Contacts of the helix formed by residues 70 - 82 (chain B) in PDB entry 2C8U
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 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A GLU 5.2 0.4 - - - +
97A LYS* 3.7 31.6 - - + +
100A GLY* 4.5 6.0 - - - -
101A GLN* 3.2 28.8 + - - +
104A ASP* 3.7 9.4 - - - +
138A ILE* 4.7 1.2 - - - +
1208A BME 6.3 0.9 - - - -
52B ARG* 3.2 33.2 + - - +
54B PRO 4.4 6.0 + - - -
69B VAL* 1.3 84.7 - - + +
71B SER* 1.3 60.0 + - - +
72B LEU 3.4 2.2 - - - -
73B ALA* 3.0 29.8 + - + +
74B ILE* 3.0 12.7 + - - +
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Residues in contact with SER 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG* 3.5 45.9 + - - +
19B SER* 6.1 0.4 - - - -
20B ILE* 3.6 23.8 - - - +
54B PRO* 4.2 14.8 + - - +
70B GLU* 1.3 71.7 - - - +
72B LEU* 1.3 66.9 + - - +
74B ILE* 3.5 5.8 + - - +
75B ALA* 2.9 28.2 + - - +
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1208A BME 4.2 9.3 - - - -
19B SER* 3.8 30.7 - - - +
70B GLU 3.4 0.6 - - - -
71B SER* 1.3 84.5 + - - +
73B ALA* 1.3 60.5 + - - +
75B ALA* 3.8 9.0 - - + +
76B ARG* 3.0 51.4 + - - +
99B ILE* 4.7 5.8 - - + -
103B GLU* 3.4 39.3 - - + +
158B LEU* 4.9 4.7 - - + -
162B VAL* 3.9 19.7 - - + -
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A TYR* 3.7 13.5 - - + -
96A GLU* 3.6 23.0 - - + +
97A LYS* 3.5 35.2 - - - +
1208A BME 5.0 3.8 - - - -
70B GLU* 3.0 15.5 + - + +
72B LEU* 1.3 75.9 - - - +
74B ILE* 1.3 59.4 + - - +
76B ARG* 3.4 3.7 + - - +
77B TYR* 3.0 29.3 + - - +
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A TYR* 3.9 6.9 - - + -
20B ILE* 4.0 24.9 - - + -
54B PRO 4.7 0.7 - - - +
55B ALA* 4.5 4.3 - - - -
56B VAL* 3.9 35.2 - - + +
68B MET* 3.4 41.3 - - + +
69B VAL* 3.7 16.8 - - - +
70B GLU 3.0 11.7 + - - +
71B SER* 3.5 6.5 - - - +
73B ALA* 1.3 74.7 - - - +
75B ALA* 1.3 62.5 + - - +
77B TYR* 3.3 4.6 + - - +
78B MET* 3.0 38.8 + - + +
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B SER 3.9 27.6 - - - +
20B ILE* 4.3 5.4 - - - +
23B THR* 3.8 5.7 - - - +
71B SER 2.9 21.0 + - - +
72B LEU* 4.0 12.6 - - + +
73B ALA 3.4 0.2 - - - -
74B ILE* 1.3 74.2 - - - +
76B ARG* 1.3 58.0 + - - +
78B MET* 3.4 4.9 + - - -
79B ALA* 2.8 31.0 + - - +
158B LEU* 3.9 18.1 - - + +
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Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ARG* 3.6 8.1 - - - +
92A TYR* 3.5 19.9 - - + +
96A GLU* 3.3 29.1 + - + -
1208A BME 3.5 29.7 + - - -
72B LEU* 3.0 50.2 + - - +
73B ALA 3.7 4.3 - - - +
74B ILE 3.3 0.2 - - - -
75B ALA* 1.3 71.7 - - - +
77B TYR* 1.3 57.6 + - - +
79B ALA* 3.7 2.5 - - - +
80B LYS* 2.8 36.6 + - - +
85B MET* 3.7 7.7 - - + +
96B GLU* 2.7 40.1 + - - -
99B ILE* 3.5 25.3 - - - +
103B GLU* 4.3 0.4 + - - -
158B LEU* 3.5 18.6 - - + -
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Residues in contact with TYR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLU* 3.2 47.3 + - + +
90A GLU* 4.0 9.4 + - + +
92A TYR* 4.2 10.0 - + - -
93A TYR* 3.5 16.6 - - + -
68B MET* 3.5 28.7 - - + -
73B ALA 3.0 14.3 + - - +
74B ILE 3.5 6.5 - - - +
76B ARG* 1.3 76.5 - - - +
78B MET* 1.3 81.3 - - + +
80B LYS* 3.7 2.1 - - - +
81B LYS* 3.0 58.0 + - + +
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Residues in contact with MET 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 4.4 12.8 - - + -
20B ILE* 5.5 3.1 - - + -
23B THR* 3.9 15.0 - - + +
24B LEU* 4.0 28.0 - - + -
56B VAL* 4.9 4.7 - - + -
58B ILE* 3.9 29.2 - - + -
68B MET* 4.1 16.4 - - - -
74B ILE* 3.0 31.3 + - + +
75B ALA* 3.8 4.5 - - - +
77B TYR* 1.3 91.3 - - + +
79B ALA* 1.3 63.3 + - - +
81B LYS* 4.3 11.7 - - - +
82B HIS* 3.1 36.9 + - + +
84B MET* 4.2 1.0 - - - +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B THR* 3.6 13.2 - - + +
75B ALA 2.8 18.8 + - - +
76B ARG 3.7 0.9 - - - +
78B MET* 1.3 74.5 - - - +
80B LYS* 1.3 62.0 + - - +
82B HIS 3.1 8.3 + - - -
83B HIS 3.1 0.2 + - - -
84B MET* 2.8 45.6 + - + +
85B MET* 3.6 24.0 - - + -
158B LEU* 4.0 8.7 - - + -
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Residues in contact with LYS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LYS* 6.0 7.2 - - - +
89A GLU* 4.3 27.1 + - + +
92A TYR* 3.8 28.7 - - + -
76B ARG 2.8 21.9 + - - +
77B TYR* 3.7 4.0 - - - +
79B ALA* 1.3 72.0 - - - +
81B LYS* 1.3 63.2 + - - +
82B HIS 3.2 1.0 + - - -
83B HIS* 3.4 21.2 + - - +
85B MET* 3.4 20.5 - - + +
86B GLY 6.1 0.7 - - - +
92B TYR* 6.4 1.8 - - + -
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLU* 3.7 28.6 + - - +
4B ASP* 5.6 3.8 + - - -
77B TYR* 3.0 47.3 + - + +
78B MET* 3.6 14.6 - - - +
79B ALA 3.3 0.2 - - - -
80B LYS* 1.3 77.3 - - - +
82B HIS* 1.3 80.9 + - + +
83B HIS* 3.8 11.3 + - - -
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Residues in contact with HIS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU* 5.8 1.5 - - + +
27B ALA* 3.7 22.7 + - + +
29B VAL* 3.7 25.1 - - + +
78B MET* 3.1 27.1 + - + -
79B ALA 3.1 6.3 + - - -
81B LYS* 1.3 102.8 + - + +
83B HIS* 1.3 72.9 + - - +
84B MET* 3.3 29.4 + - + +
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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