Contacts of the helix formed by residues 116 - 122 (chain A) in PDB entry 4E70
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 ARG 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.0 54.6 + - + +
34A GLU* 5.7 0.2 - - - +
36A ASP* 3.3 14.5 + - - +
39A ASP* 5.5 1.2 + - - -
106A LEU 4.4 0.2 + - - -
107A LEU* 3.4 28.4 + - + +
109A LYS* 3.4 43.6 - - - +
114A ASN* 2.9 22.4 + - - +
115A ALA* 1.3 77.4 - - - +
117A SER* 1.3 64.0 + - - +
119A THR* 3.2 4.0 + - - -
120A PHE* 3.0 51.4 + - + -
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Residues in contact with SER 117 (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 ASN* 4.4 2.4 + - - -
115A ALA 3.4 0.6 - - - -
116A ARG* 1.3 77.8 - - - +
118A LEU* 1.3 58.0 + - - +
120A PHE* 3.3 3.3 + - - +
121A CYS* 2.9 30.5 + - - +
174A LEU* 3.5 36.8 - - - +
177A GLU* 2.6 40.2 + - - +
178A GLY* 4.0 2.9 - - - -
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Residues in contact with LEU 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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115A ALA* 3.5 13.9 + - + +
116A ARG 3.3 0.2 - - - -
117A SER* 1.3 78.2 - - - +
119A THR* 1.3 57.4 + - - +
121A CYS* 3.6 5.6 - - + +
122A SER* 2.8 35.2 + - - -
174A LEU 5.4 0.4 - - - +
175A PHE* 5.0 2.7 - - + -
178A GLY* 3.9 24.3 - - - +
179A MET* 3.7 24.2 - - + -
182A ASP* 5.8 2.0 - - + -
268A TRP* 5.0 4.0 - - + -
403A N7I 3.6 47.8 - - + +
1013B GLN* 6.1 0.4 - - - +
1017B TRP* 3.8 27.4 - - + +
1020B PHE* 3.9 11.2 - - + -
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Residues in contact with THR 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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29A LEU* 4.3 11.6 - - + +
30A GLN* 4.8 9.2 - - - +
33A LEU* 3.5 24.7 - - + +
107A LEU* 5.7 1.4 - - - +
115A ALA* 2.8 22.5 + - - +
116A ARG 3.4 8.1 - - - -
118A LEU* 1.3 76.9 - - - +
120A PHE* 1.3 63.4 + - + +
122A SER* 3.1 1.9 + - - -
123A VAL* 3.1 30.2 + - + +
1016B VAL* 4.6 3.6 - - - +
1020B PHE* 3.1 42.6 - - + -
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Residues in contact with PHE 120 (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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30A GLN* 3.7 22.5 - - + +
33A LEU* 3.5 36.3 - - + -
34A GLU* 4.0 23.3 - - + -
116A ARG* 3.0 57.7 + - + +
117A SER* 3.8 7.0 - - - +
119A THR* 1.3 77.2 - - + +
121A CYS* 1.3 63.4 + - - +
123A VAL* 3.7 5.7 + - - +
124A HIS* 3.3 24.3 + - - +
174A LEU* 3.9 25.0 - - + +
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Residues in contact with CYS 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 SER 2.9 17.5 + - - +
118A LEU* 3.6 8.1 - - + +
120A PHE* 1.3 77.8 - - - +
122A SER* 1.3 62.3 + - - +
124A HIS* 3.2 19.9 + - - +
127A LEU* 3.4 12.0 - - - +
171A PHE* 3.7 25.6 - - - -
174A LEU* 3.9 19.7 - - + +
175A PHE* 3.9 26.0 - - - -
403A N7I 3.6 24.0 - - - -
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Residues in contact with SER 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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118A LEU 2.8 20.6 + - - -
119A THR 3.1 1.1 + - - -
121A CYS* 1.3 77.3 - - - +
123A VAL* 1.3 59.3 + - - +
124A HIS 3.3 0.6 + - - -
127A LEU* 3.8 14.5 - - - +
403A N7I 2.7 33.2 + - - -
1020B PHE* 3.2 25.7 - - - -
1021B LEU* 3.9 8.7 - - - -
1023B TYR* 2.7 29.8 + - - -
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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