Contacts of the helix formed by residues 133 - 140 (chain E) in PDB entry 4OMD
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 ASN 133 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124E LEU 4.1 0.8 + - - -
129E GLN* 5.6 2.4 - - - +
131E ASP* 2.8 20.7 + - - +
132E LEU* 1.3 80.0 - - - +
134E VAL* 1.3 62.0 + - - +
135E LYS 3.5 1.8 - - - +
136E ALA* 3.1 25.1 + - - +
430E ASP* 2.7 33.2 + - - +
432E GLY* 3.1 30.4 + - - -
433E ALA 4.2 0.4 - - - +
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Residues in contact with VAL 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E LEU* 3.3 33.7 + - + +
132E LEU* 3.9 24.9 - - + +
133E ASN* 1.3 74.5 - - - +
135E LYS* 1.3 65.3 + - - +
136E ALA 3.1 2.0 - - - -
137E ALA* 2.9 14.2 + - - +
138E TRP* 3.0 46.3 + - + +
215E VAL* 4.0 23.6 - - + -
377E ILE* 4.4 4.5 - - + -
380E LEU* 4.4 3.8 - - + -
431E ALA* 3.7 13.7 - - + -
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Residues in contact with LYS 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E TYR* 3.8 23.6 - - + -
112E GLU* 2.6 44.0 + - + +
118E PHE* 5.3 0.2 - - + -
124E LEU 3.8 3.2 + - - -
125E SER* 3.5 32.2 + - - +
133E ASN* 3.5 0.6 - - - +
134E VAL* 1.3 78.8 - - - +
136E ALA* 1.3 57.9 + - - +
138E TRP* 3.1 19.2 + - + +
139E ALA* 2.9 30.2 + - + +
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Residues in contact with ALA 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E ASN* 3.1 39.9 + - - +
134E VAL 3.1 0.4 - - - -
135E LYS* 1.3 80.8 - - - +
137E ALA* 1.3 59.4 + - - +
139E ALA* 3.6 7.7 + - - +
140E GLN* 3.3 30.2 + - - +
432E GLY* 4.1 4.7 - - - -
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Residues in contact with ALA 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E ASN 3.9 1.0 + - - -
134E VAL 2.9 10.5 + - - +
136E ALA* 1.3 77.8 - - - +
138E TRP* 1.3 64.7 + - - +
140E GLN* 3.1 13.0 + - - +
141E GLY 3.4 0.2 + - - -
142E TYR* 3.2 19.9 + - - +
380E LEU* 3.8 23.1 - - + -
431E ALA* 4.0 17.0 - - + +
432E GLY* 4.1 0.4 - - - -
435E VAL* 3.9 29.6 - - + -
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Residues in contact with TRP 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E TYR* 2.9 42.1 - - + +
113E PRO* 3.6 22.7 - - + -
118E PHE* 3.8 27.6 - + - -
124E LEU* 4.4 7.4 - - + -
125E SER* 5.6 0.2 - - - -
134E VAL* 3.0 34.5 + - + +
135E LYS* 3.1 25.1 + - + +
137E ALA* 1.3 75.8 - - - +
139E ALA* 1.3 54.4 + - - +
141E GLY* 2.7 26.3 + - - -
142E TYR 3.2 21.0 + - - -
143E THR* 4.0 10.8 - - + +
213E VAL* 3.8 11.9 - - + -
214E GLY 3.9 11.4 - - - -
215E VAL* 3.0 21.3 + - - -
217E TYR* 3.4 26.4 - + - +
380E LEU* 4.3 3.4 - - + -
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Residues in contact with ALA 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E TYR* 4.2 27.7 - - + +
135E LYS* 2.9 17.5 + - + +
136E ALA* 3.6 10.3 - - - +
138E TRP* 1.3 73.5 - - - +
140E GLN* 1.3 57.9 + - + +
141E GLY* 3.0 9.6 + - - -
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Residues in contact with GLN 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E ALA* 3.3 17.9 + - - +
137E ALA 3.1 9.5 + - - +
139E ALA* 1.3 76.6 - - + +
141E GLY* 1.3 58.6 + - - +
142E TYR* 3.5 21.7 - - + -
432E GLY* 3.3 27.7 + - - -
435E VAL* 3.4 16.5 - - - +
436E ALA* 3.8 13.1 - - - +
439E GLN* 3.7 15.7 + - - +
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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