Contacts of the helix formed by residues 115 - 124 (chain E) in PDB entry 4NAW
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 GLU 115 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77E ARG 3.6 11.7 - - - +
78E THR* 3.8 36.6 - - - +
79E ARG 3.5 4.7 - - - -
80E THR* 4.3 4.9 - - + +
113E ASP 3.6 6.5 + - - +
114E GLN* 1.3 78.4 + - - +
116E VAL* 1.3 65.5 + - - +
117E GLY 3.2 1.5 + - - +
118E THR* 3.4 24.8 + - - +
119E LEU* 3.5 14.9 + - - +
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Residues in contact with VAL 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E ILE* 4.9 3.8 - - + +
57E ILE* 4.1 21.5 - - + -
75E VAL* 3.7 16.6 - - + -
76E GLU 3.4 22.4 - - - +
77E ARG* 3.6 2.0 - - - +
79E ARG* 3.0 26.7 + - + +
80E THR 4.5 7.4 - - - +
81E ILE* 4.3 20.9 - - + -
84E LEU* 4.6 9.0 - - + -
115E GLU* 1.3 69.6 - - - +
117E GLY* 1.3 62.2 + - - +
119E LEU* 3.2 11.2 + - + +
120E TYR* 2.9 29.7 + - - +
129E LEU* 3.8 4.5 - - + +
131E LEU* 5.1 1.8 - - + -
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Residues in contact with GLY 117 (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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55E ILE* 4.3 6.7 - - - -
77E ARG* 3.0 44.8 + - - -
115E GLU 3.2 0.2 - - - -
116E VAL* 1.3 78.9 - - - +
118E THR* 1.3 61.6 + - - +
120E TYR* 3.2 5.0 + - - +
121E GLU* 3.1 28.5 + - - +
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Residues in contact with THR 118 (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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114E GLN* 4.0 15.0 - - - +
115E GLU* 3.4 25.4 + - - +
116E VAL 3.3 0.2 - - - -
117E GLY* 1.3 74.6 - - - +
119E LEU* 1.3 62.3 + - + +
121E GLU* 3.4 13.1 + - - +
122E CYS* 3.1 33.8 + - - -
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Residues in contact with LEU 119 (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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81E ILE* 3.7 33.7 - - + -
104E VAL* 4.4 12.1 - - + -
108E PHE* 4.6 2.2 - - + -
110E PRO* 4.0 17.3 - - + -
114E GLN* 3.7 28.9 - - + +
115E GLU 3.5 15.0 + - - +
116E VAL* 3.2 12.2 + - - +
118E THR* 1.3 74.4 - - + +
120E TYR* 1.3 58.0 + - - +
122E CYS* 4.8 0.2 - - - -
123E PHE* 2.7 63.1 + - + +
124E GLY 3.6 0.5 + - - -
129E LEU* 3.9 16.6 - - + +
131E LEU* 5.3 0.2 - - + -
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Residues in contact with TYR 120 (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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55E ILE* 3.5 46.4 - - + -
77E ARG* 4.1 16.4 - - - -
116E VAL 2.9 12.4 + - - +
117E GLY 3.4 9.2 - - - +
119E LEU* 1.3 75.7 - - - +
121E GLU* 1.3 67.8 + - + +
124E GLY* 2.8 33.9 + - - +
125E SER 5.1 0.9 - - - -
127E GLY* 3.6 43.6 + - - -
128E LYS* 3.7 18.6 - - - -
129E LEU* 4.0 7.6 - - + +
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Residues in contact with GLU 121 (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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77E ARG* 3.5 23.4 + - - +
117E GLY 3.1 13.9 + - - +
118E THR* 3.6 15.0 - - - +
119E LEU 3.3 0.2 - - - -
120E TYR* 1.3 85.5 - - + +
122E CYS* 1.3 64.7 + - - +
124E GLY 4.8 1.0 + - - +
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Residues in contact with CYS 122 (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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118E THR* 3.1 27.5 + - - +
121E GLU* 1.3 86.5 - - - +
123E PHE* 1.3 92.3 + - + +
124E GLY 3.7 1.2 - - - +
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Residues in contact with PHE 123 (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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104E VAL* 3.7 28.0 - - + -
105E ASN* 3.7 31.9 + - - +
108E PHE* 3.6 27.4 - + - -
114E GLN* 5.9 0.9 - - - -
119E LEU* 2.7 38.5 + - + +
122E CYS* 1.3 96.8 - - + +
124E GLY* 1.3 63.2 + - - +
125E SER* 5.1 1.4 + - - -
129E LEU* 4.2 7.9 - - + +
130E VAL 5.6 0.3 + - - -
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Residues in contact with GLY 124 (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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119E LEU 3.6 1.4 + - - -
120E TYR* 2.8 31.5 + - - +
121E GLU 5.4 1.0 - - - +
122E CYS 3.7 1.2 - - - +
123E PHE* 1.3 81.6 - - - +
125E SER* 1.3 64.3 + - - -
128E LYS 3.4 13.0 - - - -
129E LEU* 4.4 4.5 - - - -
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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