Contacts of the helix formed by residues 70 - 82 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ARG* 3.0 29.5 + - - +
54A PRO 4.4 6.0 + - - -
69A VAL* 1.3 83.3 - - + +
71A SER* 1.3 67.1 + - - +
72A LEU* 3.4 4.3 + - - +
73A ALA* 3.0 16.1 + - + -
74A ILE* 3.0 16.6 + - - +
97B LYS* 3.5 23.8 - - - +
100B GLY* 3.6 26.0 - - - +
101B GLN* 3.8 15.8 - - + +
104B ASP* 3.0 11.5 - - - +
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Residues in contact with SER 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ARG* 3.5 41.5 + - - +
19A SER* 6.2 0.4 - - - -
20A ILE* 3.6 23.3 - - - +
54A PRO* 4.0 20.7 + - - +
70A GLU* 1.3 74.0 + - - +
72A LEU* 1.3 64.1 + - - +
74A ILE* 3.4 7.3 + - - +
75A ALA* 2.9 27.6 + - - +
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A SER* 4.0 20.4 - - - +
70A GLU* 3.4 2.0 + - - -
71A SER* 1.3 83.1 + - - +
73A ALA* 1.3 60.2 + - - +
75A ALA* 3.8 8.4 - - + +
76A ARG* 3.0 49.6 + - - +
99A ILE* 4.7 4.9 - - + -
103A GLU* 3.6 39.0 - - + +
158A LEU* 4.9 3.8 - - + -
162A VAL* 3.9 26.2 - - + -
1208A BME 4.1 12.3 - - - +
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLU* 3.0 16.3 + - + +
72A LEU* 1.3 74.9 - - - +
74A ILE* 1.3 60.3 + - - +
76A ARG* 3.4 3.7 + - - +
77A TYR* 3.0 28.1 + - - +
92B TYR* 5.7 0.2 - - - -
93B TYR* 3.7 14.4 - - + -
96B GLU* 3.6 23.6 - - + +
97B LYS* 3.5 34.5 - - - +
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Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ILE* 4.1 23.1 - - + -
54A PRO 4.8 0.4 - - - +
55A ALA* 4.5 4.0 - - - -
56A VAL* 3.9 35.4 - - + +
68A MET* 3.3 43.5 - - + +
69A VAL* 3.6 17.5 - - - +
70A GLU 3.0 16.5 + - - +
71A SER* 3.5 6.3 - - - +
73A ALA* 1.3 73.0 - - - +
75A ALA* 1.3 66.1 + - - +
77A TYR* 3.2 4.9 + - - +
78A MET* 3.0 39.1 + - + +
93B TYR* 4.0 7.4 - - + -
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A SER* 3.9 27.6 - - - +
20A ILE* 4.3 5.1 - - - +
23A THR* 3.9 5.7 - - - +
71A SER 2.9 17.4 + - - +
72A LEU* 4.0 13.9 - - + +
73A ALA 3.4 0.2 - - - -
74A ILE* 1.3 77.4 - - - +
76A ARG* 1.3 57.3 + - - +
78A MET* 3.5 4.2 + - - -
79A ALA* 2.9 31.7 + - - +
158A LEU* 3.9 18.3 - - + +
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Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 3.0 48.4 + - - +
73A ALA 3.8 4.7 - - - +
74A ILE 3.3 0.2 - - - -
75A ALA* 1.3 72.4 - - - +
77A TYR* 1.3 56.9 + - - +
79A ALA* 3.7 2.0 - - - -
80A LYS* 2.7 36.9 + - - +
85A MET* 3.7 7.5 - - + +
96A GLU* 2.6 40.8 + - - -
99A ILE* 3.5 13.1 - - - +
158A LEU* 3.5 19.7 - - + -
1208A BME 2.8 44.2 + - - +
76B ARG* 3.6 7.6 - - - +
92B TYR* 3.5 19.4 - - + +
96B GLU* 3.4 30.2 + - + -
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Residues in contact with TYR 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ILE* 5.6 1.8 - - + -
66A LYS* 4.6 14.8 - - - -
68A MET* 3.5 29.8 - - + -
73A ALA 3.0 13.9 + - - +
74A ILE 3.4 7.6 - - - +
76A ARG* 1.3 76.9 - - - +
78A MET* 1.3 74.2 + - + +
80A LYS* 3.3 2.0 + - + +
81A LYS* 2.9 64.0 + - + +
89B GLU* 3.3 43.9 - - + +
90B GLU* 4.1 9.8 - - + +
92B TYR* 4.1 10.2 - + - -
93B TYR* 3.6 17.3 - - + -
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Residues in contact with MET 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 4.6 9.9 - - + -
20A ILE* 5.5 3.4 - - + -
23A THR* 3.8 19.1 - - + +
24A LEU* 4.0 30.3 - - + -
56A VAL* 4.8 5.4 - - + -
58A ILE* 4.0 27.6 - - + -
68A MET* 4.2 7.6 - - - -
74A ILE* 3.0 28.7 + - + +
75A ALA* 3.9 1.8 - - - +
77A TYR* 1.3 97.9 - - + +
79A ALA* 1.3 62.9 + - - +
81A LYS* 3.5 11.6 + - - -
82A HIS* 3.2 37.3 + - + +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A THR* 3.6 13.8 - - + +
75A ALA 2.9 20.1 + - - +
76A ARG 3.7 3.1 - - - +
78A MET* 1.3 77.2 - - - +
80A LYS* 1.3 60.2 + - - +
82A HIS 3.2 2.4 + - - -
83A HIS 3.1 4.9 + - - -
84A MET* 2.7 47.0 + - + +
85A MET* 3.8 20.0 - - + -
158A LEU* 3.9 10.8 - - + -
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Residues in contact with LYS 80 (chain A).
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 2.7 22.0 + - - +
77A TYR 3.6 3.8 - - - +
79A ALA* 1.3 71.6 - - - +
81A LYS* 1.3 62.8 + - - +
82A HIS 3.2 0.9 + - - -
83A HIS* 3.3 15.0 + - - +
84A MET 4.8 0.2 - - - +
85A MET* 3.4 18.5 - - + +
80B LYS* 6.0 6.9 - - - +
85B MET 5.6 0.4 + - - -
86B GLY 5.5 3.6 + - - -
87B GLY 5.8 0.8 - - - -
88B THR 4.2 3.4 + - - -
89B GLU* 3.8 47.8 - - + +
92B TYR* 3.5 41.0 - - + +
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Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A TYR* 2.9 62.1 + - + +
78A MET* 3.8 15.0 - - - +
79A ALA 3.3 0.4 - - - -
80A LYS* 1.3 77.2 - - - +
82A HIS* 1.3 77.8 + - + +
83A HIS* 3.9 12.6 + - - -
89B GLU* 3.2 35.4 - - + +
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Residues in contact with HIS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 5.9 1.3 - - + +
27A ALA* 3.7 21.9 + - + +
29A VAL* 3.8 25.3 - - + +
78A MET* 3.2 28.3 + - + +
79A ALA 3.2 2.6 + - - -
80A LYS 3.1 0.8 - - - -
81A LYS* 1.3 101.5 + - + +
83A HIS* 1.3 75.0 + - - +
84A MET* 3.3 31.5 + - + +
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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