Contacts of the helix formed by residues 16 - 23 (chain E) in PDB entry 1COP
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 GLN 16 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E ALA* 3.7 29.8 - - + +
12E MET* 5.8 2.7 - - + -
15E GLY* 1.3 70.9 - - - -
17E THR* 1.3 65.2 + - - +
18E LYS 3.4 0.2 - - - -
19E THR* 4.0 2.7 - - - -
20E ALA* 3.2 24.8 + - - +
27E GLN* 4.8 16.2 - - + +
30E ILE* 3.7 20.5 - - + +
31E ASN* 4.4 20.1 + - - +
34E ILE* 5.7 2.1 - - - +
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Residues in contact with THR 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E GLY* 3.1 1.9 - - - -
16E GLN* 1.3 81.0 - - - +
18E LYS* 1.3 69.6 + - + +
20E ALA* 4.0 3.9 - - - +
21E LYS* 3.2 41.7 + - + +
27E GLN* 4.2 22.1 + - + +
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Residues in contact with LYS 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E TYR* 4.6 11.0 + - - +
14E PHE* 2.6 39.0 - - + +
15E GLY* 3.5 5.5 + - - +
16E GLN 3.4 0.4 - - - -
17E THR* 1.3 83.9 - - + +
19E THR* 1.3 65.7 + - - +
21E LYS* 2.9 18.5 + - - +
22E ASP* 3.1 13.9 + - - +
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Residues in contact with THR 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E LEU* 3.6 25.1 - - + -
10E TYR* 2.7 47.3 + - + -
11E ALA* 3.4 8.4 - - + -
14E PHE* 4.9 0.2 - - - +
15E GLY 3.2 17.7 + - - -
16E GLN 4.2 2.9 - - - -
18E LYS* 1.3 78.3 - - - +
20E ALA* 1.3 61.4 + - - +
22E ASP* 3.5 1.0 + - - +
23E LEU* 3.0 49.6 + - + +
30E ILE* 4.1 6.3 - - + -
42E LEU* 3.7 0.4 - - + -
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Residues in contact with ALA 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLN 3.2 14.5 + - - +
17E THR* 4.0 5.8 - - - +
18E LYS 3.1 0.6 - - - -
19E THR* 1.3 77.9 - - - +
21E LYS* 1.3 62.0 + - + +
24E GLY* 2.7 24.2 + - - -
25E VAL* 3.0 30.8 + - - +
26E TYR 4.5 6.1 - - - +
27E GLN* 4.8 6.1 - - + +
30E ILE* 3.2 25.1 - - + +
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Residues in contact with LYS 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E THR* 3.2 30.9 + - + +
18E LYS* 2.9 13.6 + - - +
20E ALA* 1.3 82.9 - - - +
22E ASP* 1.3 60.2 + - - +
24E GLY* 3.7 7.7 + - - -
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Residues in contact with ASP 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E TYR* 3.7 18.8 + - + +
18E LYS 3.1 11.9 + - - +
19E THR* 3.5 4.9 + - - +
21E LYS* 1.3 79.6 - - - +
23E LEU* 1.3 60.5 + - - +
24E GLY 3.2 1.2 + - - -
44E ILE* 5.3 2.8 - - - +
48E GLY 4.0 12.3 - - - +
49E SER* 5.6 0.2 - - - -
50E VAL* 3.1 37.8 + - + +
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Residues in contact with LEU 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D PHE* 4.8 11.7 - - + +
59D PRO* 5.6 0.7 - - + +
62D LYS* 5.7 1.2 - - - +
7E LEU* 5.0 1.8 - - + -
10E TYR* 5.3 0.4 - - + -
19E THR* 3.0 42.3 + - + +
22E ASP* 1.3 78.6 - - + +
24E GLY* 1.3 65.2 + - - +
25E VAL* 3.2 27.7 + - + +
30E ILE* 5.2 0.2 - - + -
42E LEU* 4.2 9.6 - - + -
50E VAL* 3.3 35.7 - - + -
51E TYR* 4.5 0.9 - - - +
52E ALA* 3.6 29.6 - - + +
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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