 0.4 - - - -
135B LYS* 1.3 78.6 - - - +
137B ALA* 1.3 60.0 + - - +
139B ALA* 3.7 7.6 + - - +
140B GLN* 3.3 30.1 + - - +
432B GLY* 4.1 5.4 - - - -
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ASN 3.8 0.8 + - - -
134B VAL 2.9 10.9 + - - +
136B ALA* 1.3 77.5 - - - +
138B TRP* 1.3 65.8 + - - +
140B GLN* 3.0 21.7 + - - +
141B GLY 3.3 0.3 + - - -
142B TYR* 3.1 19.2 + - - +
380B LEU* 3.8 23.3 - - + -
431B ALA* 4.0 25.6 - - + +
432B GLY* 4.1 0.9 - - - -
435B VAL* 4.4 12.1 - - + -
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Residues in contact with TRP 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B TYR* 3.2 48.9 - + + +
113B PRO* 3.7 11.7 - - + -
118B PHE* 3.6 36.1 - + - -
124B LEU* 4.2 8.7 - - + -
134B VAL* 3.0 34.1 + - + +
135B LYS* 3.5 24.0 - - + +
137B ALA* 1.3 76.7 - - - +
139B ALA* 1.3 54.1 + - - +
141B GLY* 2.7 26.9 + - - -
142B TYR 3.2 21.7 + - - +
143B THR* 4.1 7.3 - - + +
213B VAL* 3.8 10.8 - - + -
214B GLY 3.8 15.9 - - - -
215B VAL* 2.9 22.7 + - - -
217B TYR* 3.5 24.4 - + - +
380B LEU* 4.4 2.9 - - + -
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TYR* 3.9 28.6 - - + +
135B LYS* 2.8 17.5 + - + +
136B ALA* 3.8 10.3 - - - +
138B TRP* 1.3 76.3 - - - +
140B GLN* 1.3 59.3 + - + +
141B GLY* 3.0 3.5 + - - -
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Residues in contact with GLN 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ALA* 3.3 17.9 + - - +
137B ALA 3.0 11.0 + - - +
139B ALA* 1.3 77.2 - - + +
141B GLY* 1.3 58.7 + - - +
142B TYR* 3.6 21.5 - - + -
432B GLY* 3.2 23.7 - - - +
435B VAL* 3.6 19.0 - - - +
436B ALA* 3.8 16.2 - - - +
439B GLN* 3.8 14.9 - - - +
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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