Contacts of the helix formed by residues 82 - 91 (chain E) in PDB entry 4GDK
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 PRO 82 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E ARG 4.0 3.4 - - - +
42E VAL 4.8 2.9 - - - +
43E SER 3.4 11.4 - - - +
44E TYR* 3.9 14.3 - - + +
80E HIS 3.9 5.8 - - - +
81E TYR* 1.3 88.3 - - + +
83E ILE* 1.3 66.8 + - - +
84E GLY 3.2 0.2 - - - -
85E LEU* 3.0 25.6 + - + +
86E LEU* 3.1 10.6 + - - +
260E TYR* 3.5 39.0 - - + -
262E ASP* 4.2 6.5 - - - +
266E HIS* 4.1 24.5 - - + +
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Residues in contact with ILE 83 (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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16E ILE* 4.0 10.8 - - + -
39E LEU* 3.9 25.1 - - + -
40E PRO* 3.3 26.2 - - + +
41E ARG 3.4 0.4 + - - -
43E SER 2.9 17.9 + - - +
44E TYR 3.8 9.0 - - - -
45E LEU* 3.7 26.5 - - + +
48E VAL* 3.7 30.3 - - + -
81E TYR 3.5 2.2 + - - +
82E PRO* 1.3 69.9 - - - +
84E GLY* 1.3 63.0 + - - +
86E LEU* 3.4 10.1 + - - +
87E PHE* 3.1 22.5 + - - +
98E TRP* 3.9 18.2 - - + -
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Residues in contact with GLY 84 (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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16E ILE* 3.8 9.2 - - - -
41E ARG* 2.8 45.2 + - - -
83E ILE* 1.3 73.5 - - - +
85E LEU* 1.3 56.6 + - - +
87E PHE* 3.4 0.7 + - - +
88E ASP* 3.0 34.5 + - - -
260E TYR* 3.7 9.2 - - - -
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Residues in contact with LEU 85 (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 TYR* 3.9 25.4 - - + -
82E PRO* 3.0 16.8 + - + +
84E GLY* 1.3 74.1 - - - +
86E LEU* 1.3 64.4 + - - +
88E ASP* 3.4 3.8 + - - +
89E LEU* 3.0 31.5 + - + +
190E TYR* 3.4 60.6 - - + +
260E TYR* 3.3 16.9 + - + +
266E HIS* 3.7 22.7 - - + +
268E SER* 3.6 20.4 - - - +
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Residues in contact with LEU 86 (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 LEU* 4.1 24.5 - - + -
77E LEU* 4.3 8.7 - - + -
78E LYS* 3.4 32.3 - - + +
81E TYR* 3.6 37.0 - - + +
82E PRO 3.1 9.4 + - - +
83E ILE* 3.7 12.8 - - - +
85E LEU* 1.3 80.2 - - - +
87E PHE* 1.3 58.2 + - - +
89E LEU* 3.9 6.2 - - + -
90E LEU* 3.0 50.1 + - + +
98E TRP* 3.8 13.9 - - + -
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Residues in contact with PHE 87 (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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16E ILE* 3.5 37.0 - - + -
41E ARG* 4.1 2.9 - - - -
83E ILE 3.1 9.0 + - - +
84E GLY 3.9 0.7 - - - +
85E LEU 3.2 0.2 - - - -
86E LEU* 1.3 74.7 - - - +
88E ASP* 1.3 71.9 + - - +
91E ALA* 2.8 57.3 + - + +
92E SER* 3.0 22.6 + - - -
94E SER 5.2 2.2 - - - -
95E ALA 6.0 0.7 - - - -
96E LEU* 3.6 26.5 - - + -
98E TRP* 3.6 48.2 - + + -
28F GLN* 3.8 23.3 - - - -
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Residues in contact with ASP 88 (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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41E ARG* 3.2 27.9 + - - -
84E GLY 3.0 19.7 + - - +
85E LEU* 3.9 2.4 - - - +
87E PHE* 1.3 79.4 - - - +
89E LEU* 1.3 61.0 + - - +
92E SER* 2.8 25.2 + - - -
239E MET* 3.4 18.3 - - + +
240E ILE* 4.9 0.3 - - - -
241E HIS* 3.6 9.0 + - - -
242E GLY* 2.8 30.5 + - - -
260E TYR* 4.4 1.4 + - - -
268E SER* 3.8 16.5 + - - +
270E ILE* 3.6 14.6 - - - +
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Residues in contact with LEU 89 (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 TYR* 5.8 4.9 - - + -
85E LEU* 3.0 21.5 + - + +
86E LEU* 3.9 7.4 - - + +
88E ASP* 1.3 80.4 - - - +
90E LEU* 1.3 67.2 + - + +
190E TYR* 3.9 50.9 - - + +
191E GLN* 4.3 6.7 - - - +
192E THR* 3.7 32.5 - - + +
268E SER* 4.1 14.6 - - - +
270E ILE* 4.0 17.7 - - + +
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Residues in contact with LEU 90 (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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72E TYR* 3.3 29.5 + - + -
75E THR* 4.2 26.2 - - + +
76E PRO 5.7 0.2 - - - +
77E LEU* 3.7 29.6 - - + -
86E LEU* 3.0 28.9 + - + +
89E LEU* 1.3 95.2 - - + +
91E ALA* 1.3 60.3 + - + +
92E SER 3.9 0.9 - - - -
93E SER* 4.4 8.1 + - - -
94E SER* 5.1 0.2 + - - -
98E TRP* 5.2 1.3 - - + -
192E THR* 4.3 15.7 - - + -
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Residues in contact with ALA 91 (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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72E TYR* 3.4 27.4 - - + +
87E PHE* 2.8 25.6 + - + +
90E LEU* 1.3 74.8 - - - +
92E SER* 1.3 59.3 + - - +
93E SER* 3.0 6.7 - - - +
94E SER* 2.9 28.8 + - - +
98E TRP* 3.5 28.7 - - + +
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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