Contacts of the helix formed by residues 21 - 33 (chain A) in PDB entry 2RUV
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 SER 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A PHE* 3.6 4.2 - - - -
19A CYS* 3.3 11.9 - - - +
20A LEU* 1.3 79.4 - - - +
22A LYS* 1.3 56.0 + - - +
23A GLY* 3.1 15.8 + - - -
24A HIS* 3.3 18.8 + - - +
25A LEU* 3.2 21.0 + - - +
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Residues in contact with LYS 22 (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 PHE* 3.4 52.8 - - + -
21A SER* 1.3 69.4 + - - +
23A GLY* 1.3 59.7 + - - +
25A LEU* 3.3 22.7 + - + +
26A LYS* 3.0 51.9 + - + +
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Residues in contact with GLY 23 (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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21A SER* 3.1 8.4 + - - -
22A LYS* 1.3 77.6 - - - +
24A HIS* 1.3 56.4 + - - +
26A LYS* 3.3 11.3 + - - +
27A VAL* 2.9 35.2 + - - +
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Residues in contact with HIS 24 (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 PHE* 3.7 26.4 - + - -
19A CYS* 3.9 16.8 - - + -
21A SER* 3.3 26.4 + - - +
23A GLY* 1.3 74.6 - - - +
25A LEU* 1.3 56.6 + - - +
27A VAL* 3.5 10.6 + - + +
28A HIS* 2.9 27.6 + - + +
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Residues in contact with LEU 25 (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 PHE* 3.9 17.9 - - + -
11A ALA 3.5 30.1 - - - +
12A CYS* 3.8 18.4 - - + +
17A PHE* 5.0 1.8 - - + -
19A CYS* 3.4 19.4 - - - -
21A SER 3.2 8.5 + - - +
22A LYS* 3.6 26.7 - - + +
24A HIS* 1.3 72.9 - - - +
26A LYS* 1.3 60.1 + - + +
28A HIS* 3.3 8.0 + - + +
29A ILE* 3.0 49.7 + - + +
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Residues in contact with LYS 26 (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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22A LYS* 3.0 40.1 + - + +
23A GLY* 3.6 12.1 - - - +
25A LEU* 1.3 75.4 - - + +
27A VAL* 1.3 57.9 + - + +
29A ILE* 3.9 6.8 - - + +
30A GLU* 2.9 35.0 + - - +
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Residues in contact with VAL 27 (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 GLY* 2.9 21.5 + - - +
24A HIS* 3.8 11.9 - - + +
26A LYS* 1.3 72.0 - - + +
28A HIS* 1.3 65.5 + - - +
30A GLU* 3.6 10.9 + - - +
31A ARG* 3.2 51.4 + - - +
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Residues in contact with HIS 28 (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 CYS* 3.3 12.1 - - + -
15A CYS* 3.4 4.2 - - - -
17A PHE* 3.6 47.8 - + + +
24A HIS* 2.9 21.8 + - + +
25A LEU* 3.5 5.4 - - + +
27A VAL* 1.3 75.5 - - - +
29A ILE* 1.3 62.5 + - + +
31A ARG* 5.3 0.2 - - - -
32A VAL* 2.9 57.4 + - + +
33A HIS* 3.0 5.7 + - - -
101A ZN 1.9 38.3 - - - -
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Residues in contact with ILE 29 (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 CYS* 4.7 1.1 - - - -
13A ASP* 5.0 8.7 - - + +
14A TYR* 3.9 39.3 - - + +
25A LEU* 3.0 47.2 + - + +
26A LYS* 3.9 5.8 - - - +
28A HIS* 1.3 78.9 - - + +
30A GLU* 1.3 56.9 + - - +
31A ARG 3.2 1.6 + - - -
33A HIS* 3.2 11.6 + - + -
34A LYS* 2.8 42.5 + - + +
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Residues in contact with GLU 30 (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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26A LYS* 2.9 20.1 + - - +
27A VAL* 4.0 12.0 - - - +
29A ILE* 1.3 75.5 - - - +
31A ARG* 1.3 58.9 + - + +
34A LYS* 3.0 28.3 - - + +
35A LYS* 3.4 10.4 - - - +
36A ILE* 3.6 30.4 - - + +
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Residues in contact with ARG 31 (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* 3.2 39.1 + - - +
28A HIS 4.4 0.4 - - - +
29A ILE 3.2 0.4 - - - -
30A GLU* 1.3 84.0 - - + +
32A VAL* 1.3 62.4 + - + +
34A LYS 3.4 7.2 - - - -
35A LYS* 2.8 35.9 + - - +
36A ILE* 4.1 16.5 - - + +
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Residues in contact with VAL 32 (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 CYS* 5.7 0.2 - - - -
28A HIS* 2.9 40.4 + - + +
31A ARG* 1.3 85.1 - - + +
33A HIS* 1.3 82.6 + - + +
34A LYS 4.2 1.1 - - - -
35A LYS* 5.7 0.4 + - - -
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Residues in contact with HIS 33 (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 CYS* 3.6 9.0 - - - -
14A TYR* 3.6 46.8 - + + +
15A CYS* 3.8 11.7 - - + -
28A HIS* 3.0 14.1 + + - -
29A ILE* 3.2 11.3 + - + +
32A VAL* 1.3 94.7 + - + +
34A LYS* 1.3 59.2 + - - +
101A ZN 1.9 38.0 - - - -
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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