Contacts of the helix formed by residues 24 - 33 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ASN* 3.2 43.4 + - - +
18B SER 5.2 1.5 - - - +
21B SER* 3.6 25.2 + - - +
22B SER 3.1 1.2 - - - -
23B SER* 1.3 82.8 + - - +
25B TYR* 1.3 66.6 + - - +
26B CYS 3.4 0.9 - - - -
27B ASN* 3.1 33.8 + - - +
28B LEU* 3.2 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASP* 2.7 30.7 + - - +
19A PRO* 3.4 35.2 - - + -
20A SER* 3.8 13.9 - - - -
28A LEU* 4.3 11.6 - - + +
21B SER 4.6 1.4 + - - -
22B SER 3.5 16.3 + - - +
23B SER 3.3 1.4 - - - -
24B ASN* 1.3 77.1 - - - +
26B CYS* 1.3 61.7 + - - +
28B LEU* 3.3 4.5 + - - +
29B MET* 2.8 61.6 + - + +
46B PHE* 3.8 14.0 - + - +
48B HIS* 3.3 16.5 - + - -
82B THR* 3.7 36.6 - - + -
99B THR* 4.1 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 1.3 80.1 - - - +
27B ASN* 1.3 55.3 + - - +
29B MET* 4.6 1.1 - - - -
30B MET* 2.8 40.1 + - - +
82B THR* 3.7 13.0 - - - -
84B CYS* 2.0 53.8 - - + -
97B TYR* 3.6 20.9 - - + -
98B LYS 4.3 0.4 - - - +
99B THR* 3.0 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B SER 4.7 1.8 + - - -
24B ASN* 3.1 36.0 + - - +
26B CYS* 1.3 76.0 - - - +
28B LEU* 1.3 64.6 + - + +
30B MET* 4.1 1.4 - - - +
31B CYS* 3.3 22.9 + - - +
36B THR* 5.6 0.9 - - - +
95B CYS 3.9 5.3 - - - +
96B ALA* 3.4 11.2 - - - +
97B TYR* 2.7 48.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 4.5 17.5 - - + +
28A LEU* 3.9 31.6 - - + -
29A MET* 3.4 42.6 - - + -
32A CYS* 4.0 11.6 - - + +
17B ASN* 5.0 3.8 - - - +
24B ASN* 3.2 31.7 + - + +
25B TYR* 3.9 5.4 - - - +
27B ASN* 1.3 75.5 - - + +
29B MET* 1.3 55.6 + - - +
31B CYS* 3.3 4.7 + - - +
32B CYS* 2.7 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASP* 3.8 11.0 - - - +
28A LEU* 3.6 26.0 - - + -
25B TYR* 2.8 61.5 + - + +
26B CYS 4.0 0.4 - - - +
28B LEU* 1.3 70.3 - - - +
30B MET* 1.3 60.5 + - - +
32B CYS* 4.3 4.9 - - - -
33B ARG* 2.8 76.6 + - + +
46B PHE* 3.6 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B CYS 2.8 29.1 + - - +
27B ASN 4.1 0.9 - - - +
29B MET* 1.3 71.7 - - - +
31B CYS* 1.3 59.0 + - - +
33B ARG 3.9 0.2 + - - -
34B LYS 3.7 1.0 + - - -
35B MET* 2.9 58.3 + - + +
36B THR* 3.8 7.2 + - + -
41B LYS* 3.7 17.0 - - + +
44B ASN* 3.7 38.1 - - + +
46B PHE* 3.9 9.0 - - - -
84B CYS* 4.4 9.2 - - + -
97B TYR* 3.5 52.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A CYS* 2.0 58.8 - - - -
34A LYS* 6.3 0.7 - - - -
27B ASN 3.3 17.2 + - - +
28B LEU 3.5 0.9 - - - +
29B MET 3.1 0.6 - - - -
30B MET* 1.3 78.2 - - - +
32B CYS* 1.3 64.4 + - - +
34B LYS* 3.2 24.0 + - - -
36B THR* 3.6 18.6 + - + +
37B GLN* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 4.0 10.3 - - - +
31A CYS* 2.0 57.5 - - + -
32A CYS* 3.8 11.9 - - - +
28B LEU 2.7 22.3 + - - +
29B MET* 3.8 12.6 - - - +
31B CYS* 1.3 72.9 - - - +
33B ARG* 1.3 75.0 + - - +
34B LYS* 3.2 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLU 3.6 6.7 + - - -
10A ARG* 2.8 60.5 + - - +
13A MET 2.8 30.3 + - - +
14A ASP* 3.9 11.9 + - - +
29B MET* 2.8 57.1 + - + +
31B CYS 3.2 0.2 - - - -
32B CYS* 1.3 82.9 - - - +
34B LYS* 1.3 70.4 + - - +
35B MET* 3.4 24.4 + - + +
46B PHE* 4.1 6.7 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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