Contacts of the helix formed by residues 68 - 78 (chain A) in PDB entry 3CP5
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 GLY 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLU* 3.3 22.6 + - - +
67A ARG* 1.3 77.0 - - - +
69A PRO* 1.3 75.3 - - - +
70A VAL 3.3 2.7 - - - -
71A TYR* 3.4 5.0 + - - +
72A ILE* 3.1 21.9 + - - +
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Residues in contact with PRO 69 (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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11A GLU* 3.4 8.7 - - - +
23A VAL* 3.7 24.7 - - + -
25A LEU* 5.0 10.3 - - + -
67A ARG 4.6 0.7 - - - +
68A GLY* 1.3 81.5 - - - +
70A VAL* 1.3 61.1 + - + +
72A ILE* 3.3 3.2 + - + +
73A MET* 2.9 35.6 + - - +
114A LEU* 3.8 31.8 - - + +
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Residues in contact with VAL 70 (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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11A GLU* 2.9 22.6 + - + +
15A ALA* 3.8 24.0 - - + +
20A VAL* 3.5 28.7 - - + +
21A LYS 3.8 20.4 - - - +
22A GLN* 4.1 9.6 - - - -
23A VAL* 4.3 11.2 - - + +
69A PRO* 1.3 75.3 - - + +
71A TYR* 1.3 66.6 + - - +
73A MET* 3.4 6.0 + - - +
74A ASN* 3.0 30.1 + - - +
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Residues in contact with TYR 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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10A PRO* 4.9 3.6 - - + +
11A GLU* 3.0 19.1 + - - +
14A ALA* 3.6 13.3 - - + +
67A ARG* 3.7 26.2 - - + -
68A GLY 3.6 7.0 - - - +
70A VAL* 1.3 76.1 - - - +
72A ILE* 1.3 67.3 + - + +
74A ASN* 3.9 0.3 - - - -
75A VAL* 3.0 41.5 + - + +
82A MET* 3.4 26.0 - - + +
86A HIS* 3.8 34.3 - + - -
88A VAL* 3.4 18.4 - - + +
89A MET* 3.4 20.9 - - + +
92A LEU* 4.1 0.2 - - - +
202A HEC 2.7 37.0 + - + -
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Residues in contact with ILE 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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63A VAL* 3.8 28.7 - - + +
64A THR* 3.7 28.9 - - + -
67A ARG* 3.9 16.2 - - + +
68A GLY 3.1 18.4 + - - +
69A PRO* 3.8 4.3 - - + +
70A VAL 3.3 0.2 - - - -
71A TYR* 1.3 82.4 - - + +
73A MET* 1.3 61.4 + - - +
75A VAL* 3.5 3.2 + - - +
76A MET* 3.3 40.1 + - + +
114A LEU* 4.0 16.4 - - + -
117A LEU* 4.1 14.6 - - + -
202A HEC 4.3 14.4 - - + +
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Residues in contact with MET 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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20A VAL* 4.1 22.4 - - + -
23A VAL* 4.0 19.1 - - + -
69A PRO 2.9 22.3 + - - +
70A VAL 3.8 3.8 - - - +
72A ILE* 1.3 75.2 - - - +
74A ASN* 1.3 60.1 + - - +
76A MET* 3.3 9.5 + - - +
77A LEU* 3.0 32.4 + - + +
107A GLU* 3.8 26.9 - - + +
110A ALA* 3.6 31.0 - - + +
111A ARG* 3.7 30.1 - - + +
114A LEU* 4.2 15.7 - - + -
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Residues in contact with ASN 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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14A ALA 3.0 21.4 + - - -
18A GLY 3.3 21.0 - - - +
19A PRO* 3.2 6.8 - - - +
20A VAL* 2.8 51.0 + - - +
70A VAL* 3.0 21.6 + - - +
71A TYR 4.1 0.9 - - - +
73A MET* 1.3 73.1 - - - +
75A VAL* 1.3 61.4 + - - +
77A LEU* 4.3 1.7 - - - +
78A ASN* 2.8 35.7 + - - +
82A MET* 3.5 17.7 - - + +
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Residues in contact with VAL 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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71A TYR* 3.0 50.5 + - + +
72A ILE 3.8 4.9 - - - +
74A ASN* 1.3 76.2 - - - +
76A MET* 1.4 60.9 + - - +
79A PRO* 3.2 25.8 - - - +
82A MET* 3.9 12.8 - - + +
89A MET* 3.8 25.6 - - + -
100A MET* 3.6 21.8 - - + +
202A HEC 3.7 29.4 - - + -
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Residues in contact with MET 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 ILE* 3.3 34.7 + - + +
73A MET* 3.3 13.8 + - - +
75A VAL* 1.4 80.3 - - - +
77A LEU* 1.3 59.7 + - - +
79A PRO* 3.8 3.8 - - - +
100A MET* 4.1 6.1 - - - -
102A ASP* 5.6 0.3 - - - +
103A MET* 3.7 20.1 + - - +
105A LEU* 3.7 17.2 - - + +
110A ALA* 3.4 38.4 - - + +
113A ILE* 3.7 39.0 - - + -
114A LEU* 4.1 5.6 - - - +
117A LEU* 4.8 0.4 - - + -
202A HEC 3.6 31.9 - - + -
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Residues in contact with LEU 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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19A PRO* 4.1 20.6 - - + +
20A VAL* 3.7 28.9 - - + -
73A MET* 3.0 22.1 + - + +
74A ASN 4.5 0.2 - - - +
76A MET* 1.3 77.0 - - - +
78A ASN* 1.3 59.4 + - - +
79A PRO* 3.6 4.0 - - - +
102A ASP* 4.7 10.4 - - - +
105A LEU* 3.4 32.7 - - + +
106A SER 3.6 20.6 - - - +
107A GLU* 3.9 13.2 - - + +
110A ALA* 3.9 18.4 - - + -
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Residues in contact with ASN 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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17A ILE* 4.0 11.7 + - - +
18A GLY 3.0 22.3 + - - +
19A PRO* 3.5 16.4 - - + +
74A ASN 2.8 16.7 + - - +
77A LEU* 1.3 79.4 - - - +
79A PRO* 1.3 68.2 - - - +
80A ASN* 3.2 2.6 + - - +
81A GLY* 3.2 26.0 + - - -
82A MET* 3.0 13.6 + - + +
85A ARG* 4.7 3.4 - - - +
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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