Contacts of the helix formed by residues 91 - 98 (chain E) in PDB entry 3EXG
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 91 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87E THR* 3.6 28.5 - - + -
88E ALA 4.2 7.0 - - - +
89E TYR 3.1 6.7 + - - +
90E ARG* 1.3 74.2 - - - +
92E HIS* 1.3 69.1 + - + +
93E GLY 3.1 4.2 + - - -
94E PHE* 3.1 6.2 + - - +
95E THR* 2.9 26.2 + - - +
123E SER 5.4 2.0 - - - +
124E MET 5.5 0.4 - - - +
126E MET* 4.8 6.3 - - + -
131E PHE* 4.1 10.5 - - + -
134E GLY* 4.2 9.0 - - - +
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Residues in contact with HIS 92 (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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45E MET* 4.6 8.6 - - - +
46E GLU* 3.2 30.8 + - - +
62E CYS* 4.4 8.5 - - - -
63E HIS 3.3 28.8 + - - -
64E LEU* 4.6 1.1 - - + +
89E TYR 4.8 1.0 + - - -
90E ARG 3.7 1.6 - - - -
91E ALA* 1.3 78.1 - - - +
93E GLY* 1.3 62.9 + - - +
95E THR* 3.5 3.4 + - - -
96E PHE* 3.2 18.5 + - - +
105E ILE* 3.7 20.3 - - + +
109E LEU* 4.0 25.1 - - + +
123E SER* 2.9 34.7 + - - -
126E MET* 3.5 27.6 - - + -
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Residues in contact with GLY 93 (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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42E VAL* 4.1 13.9 - - - -
45E MET* 6.0 0.4 - - - -
46E GLU* 5.8 0.2 - - - -
65E CYS* 3.8 26.5 - - - -
72E CYS* 4.0 15.5 - - - -
90E ARG 4.9 0.4 + - - -
91E ALA 3.1 0.8 - - - -
92E HIS* 1.3 74.1 - - - +
94E PHE* 1.3 67.8 + - - +
96E PHE* 3.0 4.5 + - - +
97E THR* 3.0 25.3 + - - +
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Residues in contact with PHE 94 (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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65E CYS* 6.4 1.6 - - + -
71E CYS* 4.5 1.1 - - + -
72E CYS* 3.4 38.4 - - + -
75E LEU* 3.8 19.7 - - + -
76E GLU* 6.1 0.2 - - - -
85E LEU* 3.8 24.2 - - + -
87E THR* 4.5 12.3 - - + -
90E ARG 4.5 16.4 - - - -
91E ALA* 3.1 6.1 + - - +
93E GLY* 1.3 75.8 - - - +
95E THR* 1.3 63.0 + - - +
96E PHE 2.9 1.4 + - - -
97E THR* 3.0 19.3 + - - -
98E ARG* 3.2 18.7 + - + +
131E PHE* 3.9 20.2 - - + -
164E LEU* 3.3 31.0 - - + -
194E GLU* 3.8 18.2 - - - -
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Residues in contact with THR 95 (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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91E ALA* 2.9 17.0 + - - +
92E HIS 3.6 5.6 - - - -
94E PHE* 1.3 76.1 - - - +
96E PHE* 1.3 58.3 + - - +
98E ARG* 3.9 3.5 + - - +
99E GLY 3.8 2.6 + - - -
100E LEU* 3.2 53.0 + - + +
105E ILE* 3.5 17.5 - - + -
126E MET* 3.3 31.2 - - + +
128E ALA* 5.3 0.9 - - + -
131E PHE* 3.5 27.0 - - + -
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Residues in contact with PHE 96 (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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38E MET* 4.1 25.1 - - + -
41E THR* 3.5 30.7 - - + -
42E VAL* 3.8 22.0 - - + -
45E MET* 4.5 7.6 - - + -
92E HIS 3.2 11.8 + - - +
93E GLY 3.0 8.1 + - - +
95E THR* 1.3 73.6 - - - +
97E THR* 1.3 61.6 + - + +
98E ARG 2.6 16.9 + - - -
99E GLY* 3.0 13.0 + - - -
100E LEU 3.3 24.4 - - - +
101E SER* 5.1 0.9 - - - -
102E VAL* 3.7 29.2 - - + -
105E ILE* 3.7 7.6 - - + +
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Residues in contact with THR 97 (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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38E MET* 4.8 12.8 - - - +
42E VAL* 4.4 2.0 - - + -
72E CYS* 3.8 38.1 + - + +
73E VAL* 4.0 17.5 - - + -
76E GLU* 3.0 38.2 + - - +
93E GLY 3.0 12.6 + - - +
94E PHE* 3.0 20.4 + - - -
96E PHE* 1.3 85.7 - - + +
98E ARG* 1.3 55.2 + - - +
99E GLY 3.6 1.2 + - - -
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Residues in contact with ARG 98 (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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76E GLU* 3.3 32.7 + - - +
79E ILE* 4.0 10.8 - - - +
80E ASN 3.5 14.8 + - - -
81E PRO* 3.3 24.7 + - - +
83E ASP 3.0 23.6 + - - -
84E HIS* 4.1 0.8 - - - +
85E LEU* 4.0 19.7 - - + +
94E PHE* 3.2 21.3 + - + +
95E THR* 4.2 4.9 - - - +
96E PHE 2.6 6.7 + - - -
97E THR* 1.3 77.0 - - - +
99E GLY* 1.3 54.5 + - - -
100E LEU 3.8 2.0 + - - -
128E ALA* 4.4 8.6 - - + +
129E LYS* 4.3 21.5 + - - +
130E ASN* 3.1 20.1 + - - +
131E PHE* 4.2 33.4 - - + -
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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