Contacts of the helix formed by residues 82 - 93 (chain E) in PDB entry 7CR3
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 SER 82 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339D LEU* 6.5 0.2 - - - -
548D PHE* 5.7 7.2 - - - -
552D LYS* 4.9 8.5 - - - -
77E MET* 5.0 3.0 + - - +
80E THR* 2.5 31.6 + - - -
81E ASP* 1.3 73.3 - - - +
83E GLU* 1.3 58.5 + - - +
84E GLU 3.6 1.6 - - - -
85E GLU* 3.8 25.8 - - - -
86E ILE* 3.0 31.2 + - - +
147E THR* 3.3 17.0 - - - +
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Residues in contact with GLU 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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153D ARG* 3.6 31.9 + - - +
81E ASP* 3.5 3.5 - - - +
82E SER* 1.3 75.8 - - - +
84E GLU* 1.3 72.2 + - - +
86E ILE* 3.3 2.0 - - - +
87E ARG* 2.5 61.2 + - - +
143E VAL* 3.2 38.7 - - - +
144E GLN* 3.5 10.5 - - - +
147E THR* 3.8 11.7 - - + +
148E ALA 4.2 1.9 + - - -
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Residues in contact with GLU 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556D LYS* 4.4 13.3 + - - +
81E ASP* 3.0 39.8 - - - +
83E GLU* 1.3 81.2 + - - +
85E GLU* 1.3 60.9 + - - +
87E ARG* 3.8 10.7 - - - +
88E GLU* 2.9 47.5 + - + +
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Residues in contact with GLU 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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339D LEU* 4.0 5.6 - - + +
552D LYS* 2.9 52.6 - - - +
555D PHE* 3.3 31.7 - - + -
556D LYS* 3.2 37.7 - - - +
81E ASP 4.9 1.8 - - - +
82E SER* 3.8 28.1 - - - +
83E GLU 3.2 0.8 - - - -
84E GLU* 1.3 84.7 - - - +
86E ILE* 1.3 57.7 + - - +
88E GLU* 3.3 7.9 + - - +
89E ALA* 3.0 22.3 + - - +
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Residues in contact with ILE 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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339D LEU* 3.9 18.1 - - + +
340D ILE* 4.9 10.3 - - + -
343D ALA* 4.5 20.6 - - + -
548D PHE* 5.9 2.5 - - + -
77E MET* 5.8 4.0 - - - -
82E SER* 3.0 23.5 + - - +
83E GLU* 3.3 7.9 - - - +
85E GLU* 1.3 74.0 - - - +
87E ARG* 1.3 63.8 + - - +
89E ALA* 3.4 0.7 + - - +
90E PHE* 2.9 56.5 + - + -
142E PHE* 6.0 4.9 - - + -
143E VAL* 3.5 24.9 - - + -
147E THR* 3.8 19.7 - - + +
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Residues in contact with ARG 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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87D ARG* 3.9 31.0 - - - +
83E GLU* 2.5 63.5 + - - +
84E GLU* 3.8 9.3 - - - +
86E ILE* 1.3 75.0 - - - +
88E GLU* 1.3 60.4 + - + +
90E PHE* 3.4 2.8 + - - +
91E ARG* 2.9 27.8 + - - +
139E TYR* 3.5 36.8 + - + +
140E GLU* 4.5 8.3 - - - -
143E VAL* 3.6 23.1 - - + +
144E GLN* 4.4 14.1 - - - +
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Residues in contact with GLU 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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332D ARG* 5.8 0.3 + - - -
555D PHE* 4.1 10.1 - - + -
556D LYS* 4.7 2.3 + - - -
559D LEU* 4.0 24.9 - - + +
560D ARG* 5.6 1.2 + - - -
84E GLU* 2.9 39.9 + - + +
85E GLU* 3.6 9.8 - - - +
87E ARG* 1.3 75.2 - - + +
89E ALA* 1.3 64.6 + - - +
91E ARG* 3.0 27.2 + - - +
92E VAL* 3.0 27.9 + - - +
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Residues in contact with ALA 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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336D ALA* 3.5 34.2 - - + +
339D LEU* 3.6 31.4 - - + -
340D ILE* 4.5 7.6 - - + +
555D PHE* 3.5 17.8 - - + -
85E GLU 3.0 6.3 + - - -
86E ILE* 3.7 5.8 - - - +
88E GLU* 1.3 76.7 - - - +
90E PHE* 1.3 60.9 + - - +
92E VAL 3.6 4.9 + - - -
93E PHE* 3.6 11.8 - - - -
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Residues in contact with PHE 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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340D ILE* 3.7 36.3 - - + -
86E ILE* 2.9 41.6 + - + +
87E ARG 3.7 0.7 - - - +
89E ALA* 1.3 73.8 - - - +
91E ARG* 1.3 53.8 + - - +
93E PHE* 3.0 9.2 + - + +
94E ASP* 2.6 35.2 + - - +
101E ILE* 4.8 12.6 - - + +
106E LEU* 5.8 8.1 - - + -
110E MET* 6.1 0.9 - - + -
129E ALA* 5.9 1.8 - - + -
137E VAL* 6.1 3.1 - - + -
139E TYR* 3.5 42.6 - + + -
142E PHE* 4.2 20.4 - + - -
143E VAL* 3.6 29.2 - - + -
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Residues in contact with ARG 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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330D GLU* 4.0 18.0 + - - +
332D ARG* 4.1 26.3 - - - +
559D LEU* 5.3 0.4 - - - +
87E ARG 2.9 15.9 + - - +
88E GLU* 3.0 39.2 + - - +
90E PHE* 1.3 76.4 - - - +
92E VAL* 1.3 81.8 + - - +
94E ASP* 2.9 39.2 + - + +
97E GLY* 6.1 2.5 - - - -
139E TYR* 5.1 6.7 - - - +
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Residues in contact with VAL 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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330D GLU* 4.1 29.4 - - + +
332D ARG* 3.6 21.5 - - + -
333D ARG* 3.7 36.3 - - + +
336D ALA* 4.2 7.2 - - + -
555D PHE* 5.0 1.3 - - + -
88E GLU 3.0 18.6 + - - +
89E ALA* 3.9 10.1 - - - +
90E PHE 3.3 0.4 - - - -
91E ARG* 1.3 96.7 - - - +
93E PHE* 1.3 62.8 + - + +
94E ASP 4.7 1.6 - - - -
95E LYS* 4.3 8.7 - - - +
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Residues in contact with PHE 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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333D ARG* 3.1 38.6 - - + -
336D ALA* 3.7 5.8 - - + -
337D ALA* 3.2 42.0 - - + -
340D ILE* 4.7 7.9 - - + -
89E ALA 3.6 12.8 - - - -
90E PHE* 3.0 12.7 + - + +
92E VAL* 1.3 76.6 - - - +
94E ASP* 1.3 58.5 + - - +
95E LYS* 3.2 41.7 + - - +
101E ILE* 3.3 23.6 - - + +
109E VAL* 3.5 23.6 - - + -
113E LEU* 3.7 8.5 - - + -
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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