Contacts of the helix formed by residues 116 - 122 (chain A) in PDB entry 1EVW
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 ALA 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A THR 4.1 7.1 + - - +
95A THR* 4.8 14.0 + - + +
115A SER* 1.3 75.6 - - - +
117A ASP* 1.3 63.8 + - - +
119A ASN* 3.6 8.4 - - - +
120A LYS* 3.2 26.3 + - - +
12F A 6.1 0.5 - - - +
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Residues in contact with ASP 117 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LYS* 4.9 14.3 + - + -
115A SER* 3.2 7.3 + - - +
116A ALA* 1.3 79.9 - - - +
118A ASP* 1.3 70.4 + - - +
120A LYS* 3.2 6.8 + - - +
121A GLY 2.9 19.1 + - - -
124B TRP* 3.2 22.2 - - + +
144B LEU* 4.0 28.4 - - + +
12E A 5.4 6.5 - - - +
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Residues in contact with ASP 118 (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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114A GLU* 3.7 23.5 - - + +
115A SER* 3.2 20.4 + - - +
117A ASP* 1.3 79.2 - - - +
119A ASN* 1.3 64.8 + - - +
121A GLY* 3.2 10.4 + - - -
122A ARG* 3.4 13.0 + - - +
134A HIS* 4.3 9.8 + - + +
124B TRP* 5.1 5.2 + - - +
144B LEU 5.7 0.7 - - - +
148B GLY* 3.4 15.5 - - - -
149B ALA* 2.9 30.8 + - - +
150B THR* 3.9 7.3 + - - -
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Residues in contact with ASN 119 (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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95A THR* 4.1 4.7 + - - +
96A ALA 3.9 0.4 + - - -
97A SER* 2.8 29.5 + - - +
98A HIS 5.1 0.3 - - - +
101A HIS* 5.3 0.2 - - - -
114A GLU* 3.4 3.7 + - - -
115A SER 3.2 15.7 + - - +
116A ALA* 3.6 8.4 - - - +
118A ASP* 1.3 80.9 - - - +
120A LYS* 1.3 64.8 + - - +
122A ARG* 3.3 16.8 + - - +
123A ASN 4.1 1.2 + - - -
603A MG 2.3 29.3 - - - -
12F A 2.8 24.9 + - - +
13O G 2.8 29.4 + - - -
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Residues in contact with LYS 120 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ALA 3.2 11.8 + - - +
117A ASP* 3.2 12.2 + - - +
119A ASN* 1.3 79.9 - - - +
121A GLY* 1.3 57.3 + - - +
123A ASN* 2.8 42.4 + - - +
124A TRP* 3.6 9.2 - - + -
120B LYS* 3.9 32.6 - - + +
124B TRP* 3.8 20.0 - - + -
11E T 4.2 17.2 + - - -
10F T 5.8 0.6 + - - -
11F A 4.9 11.6 + - - -
12F A 4.7 30.7 + - + +
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Residues in contact with GLY 121 (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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117A ASP 2.9 10.7 + - - -
118A ASP 3.2 5.1 + - - -
120A LYS* 1.3 71.3 - - - +
122A ARG* 1.3 62.6 + - - +
123A ASN 2.9 6.8 + - - -
124A TRP* 2.9 16.1 + - - +
125A CYS* 3.5 6.4 + - - +
134A HIS* 4.4 7.2 - - - -
124B TRP* 3.4 41.1 - - - +
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Residues in contact with ARG 122 (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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97A SER* 4.6 3.8 - - - -
98A HIS 4.9 4.3 - - - -
99A LEU* 3.9 26.0 - - - +
101A HIS* 4.0 15.6 + - + +
112A CYS* 4.2 4.0 - - - -
114A GLU* 2.6 43.6 + - - -
118A ASP 3.4 4.7 + - - +
119A ASN 3.3 12.2 + - - +
120A LYS 3.2 0.6 - - - -
121A GLY* 1.3 75.6 - - - +
123A ASN* 1.3 61.9 + - - +
124A TRP 3.0 1.2 + - - -
125A CYS* 3.0 14.8 + - - +
134A HIS* 3.6 34.6 + - + +
136A VAL* 3.2 33.7 + - - +
138A CYS* 3.5 32.1 - - - +
142A GLY* 3.3 12.1 + - - -
150B THR* 3.4 10.9 + - - -
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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