Contacts of the helix formed by residues 26 - 34 (chain A) in PDB entry 1RJV
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 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ALA 4.6 6.4 + - - +
19A PHE* 3.6 7.1 - - - -
24A SER* 2.9 13.1 + - - +
25A PHE* 1.3 65.2 - - - +
27A HIS* 1.3 50.8 + - - +
28A LYS* 3.4 22.2 - - - +
29A LYS* 2.6 57.3 + - + +
30A PHE* 2.8 33.6 + - - +
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Residues in contact with HIS 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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19A PHE* 3.6 13.2 - - + -
25A PHE* 2.8 46.1 + + + +
26A ASP* 1.3 69.0 - - - +
28A LYS* 1.3 101.2 + - + +
30A PHE* 3.6 0.2 - - - +
31A PHE* 2.9 29.3 + - + -
86A LEU* 4.3 10.7 - - + +
89A ALA* 4.4 21.6 - - + +
103A PHE* 5.0 6.1 - - + -
106A LEU* 3.4 33.1 + - + +
107A VAL* 3.3 17.7 - - + +
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Residues in contact with LYS 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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26A ASP* 3.4 16.1 - - - +
27A HIS* 1.3 117.2 + - + +
29A LYS* 1.3 57.1 + - - +
31A PHE* 3.6 2.9 + - - +
32A GLN* 2.8 34.8 + - - +
106A LEU 4.3 3.8 - - - +
107A VAL* 3.9 16.2 - - - +
109A GLU* 4.9 0.9 - - + -
110A SER* 3.5 48.0 - - - +
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Residues in contact with LYS 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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18A ALA* 4.9 5.2 - - + -
26A ASP* 2.6 46.4 + - + +
28A LYS* 1.3 73.5 - - - +
30A PHE* 1.3 53.8 + - - +
32A GLN* 3.2 10.5 + - + +
33A MET* 2.8 61.0 + - + +
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Residues in contact with PHE 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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12A ILE* 5.7 0.2 - - + -
15A ALA* 3.1 46.6 - - + +
16A VAL 3.9 1.8 - - - -
18A ALA* 4.2 11.2 - - + +
19A PHE* 3.1 54.5 - + + -
26A ASP 2.8 10.8 + - - +
27A HIS 3.6 1.6 - - - +
29A LYS* 1.3 70.2 - - - +
31A PHE* 1.3 69.2 + + - +
32A GLN 3.1 0.5 + - - -
33A MET* 3.1 1.7 + - - +
34A VAL* 2.8 54.4 + - + +
36A LEU* 4.1 2.5 - - + -
68A LEU* 4.4 3.1 - - + -
71A PHE* 3.3 52.5 - + + -
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Residues in contact with PHE 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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19A PHE* 5.7 0.9 - + - -
27A HIS* 2.9 30.5 + - + +
28A LYS 3.9 1.6 - - - +
29A LYS 3.4 0.4 - - - -
30A PHE* 1.3 81.9 - + - +
32A GLN* 1.3 57.2 + - - +
34A VAL* 3.6 6.3 - - - -
35A GLY 3.7 0.7 - - - -
36A LEU* 3.1 65.8 + - + -
37A LYS* 3.5 18.3 + - + +
44A VAL* 5.0 4.7 - - + -
47A VAL* 5.0 3.1 - - + -
71A PHE* 4.8 1.3 - + - -
103A PHE* 3.5 70.0 - + - -
104A SER* 4.2 6.5 - - - -
107A VAL* 3.2 32.1 - - + -
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Residues in contact with GLN 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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28A LYS* 2.8 23.8 + - - +
29A LYS* 3.2 12.2 + - + +
30A PHE 3.1 0.6 - - - -
31A PHE* 1.3 75.3 - - - +
33A MET* 1.3 59.8 + - + +
35A GLY* 2.9 21.0 + - - -
37A LYS* 3.3 29.2 - - - +
107A VAL 4.0 0.2 + - - -
110A SER* 2.8 29.5 + - - -
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Residues in contact with MET 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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11A ASP* 3.6 19.9 - - - +
14A LYS* 4.3 37.4 - - + +
15A ALA* 4.6 6.3 - - - +
18A ALA* 4.4 17.7 - - + +
29A LYS* 2.8 42.8 + - + +
30A PHE* 3.8 4.9 - - - +
32A GLN* 1.3 71.9 - - + +
34A VAL* 1.3 57.7 + - - +
35A GLY 3.3 0.7 + - - -
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Residues in contact with VAL 34 (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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3A MET* 6.2 0.4 - - + -
7A LEU* 4.9 7.8 - - + +
8A ASN* 5.2 0.2 - - - +
11A ASP* 3.3 24.1 + - - +
12A ILE* 3.5 32.6 - - + +
15A ALA* 3.4 23.3 - - + +
30A PHE* 2.8 35.1 + - + +
31A PHE* 3.6 3.1 - - - -
33A MET* 1.3 71.3 - - - +
35A GLY* 1.3 58.7 + - - +
36A LEU* 3.3 45.4 + - + +
39A LYS* 5.1 1.9 - - - -
71A PHE* 5.6 1.6 - - + -
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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