Contacts of the helix formed by residues 12 - 20 (chain A) in PDB entry 4RHW
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 HIS 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A CYS* 3.0 30.8 + - - +
9A LEU 3.6 1.6 - - - -
10A LEU 3.2 0.4 - - - -
11A GLN* 1.3 109.7 + - + +
13A ARG* 1.3 63.8 + - - +
14A GLU 3.3 3.5 + - - -
15A ALA* 3.3 7.8 + - - +
16A LEU* 3.1 31.3 + - + +
86A LEU* 3.3 66.8 + - + +
87A LEU* 4.6 2.7 - - + -
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Residues in contact with ARG 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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9A LEU 3.1 15.1 + - - +
10A LEU* 2.8 44.7 + - - +
11A GLN 3.4 2.8 + - - -
12A HIS* 1.3 78.2 - - - +
14A GLU* 1.3 63.1 + - + +
16A LEU* 3.3 8.6 + - - +
17A GLU* 2.8 63.7 + - + +
57A ILE* 4.2 14.9 - - + +
58A LYS* 4.3 20.8 - - - +
61A LEU* 3.9 18.3 - - - +
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Residues in contact with GLU 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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11A GLN 5.2 0.8 + - - +
12A HIS 3.3 0.4 - - - -
13A ARG* 1.3 82.5 - - + +
15A ALA* 1.3 64.6 + - - +
17A GLU* 3.4 14.1 + - - +
18A LYS* 3.1 48.1 + - - +
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Residues in contact with ALA 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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12A HIS* 3.3 11.4 + - - +
14A GLU* 1.3 77.2 - - - +
16A LEU* 1.3 64.5 + - - +
18A LYS* 3.2 22.0 + - - +
19A ASP* 3.4 19.1 + - - +
83A LEU* 4.0 8.2 - - + +
86A LEU* 4.0 24.0 - - + -
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Residues in contact with LEU 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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9A LEU* 3.7 31.4 - - + +
12A HIS* 3.1 30.7 - - + +
13A ARG* 3.5 10.1 - - - +
14A GLU 3.3 0.2 - - - -
15A ALA* 1.3 77.8 - - - +
17A GLU* 1.3 61.3 + - - +
20A ILE* 3.1 43.2 + - + +
53A ALA* 4.1 0.2 - - - +
57A ILE* 3.7 18.6 - - + -
71A PHE* 4.9 1.6 - - + -
75A LEU* 4.6 2.0 - - + -
83A LEU* 4.2 31.9 - - + +
86A LEU* 5.5 1.1 - - + -
87A LEU* 4.0 25.4 - - + -
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Residues in contact with GLU 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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13A ARG* 2.8 58.5 + - + +
14A GLU* 3.8 13.1 - - - +
15A ALA 3.3 0.2 - - - -
16A LEU* 1.3 76.5 - - - +
18A LYS* 1.3 62.6 + - + +
49A GLN* 3.5 4.5 + - - -
50A GLN* 3.4 33.7 - - + +
53A ALA* 3.5 10.7 - - - +
54A ALA* 3.8 27.7 - - - +
57A ILE* 3.8 16.0 - - + +
58A LYS* 5.0 3.6 + - - -
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Residues in contact with LYS 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 GLU* 3.1 40.7 + - - +
15A ALA* 3.2 11.4 + - - +
17A GLU* 1.3 79.6 - - + +
19A ASP* 1.3 67.8 + - - +
49A GLN* 3.4 17.1 + - - +
50A GLN* 4.0 22.3 - - - +
1E MET 6.0 1.8 - - - -
3E GLU* 5.1 13.0 + - - +
6E ARG* 4.2 25.4 + - - +
64E THR* 4.1 4.5 - - - +
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Residues in contact with ASP 19 (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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15A ALA* 3.4 11.4 + - - +
17A GLU 3.3 0.2 - - - -
18A LYS* 1.3 82.0 - - - +
20A ILE* 1.3 65.9 + - - +
21A LYS 3.2 3.1 + - - -
49A GLN* 3.9 1.6 - - - -
80A TYR* 3.6 7.0 - - - -
83A LEU* 3.9 30.0 - - + +
1E MET 4.4 9.9 + - - -
6E ARG* 2.7 31.7 + - - -
63E GLU 3.6 3.0 - - - +
64E THR* 3.1 46.8 - - - +
66E GLY* 4.8 5.0 + - - -
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Residues in contact with ILE 20 (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 LEU* 3.1 31.2 + - + +
19A ASP* 1.3 75.3 - - - +
21A LYS* 1.3 62.1 + - - +
22A THR* 3.5 29.6 + - + +
25A ILE* 4.2 12.3 - - + -
49A GLN* 2.9 23.7 + - - +
53A ALA* 3.7 12.7 - - + +
56A LEU* 4.8 4.7 - - + -
57A ILE* 4.5 7.2 - - + -
71A PHE* 3.5 37.0 - - + -
75A LEU* 4.1 13.2 - - + -
80A TYR* 4.2 4.9 - - + -
83A LEU* 4.0 16.4 - - + -
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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