Contacts of the helix formed by residues 78 - 94 (chain E) in PDB entry 4CQM
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 GLU 78 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E ASP* 3.1 35.9 + - - +
77E SER* 1.3 82.3 - - - +
79E ALA* 1.3 65.4 + - - +
80E ARG* 3.4 3.1 - - + +
81E ALA* 4.1 13.6 - - + +
82E ALA* 3.1 24.3 + - - +
129E LYS* 6.0 0.2 - - - +
133E LEU* 3.6 1.9 - - - +
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Residues in contact with ALA 79 (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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77E SER 3.9 0.4 + - - -
78E GLU* 1.3 70.2 - - - +
80E ARG* 1.3 66.3 + - + +
82E ALA* 3.4 2.6 + - - +
83E ARG* 3.0 25.3 + - - +
129E LYS* 5.5 5.0 - - - +
133E LEU* 3.7 27.2 - - + +
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Residues in contact with ARG 80 (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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78E GLU* 3.4 2.8 - - + +
79E ALA* 1.3 79.1 - - + +
81E ALA* 1.3 54.6 + - - +
83E ARG* 3.2 4.7 + - - +
84E CYS* 2.8 40.1 + - + +
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Residues in contact with ALA 81 (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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74E ALA* 3.6 11.4 - - + +
75E ASP* 3.3 36.1 - - + +
78E GLU* 3.5 17.7 + - + +
79E ALA 3.4 0.4 - - - -
80E ARG* 1.3 78.4 - - - +
82E ALA* 1.3 62.1 + - - +
84E CYS* 4.2 4.3 - - - +
85E LEU* 3.2 22.9 + - - +
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Residues in contact with ALA 82 (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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74E ALA* 5.5 0.2 - - - -
75E ASP 4.4 1.1 + - - -
76E VAL* 4.2 11.4 - - - +
78E GLU 3.1 17.5 + - - +
79E ALA 3.8 3.1 - - - +
81E ALA* 1.3 75.7 - - - +
83E ARG* 1.3 64.6 + - - +
85E LEU* 3.4 21.0 - - - +
86E LEU* 3.5 16.5 + - - +
133E LEU* 3.6 37.5 - - + +
134E VAL* 4.4 6.1 - - + +
137E ALA* 4.0 2.5 - - - +
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Residues in contact with ARG 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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79E ALA 3.0 17.7 + - - +
80E ARG* 3.8 4.5 - - - +
82E ALA* 1.3 73.8 - - - +
84E CYS* 1.3 66.1 + - - +
85E LEU 3.2 0.7 + - - -
86E LEU* 3.2 14.4 + - - +
87E GLU* 3.3 46.3 + - - +
137E ALA* 4.4 14.5 - - + +
140E GLN* 4.4 23.8 + - - +
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Residues in contact with CYS 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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80E ARG* 2.8 23.1 + - + +
81E ALA* 4.4 4.3 - - - +
83E ARG* 1.3 73.5 - - - +
85E LEU* 1.3 57.1 + - - +
87E GLU* 3.3 16.8 + - - +
88E GLN* 2.8 53.3 + - - +
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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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15E LEU* 4.3 15.0 - - + -
17E THR* 4.7 7.9 - - + -
41E CYS* 3.6 31.9 - - + -
72E PHE* 3.7 31.2 - - + -
73E GLN 5.2 0.2 - - - +
74E ALA* 4.1 11.0 - - + -
76E VAL* 5.4 1.8 - - + -
81E ALA 3.2 20.4 + - - +
82E ALA* 3.4 9.2 - - - +
83E ARG 3.1 0.2 - - - -
84E CYS* 1.3 77.5 - - - +
86E LEU* 1.3 73.1 + - + +
88E GLN* 3.1 9.9 + - - +
89E VAL* 3.0 40.2 + - + +
134E VAL* 5.1 7.6 - - + -
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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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15E LEU* 3.7 32.3 - - + -
82E ALA 3.5 14.1 - - - +
83E ARG 3.2 9.6 + - - +
85E LEU* 1.3 85.6 - - + +
87E GLU* 1.3 58.6 + - + +
89E VAL* 4.1 3.1 - - + +
90E GLN* 3.0 41.1 + - - +
97E PRO* 4.0 25.1 - - + -
134E VAL* 4.4 9.4 - - - +
137E ALA* 3.7 35.2 - - + +
138E ALA* 4.1 18.8 - - + +
141E ALA* 4.6 3.8 - - + -
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Residues in contact with GLU 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E ARG* 3.3 48.0 + - - +
84E CYS* 3.3 19.6 + - - +
85E LEU 3.1 0.6 - - - -
86E LEU* 1.3 79.6 - - + +
88E GLN* 1.3 58.9 + - - +
89E VAL 3.4 0.4 - - - -
90E GLN* 4.1 11.5 - - - +
91E ALA* 3.1 29.6 + - - +
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Residues in contact with GLN 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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72E PHE* 3.5 31.3 - - + +
73E GLN 4.7 11.6 + - - +
84E CYS* 2.8 42.7 + - - +
85E LEU* 3.1 8.3 + - - +
87E GLU* 1.3 76.7 - - - +
89E VAL* 1.3 59.4 + - - +
91E ALA* 3.5 4.3 + - - +
92E CYS* 3.0 28.9 + - - +
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Residues in contact with VAL 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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13E LEU* 4.4 4.5 - - + -
15E LEU* 4.3 13.0 - - + -
39E ALA* 4.1 8.3 - - + -
72E PHE* 3.7 33.7 - - + -
85E LEU* 3.0 25.4 + - + +
86E LEU* 4.3 5.4 - - - +
88E GLN* 1.3 74.9 - - - +
90E GLN* 1.3 59.9 + - - +
92E CYS 3.0 1.0 + - - -
93E PHE* 2.9 49.5 + - + +
97E PRO* 3.7 28.3 - - + -
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Residues in contact with GLN 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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86E LEU* 3.0 31.1 + - - +
87E GLU* 4.1 13.8 - - - +
89E VAL* 1.3 77.6 - - - +
91E ALA* 1.3 56.2 + - - +
94E SER* 2.7 34.5 + - - -
95E ARG 3.5 21.6 + - - +
96E PRO* 3.8 9.9 - - + +
97E PRO* 4.4 3.4 - - + -
141E ALA* 3.6 26.2 - - - +
145E ASN* 2.9 29.5 + - - -
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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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87E GLU 3.1 20.8 + - - +
88E GLN* 3.9 4.9 - - - +
89E VAL 3.3 0.2 - - - -
90E GLN* 1.3 76.9 - - - +
92E CYS* 1.3 60.5 + - - +
94E SER* 4.3 6.1 + - - +
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Residues in contact with CYS 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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70E ALA* 4.2 9.2 - - - -
72E PHE* 3.8 17.9 - - + -
88E GLN 3.0 18.2 + - - +
89E VAL 3.0 5.6 + - - +
91E ALA* 1.3 80.6 - - - +
93E PHE* 1.3 84.6 + - + +
94E SER* 3.7 1.1 + - - -
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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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13E LEU* 3.8 34.1 - - + -
37E THR* 4.9 4.0 - - - -
38E VAL 5.1 1.1 - - - -
39E ALA* 4.1 9.4 - - + -
68E ASN* 3.2 38.4 - - + -
69E HIS* 5.0 0.4 - - - -
70E ALA* 3.7 25.6 - - + -
72E PHE* 4.0 18.6 - + - -
89E VAL* 2.9 37.8 + - + +
92E CYS* 1.3 93.5 - - + +
94E SER* 1.3 72.4 + - - +
95E ARG* 3.1 17.9 + - + +
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Residues in contact with SER 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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90E GLN 2.7 14.8 + - - -
91E ALA 4.3 5.9 + - - -
92E CYS 3.7 1.5 + - - -
93E PHE* 1.3 79.9 - - - +
95E ARG* 1.3 58.2 + - - +
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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