Contacts of the helix formed by residues 114 - 126 (chain E) in PDB entry 3E4U
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 MET 114 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53E CYS* 3.6 25.4 - - + +
54E SER* 4.1 3.1 - - - -
86E LEU* 3.6 26.0 - - + -
89E PHE* 3.7 28.9 - - + -
90E MET* 3.8 22.4 - - + -
109E ALA* 2.8 13.8 + - + +
112E LEU* 3.5 40.8 - - - +
113E GLN* 1.3 75.5 - - - +
115E GLU* 1.3 64.2 + - - +
116E HIS 3.4 2.5 + - - -
117E VAL* 3.5 8.9 + - + -
118E VAL* 3.4 22.4 + - - +
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Residues in contact with GLU 115 (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 MET* 6.1 0.9 - - - +
113E GLN 3.6 6.4 + - - +
114E MET* 1.3 73.2 - - - +
116E HIS* 1.3 69.9 + - + +
118E VAL* 3.2 18.0 + - - +
119E ASP* 3.0 47.1 + - - +
122E ARG* 6.4 0.2 - - - -
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Residues in contact with HIS 116 (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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65A LEU* 3.3 24.9 + - - -
67A CYS* 2.8 33.9 - - - -
114E MET 3.4 0.4 - - - -
115E GLU* 1.3 85.5 + - + +
117E VAL* 1.3 57.2 + - + +
119E ASP* 3.6 16.8 + - + +
120E THR* 2.6 34.5 + - - -
11F PHE* 4.2 4.9 - - + -
13F ARG* 4.9 13.4 + - - -
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Residues in contact with VAL 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E LEU* 3.9 19.7 - - + -
89E PHE* 3.5 43.7 - - + -
95E LEU* 3.5 22.4 - - + -
105E VAL* 4.4 1.8 - - + -
109E ALA* 4.1 9.0 - - + -
114E MET* 3.5 18.3 + - + +
115E GLU 3.4 0.8 - - - -
116E HIS* 1.3 73.9 - - + +
118E VAL* 1.3 60.2 + - - +
120E THR* 3.3 5.1 + - - -
121E CYS* 2.9 35.9 + - - -
11F PHE* 4.2 9.0 - - + -
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Residues in contact with VAL 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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106E MET* 3.9 18.3 - - + +
109E ALA* 3.5 19.7 - - + +
110E MET* 3.6 31.9 - - + +
114E MET 3.4 16.8 - - - +
115E GLU* 3.2 18.8 + - - +
117E VAL* 1.3 75.5 - - - +
119E ASP* 1.3 64.2 - - - +
121E CYS* 3.0 19.4 + - - +
122E ARG* 3.1 36.9 + - - +
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Residues in contact with ASP 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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67A CYS* 5.8 1.1 - - - -
115E GLU* 3.0 38.4 + - - +
116E HIS* 3.7 18.3 - - + +
118E VAL* 1.3 76.4 - - - +
120E THR* 1.3 61.3 + - - +
122E ARG* 3.7 25.4 + - - +
123E LYS* 3.4 34.0 + - - +
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Residues in contact with THR 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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67A CYS* 4.3 3.1 - - - +
69A LEU* 3.9 28.1 - - + +
95E LEU* 4.7 4.5 - - + -
97E LEU* 4.9 0.6 - - + +
116E HIS 2.6 22.9 + - - -
117E VAL 3.6 4.7 - - - -
118E VAL 3.1 0.8 - - - -
119E ASP* 1.3 75.1 - - - +
121E CYS* 1.3 66.6 + - - +
123E LYS* 3.2 19.8 + - + +
124E PHE* 3.4 12.0 + - - +
9F ILE* 4.2 22.9 - - + -
11F PHE* 3.4 26.2 - - + -
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Residues in contact with CYS 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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95E LEU* 4.6 0.7 - - - -
97E LEU* 4.1 15.5 - - - -
102E ILE* 3.2 28.3 - - + +
105E VAL* 3.3 33.9 - - - -
106E MET* 3.2 39.4 - - + +
117E VAL* 2.9 26.6 + - - -
118E VAL 3.4 7.4 - - - +
120E THR* 1.3 76.3 - - - +
122E ARG* 1.3 61.7 + - - +
123E LYS 3.3 0.2 + - - -
124E PHE 3.4 0.7 + - - -
125E ILE* 3.3 7.6 + - - +
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Residues in contact with ARG 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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106E MET* 3.7 19.5 - - - +
110E MET* 4.8 11.3 - - - +
115E GLU* 6.4 0.4 - - - -
118E VAL* 3.1 30.3 + - - +
119E ASP* 3.7 31.3 + - - +
120E THR 3.3 0.2 - - - -
121E CYS* 1.3 74.8 - - - +
123E LYS* 1.3 63.5 + - + +
125E ILE* 3.5 5.9 + - + +
126E LYS* 3.4 38.3 + - + +
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Residues in contact with LYS 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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66A LYS* 4.1 34.2 - - - +
69A LEU* 5.6 3.4 - - + -
73A ASN* 4.3 25.9 + - + +
119E ASP* 3.4 26.1 + - - +
120E THR* 3.2 12.7 + - + +
122E ARG* 1.3 78.5 - - + +
124E PHE* 1.3 58.7 + - - +
126E LYS* 2.9 29.1 + - - +
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Residues in contact with PHE 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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73A ASN* 4.1 16.4 - - - +
97E LEU* 4.1 14.6 - - + -
102E ILE* 3.2 25.8 - - + -
120E THR 3.4 5.4 + - - +
121E CYS 3.4 0.6 + - - +
123E LYS* 1.3 78.0 - - - +
125E ILE* 1.3 68.8 + - - +
127E ALA* 3.8 13.7 - - - +
9F ILE* 5.4 3.8 - - + -
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Residues in contact with ILE 125 (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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102E ILE* 4.0 15.7 - - + +
103E MET* 2.8 38.8 - - + -
106E MET* 3.4 15.5 - - + -
121E CYS 3.3 11.7 + - - +
122E ARG* 3.6 9.6 - - + +
123E LYS 3.3 0.2 - - - -
124E PHE* 1.3 80.5 - - - +
126E LYS* 1.3 68.8 + - + +
127E ALA* 3.1 10.6 + - - +
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Residues in contact with LYS 126 (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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73A ASN* 5.2 4.9 - - - +
75A ASP* 5.8 6.0 - - - +
122E ARG* 3.4 24.0 - - - +
123E LYS* 2.9 21.2 + - - +
124E PHE 3.3 0.6 - - - -
125E ILE* 1.3 81.1 - - + +
127E ALA* 1.3 57.9 + - - +
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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