Contacts of the helix formed by residues 24 - 33 (chain A) in PDB entry 1R5C
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 ASN 24 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER 3.3 7.9 + - - +
19A PRO* 4.0 19.0 + - - +
21A SER* 2.9 36.0 + - - +
22A SER 2.9 0.4 - - - -
23A SER* 1.3 83.9 + - - +
25A TYR* 1.3 63.6 + - - +
26A CYS 3.3 2.9 - - - -
27A ASN* 3.0 33.4 + - - +
28A LEU* 3.0 27.9 + - + +
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Residues in contact with TYR 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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21A SER 4.0 1.0 + - - -
22A SER* 3.0 18.4 + - - +
23A SER 3.4 0.6 - - - -
24A ASN* 1.3 77.5 - - - +
26A CYS* 1.3 62.6 + - - +
28A LEU* 3.3 4.7 + - - +
29A MET* 2.8 57.5 + - + +
46A PHE* 3.9 13.5 - + - +
48A HIS* 3.2 17.0 - + - -
82A THR* 3.8 36.1 - - + -
99A THR* 4.1 5.8 - - + +
14B ASP* 2.4 35.0 + - - +
17B ASN* 4.4 9.2 - - - -
18B SER 5.0 0.9 - - - -
19B PRO* 3.6 35.0 - - + +
28B LEU* 4.5 11.8 - - + +
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Residues in contact with CYS 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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25A TYR* 1.3 78.6 - - - +
27A ASN* 1.3 61.5 + - - +
29A MET* 4.5 1.8 - - - +
30A MET* 2.8 36.9 + - - +
82A THR* 3.8 10.8 - - - -
84A CYS* 2.0 55.9 - - - -
97A TYR* 3.6 20.0 - - + -
99A THR* 3.1 33.9 + - - +
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Residues in contact with ASN 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 SER 5.0 1.4 + - - -
24A ASN* 3.0 32.1 + - - +
26A CYS* 1.3 78.0 - - - +
28A LEU* 1.3 68.1 + - + +
30A MET* 4.2 1.4 - - - +
31A CYS* 3.4 21.1 + - - +
36A THR* 5.4 1.0 - - - +
95A CYS 4.5 6.0 + - - +
96A ALA* 3.6 10.9 - - - +
97A TYR* 2.7 46.5 + - - +
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Residues in contact with LEU 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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14A ASP* 5.8 0.9 - - - +
19A PRO 4.7 1.6 - - - +
24A ASN* 3.0 29.6 + - + +
25A TYR* 3.9 2.7 - - - +
27A ASN* 1.3 81.1 - - + +
29A MET* 1.3 59.5 + - - +
31A CYS* 3.3 4.3 + - - +
32A CYS* 2.8 31.2 + - - +
25B TYR* 4.3 19.1 - - + +
28B LEU* 3.9 32.3 - - + +
29B MET* 3.6 39.7 - - + -
32B CYS* 4.0 9.4 - - + +
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Residues in contact with MET 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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25A TYR* 2.8 50.6 + - + +
26A CYS 4.2 0.9 - - - +
28A LEU* 1.3 71.0 - - - +
30A MET* 1.3 62.1 + - - +
32A CYS* 4.2 3.4 - - - -
33A ARG* 2.8 76.1 + - + +
46A PHE* 3.8 30.7 - - + -
14B ASP* 3.6 22.9 - - - +
17B ASN* 5.6 0.4 - - - -
28B LEU* 3.4 28.9 - - + -
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Residues in contact with MET 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 CYS 2.8 30.0 + - - +
27A ASN 4.2 0.9 - - - +
29A MET* 1.3 73.6 - - - +
31A CYS* 1.3 57.5 + - - +
33A ARG 4.1 0.2 - - - -
34A LYS 3.7 0.5 + - - -
35A MET* 2.9 58.8 + - + +
36A THR* 3.6 7.6 + - + -
41A LYS* 3.8 25.8 - - + +
44A ASN* 3.6 42.4 - - + -
46A PHE* 4.0 7.0 - - - -
84A CYS* 4.3 9.0 - - + -
97A TYR* 3.8 39.9 - - + +
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Residues in contact with CYS 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 ASN 3.4 16.8 + - - +
28A LEU 3.3 1.5 + - - +
29A MET 3.1 0.4 - - - -
30A MET* 1.3 77.6 - - - +
32A CYS* 1.3 65.6 + - - +
34A LYS* 3.0 14.7 + - - -
36A THR* 3.5 20.1 + - + +
37A GLN* 5.2 1.6 + - - -
32B CYS* 2.0 57.7 - - - -
34B LYS* 4.3 11.0 + - - -
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Residues in contact with CYS 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 LEU 2.8 20.6 + - - +
29A MET* 3.8 7.2 - - - +
31A CYS* 1.3 73.2 - - - +
33A ARG* 1.3 72.6 + - - +
34A LYS* 3.0 20.3 + - - +
28B LEU* 4.0 17.5 - - + +
31B CYS* 2.0 61.2 - - + +
32B CYS* 3.8 10.7 - - - +
34B LYS* 5.1 2.3 + - - -
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Residues in contact with ARG 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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29A MET* 2.8 56.9 + - + +
30A MET 4.1 0.2 - - - -
32A CYS* 1.3 78.8 - - - +
34A LYS* 1.3 64.0 + - - +
35A MET* 3.4 19.7 + - + +
46A PHE* 4.1 6.8 - - + -
9B GLU 3.4 8.3 + - - -
10B ARG* 2.8 76.9 + - - +
13B MET 2.8 29.9 + - - -
14B ASP* 4.1 10.1 + - - +
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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