Contacts of the helix formed by residues 47 - 54 (chain A) in PDB entry 2CH0
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 ILE 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A PRO* 1.4 70.3 - - - +
48A PRO* 1.4 60.8 - - + +
49A HIS 3.3 1.7 + - - -
50A VAL 3.4 3.6 + - - -
51A ARG* 2.8 65.5 + - + +
83A THR* 4.8 2.5 - - + -
94A LEU* 3.2 50.0 + - + +
95A VAL 4.2 9.6 - - - -
96A TRP* 3.6 35.0 - - + -
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Residues in contact with PRO 48 (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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46A PRO* 4.1 10.5 - - + -
47A ILE* 1.4 92.4 - - + +
49A HIS* 1.4 57.0 + - - -
50A VAL 3.3 0.2 - - - -
51A ARG* 3.6 15.7 - - + +
52A ASP* 2.5 45.7 + - + +
64A LYS* 3.6 29.8 - - + +
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Residues in contact with HIS 49 (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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27A VAL* 4.2 6.5 - - + -
31A HIS* 3.3 38.1 - + - -
42A GLN* 4.3 12.8 + - - +
45A MET* 3.3 47.6 - - + +
46A PRO* 3.2 30.5 + - + +
48A PRO* 1.4 70.2 - - - +
50A VAL* 1.4 59.3 + - - +
52A ASP* 3.5 10.4 - - - +
53A SER* 2.5 49.4 + - - -
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Residues in contact with VAL 50 (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 ILE* 3.2 52.3 - - + +
27A VAL* 4.8 2.0 - - + -
28A LEU* 4.2 17.7 - - + -
45A MET* 3.7 23.1 - - + -
47A ILE 3.4 0.8 + - - +
49A HIS* 1.4 92.6 - - + +
51A ARG* 1.4 60.6 + - - +
53A SER* 3.3 16.0 + - - -
54A LEU* 3.9 0.2 - - - +
67A TRP* 4.3 1.1 - - + -
81A VAL* 5.5 0.2 - - + -
96A TRP* 3.6 39.9 - - + -
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Residues in contact with ARG 51 (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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47A ILE* 2.8 49.8 + - + +
48A PRO* 3.5 11.0 - - + -
50A VAL* 1.4 70.6 - - - +
52A ASP* 1.4 54.3 + - - +
54A LEU* 2.9 30.7 - - - +
64A LYS* 3.3 49.0 + - + +
65A LYS* 5.1 4.4 - - - +
67A TRP* 3.4 30.5 - - + +
68A ASP* 3.3 26.4 + - - +
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Residues in contact with ASP 52 (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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46A PRO* 5.8 0.7 - - - +
48A PRO* 2.5 44.7 + - + +
49A HIS* 3.5 9.8 - - - +
51A ARG* 1.4 67.6 - - - +
53A SER* 1.4 60.2 + - - +
54A LEU* 3.1 8.3 + - - +
55A ILE 2.6 30.3 + - - +
56A GLN* 4.8 1.4 - - - -
60A ARG* 4.2 24.5 - - + -
61A LYS* 5.9 0.4 - - - +
64A LYS* 5.8 0.9 - - - -
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Residues in contact with SER 53 (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 LYS* 5.2 3.1 - - - +
24A ILE* 4.6 3.8 - - - -
27A VAL* 3.8 29.0 - - - +
31A HIS* 5.5 0.2 + - - -
49A HIS* 2.5 40.4 + - - -
50A VAL* 3.3 13.8 + - - -
52A ASP* 1.4 74.0 + - - +
54A LEU* 1.4 61.4 + - - +
55A ILE 3.2 1.2 + - - -
56A GLN* 3.5 18.0 + - - +
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Residues in contact with LEU 54 (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 MET* 3.5 21.8 - - + +
23A LYS* 4.7 17.8 + - + +
24A ILE* 3.8 21.9 - - + +
50A VAL 3.9 0.8 + - - -
51A ARG* 2.9 40.2 - - - +
52A ASP 3.6 2.0 - - - +
53A SER* 1.4 75.6 - - - +
55A ILE* 1.4 80.5 + - + +
56A GLN* 4.8 0.9 - - - -
60A ARG 2.8 30.7 - - - +
63A MET* 3.7 32.6 - - + +
64A LYS* 3.8 11.2 - - - +
67A TRP* 4.1 6.5 - - + -
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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