Contacts of the helix formed by residues 10 - 18 (chain A) in PDB entry 2CWE
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 ASP 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ILE* 3.6 1.5 - - + +
9A THR* 1.3 77.5 + - - +
11A PRO* 1.3 67.2 - - - +
12A GLU* 2.9 29.0 + - - +
13A VAL* 2.7 52.8 - - + +
14A ILE* 3.0 8.0 - - - +
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Residues in contact with PRO 11 (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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9A THR 3.1 10.9 - - - +
10A ASP* 1.3 90.5 - - - +
12A GLU* 1.3 64.9 + - + +
14A ILE* 3.2 3.9 + - + +
15A LYS* 2.8 38.9 + - - +
92A LEU* 5.1 7.4 - - + +
94A ASP* 3.9 36.6 - - + +
97A LEU* 4.0 16.2 - - + -
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Residues in contact with GLU 12 (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 ASP* 2.9 13.5 + - - +
11A PRO* 1.3 83.7 - - + +
13A VAL* 1.3 62.8 + - + +
15A LYS* 2.7 39.9 + - - +
16A VAL* 3.1 26.3 + - + +
94A ASP* 4.5 1.6 - - - +
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Residues in contact with VAL 13 (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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8A ILE* 3.0 26.5 - - + -
10A ASP* 2.7 49.8 + - + +
12A GLU* 1.3 74.5 - - + +
14A ILE* 1.3 61.4 + - - +
16A VAL* 2.8 30.2 + - - +
17A MET* 2.9 17.0 + - - +
59A GLU 5.4 0.4 - - - +
60A ALA* 3.8 35.7 - - + +
62A LEU* 4.5 3.5 - - + +
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Residues in contact with ILE 14 (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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8A ILE* 3.3 35.9 - - + +
9A THR* 4.1 6.3 - - - -
10A ASP 3.0 19.7 + - - +
11A PRO* 3.4 7.9 - - + +
13A VAL* 1.3 81.5 - - - +
15A LYS* 1.3 63.4 + - - +
17A MET* 2.9 22.4 + - - +
18A LEU* 3.0 30.0 + - + +
88A ILE* 3.8 22.7 - - + -
89A ASN 3.7 28.3 - - - +
90A LEU* 4.9 2.7 - - + -
97A LEU* 4.0 24.2 - - + -
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Residues in contact with LYS 15 (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 PRO* 2.8 25.4 + - - +
12A GLU* 2.7 40.9 + - - +
14A ILE* 1.3 76.3 - - - +
16A VAL* 1.3 62.1 + - + +
18A LEU* 3.7 16.2 + - - +
19A GLU* 3.9 7.6 + - - +
22A ARG* 5.3 0.3 + - - -
94A ASP* 3.4 32.9 + - - -
96A GLU* 3.8 28.5 + - - +
97A LEU* 3.8 16.2 - - + -
100A ILE* 4.3 12.6 - - + -
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Residues in contact with VAL 16 (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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12A GLU* 3.1 17.7 - - + +
13A VAL* 2.8 15.2 + - - +
15A LYS* 1.3 77.7 - - + +
17A MET* 1.3 58.7 + - - -
19A GLU* 3.3 9.4 + - - +
22A ARG* 3.2 30.8 - - - +
56A LYS* 3.6 45.8 - - + +
57A LEU* 4.2 4.9 - - + +
60A ALA* 4.1 10.8 - - + -
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Residues in contact with MET 17 (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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8A ILE* 4.1 12.1 - - - -
13A VAL 2.9 13.0 + - - +
14A ILE* 3.3 14.1 - - - +
16A VAL* 1.3 75.6 - - - +
18A LEU* 1.3 69.8 + - + +
19A GLU 3.2 7.6 + - - +
22A ARG* 4.3 1.7 - - - -
23A ARG* 3.7 21.7 + - - +
26A LEU* 4.6 12.2 - - + +
62A LEU* 3.0 41.7 - - + -
86A PHE* 3.8 30.7 - - + +
88A ILE* 3.6 32.8 - - + -
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Residues in contact with LEU 18 (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 ILE* 3.0 35.2 + - + +
15A LYS* 4.0 6.3 - - - +
16A VAL 3.3 0.8 - - - -
17A MET* 1.3 79.3 - - + +
19A GLU* 1.3 65.8 + - - +
20A ASP* 3.0 5.5 + - - -
23A ARG* 3.8 31.1 + - - +
88A ILE* 5.0 12.6 - - + -
90A LEU* 4.9 2.7 - - + -
97A LEU* 4.6 3.8 - - + -
100A ILE* 3.9 37.2 - - + -
104A ARG* 4.6 18.8 - - - +
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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