Contacts of the helix formed by residues 68 - 77 (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 GLN 68 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65E CYS* 2.9 26.3 + - + +
67E GLY* 1.3 82.2 - - - +
69E GLU* 1.3 55.8 + - - +
70E ALA 3.0 6.1 - - - -
71E CYS* 2.8 35.4 + - + +
72E CYS* 3.9 4.5 + - - -
90E ARG* 3.8 19.5 - - - +
194E GLU* 3.7 23.0 - - - +
196E ASN* 3.1 42.0 - - - +
227E GLY 5.2 1.1 - - - -
257E THR* 3.5 25.3 - - + +
258E TYR 4.0 4.5 - - - +
259E ARG* 3.8 13.5 - - + +
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Residues in contact with GLU 69 (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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39E MET* 3.9 32.9 - - + +
42E VAL* 3.4 30.3 - - + -
43E ARG* 2.5 46.1 + - - +
65E CYS* 4.7 1.8 - - - +
66E ASP* 3.2 9.3 - - - +
67E GLY* 2.9 25.9 + - - -
68E GLN* 1.3 71.0 + - - +
70E ALA* 1.3 56.0 + - - +
71E CYS 3.0 1.8 - - - -
72E CYS* 4.3 8.5 - - - -
73E VAL* 3.2 34.1 + - + +
287E PRO* 3.4 7.4 - - + +
288E ILE* 4.8 1.1 - - - -
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Residues in contact with ALA 70 (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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39E MET* 4.2 8.3 - - - -
67E GLY 5.9 0.2 - - - +
68E GLN 2.8 1.0 + - - -
69E GLU* 1.3 77.4 - - - +
71E CYS* 1.3 59.5 + - - +
74E GLY* 3.0 24.6 + - - +
227E GLY 3.1 23.1 - - - +
228E MET 3.7 2.5 - - - -
229E ASP 4.1 0.2 - - - -
230E ILE* 3.6 27.3 - - + +
233E VAL* 3.5 10.2 - - - +
287E PRO* 3.6 22.9 - - + +
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Residues in contact with CYS 71 (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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68E GLN* 2.8 16.8 + - + +
70E ALA* 1.3 79.7 - - - +
72E CYS* 1.3 63.7 + - - +
73E VAL 3.2 0.4 - - - -
75E LEU* 2.8 40.0 + - - +
94E PHE* 4.7 3.4 - - + -
194E GLU* 4.1 20.6 - - - +
227E GLY* 3.6 24.0 - - - -
233E VAL* 4.3 1.3 - - - -
255E LEU* 3.9 31.6 - - + -
257E THR* 4.7 11.4 - - - -
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Residues in contact with CYS 72 (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* 4.7 4.3 - - - -
65E CYS* 5.0 7.2 - - - -
68E GLN 4.5 2.0 - - - -
69E GLU* 4.1 17.3 - - - -
71E CYS* 1.3 80.2 - - - +
73E VAL* 1.3 68.3 + - - +
75E LEU* 4.0 0.3 - - - +
76E GLU* 3.1 24.9 + - - +
93E GLY* 4.0 22.7 - - - -
94E PHE* 3.4 42.8 - - + +
97E THR* 3.8 19.1 + - + +
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Residues in contact with VAL 73 (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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35E TYR* 4.2 18.4 - - + +
38E MET* 3.9 42.8 - - + +
39E MET* 3.7 20.4 - - + +
42E VAL* 4.9 1.3 - - + -
69E GLU* 3.2 20.0 + - + +
72E CYS* 1.3 83.1 - - - +
74E GLY* 1.3 63.2 + - - +
76E GLU* 3.5 3.0 + - - +
77E ALA* 3.2 20.3 + - - +
97E THR* 4.0 15.0 - - + -
230E ILE* 3.9 14.8 - - + -
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Residues in contact with GLY 74 (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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70E ALA 3.0 23.7 + - - -
71E CYS 3.2 0.2 + - - -
73E VAL* 1.3 78.3 - - - +
75E LEU* 1.3 62.1 + - - +
77E ALA* 3.2 13.8 + - - +
78E GLY* 3.3 7.1 + - - -
230E ILE* 3.7 18.0 - - - +
233E VAL* 3.4 16.3 - - - +
234E ARG* 3.6 11.4 - - - -
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Residues in contact with LEU 75 (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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71E CYS 2.8 21.9 + - - +
72E CYS* 4.0 3.1 - - - +
74E GLY* 1.3 68.0 - - - +
76E GLU* 1.3 57.0 + - - +
78E GLY* 2.6 28.9 + - - -
79E ILE* 3.4 11.7 + - - +
85E LEU* 4.5 3.4 - - + -
94E PHE* 3.8 27.6 - - + -
162E LEU* 4.1 17.3 - - + -
164E LEU* 4.0 7.9 - - + -
192E ILE* 3.9 22.7 - - + -
233E VAL* 3.1 28.7 - - + -
237E THR* 3.6 18.6 - - - +
253E MET* 4.2 2.7 - - + -
255E LEU* 3.6 21.8 - - + -
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Residues in contact with GLU 76 (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* 5.1 12.3 - - + -
72E CYS 3.1 16.7 + - - +
73E VAL* 3.8 5.4 - - - +
75E LEU* 1.3 77.2 - - - +
77E ALA* 1.3 61.3 + - - +
79E ILE* 3.3 28.4 - - - +
81E PRO* 4.9 7.6 - - - +
85E LEU* 5.9 1.9 - - - +
94E PHE* 6.1 0.3 - - - -
97E THR* 3.0 36.7 + - - +
98E ARG* 3.3 44.0 + - - +
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Residues in contact with ALA 77 (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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34E LYS* 5.5 4.9 - - - +
35E TYR* 3.4 39.2 + - + +
73E VAL 3.2 10.0 + - - +
74E GLY* 3.2 11.6 + - - +
75E LEU 2.8 0.8 + - - -
76E GLU* 1.3 77.6 - - - +
78E GLY* 1.3 59.7 + - - +
79E ILE 3.4 1.3 + - - -
230E ILE* 5.4 0.7 - - + -
234E ARG* 3.7 11.4 - - + -
238E ARG* 2.8 26.0 + - - -
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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