Contacts of the helix formed by residues 23 - 32 (chain A) in PDB entry 1RRP
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 LYS 23 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.0 40.3 - - + +
16A VAL* 3.3 14.6 - - - +
17A GLY* 2.7 48.8 + - - +
18A ASP 3.6 0.6 + - - -
19A GLY* 3.6 3.4 - - - -
21A THR* 3.3 11.7 - - - +
22A GLY* 1.3 71.5 - - - +
24A THR* 1.3 60.5 + - - +
26A PHE* 3.3 11.0 - - - +
27A VAL* 3.3 4.2 + - - +
65A ASP* 3.7 3.4 - - - +
66A THR 3.6 21.8 - - - -
67A ALA 4.3 4.0 - - - -
89A MET* 3.9 16.9 - - + -
250A GNP 2.7 48.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 1.3 70.8 - - - +
25A THR* 1.3 69.4 + - - +
26A PHE 2.9 2.4 + - - -
27A VAL* 3.0 3.7 + - + +
28A LYS* 2.8 50.2 + - + +
40A VAL 5.8 0.9 - - - +
42A THR* 2.6 21.4 + - + +
46A GLU* 5.8 3.8 - - - +
48A HIS* 5.5 1.8 - - - +
65A ASP* 2.5 29.4 + - - +
250A GNP 2.9 11.6 + - - +
251A MG 2.7 17.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLY 3.0 1.5 + - - -
24A THR* 1.3 76.3 - - - +
26A PHE* 1.3 65.4 + - - +
28A LYS* 3.9 5.6 - - - +
29A ARG* 3.2 19.9 + - - +
34A GLU 4.7 0.5 - - - +
35A PHE* 3.7 37.9 - - + -
36A GLU* 4.0 27.1 + - + +
151A ALA* 4.2 1.5 - - + +
250A GNP 2.9 53.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 4.4 3.1 - - + -
22A GLY 2.8 12.0 + - - +
23A LYS 3.3 9.4 - - - +
24A THR 2.9 0.2 + - - -
25A THR* 1.3 76.6 - - - +
27A VAL* 1.3 76.3 + - + +
29A ARG* 3.1 14.0 + - - +
30A HIS* 3.3 37.7 + + - -
87A ILE* 3.8 26.2 - - + -
89A MET* 3.6 26.9 - - + -
120A CYS* 5.6 0.2 - - - -
122A ASN* 5.9 0.7 - - - +
149A ILE* 4.0 18.2 - - + -
151A ALA* 3.9 15.7 - - + +
157A PHE* 3.5 28.5 - + + -
160A PRO* 4.2 13.7 - - + -
161A PHE* 3.7 18.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.5 19.3 - - + -
23A LYS 3.4 13.9 - - - +
24A THR* 3.0 6.6 + - - +
26A PHE* 1.3 79.4 - - + +
28A LYS* 1.3 59.2 + - + +
29A ARG 2.8 11.1 + - - -
30A HIS* 3.0 17.1 + - - +
31A LEU* 3.1 11.4 + - + +
48A HIS* 4.4 31.2 - - + +
50A LEU* 4.4 19.1 - - + -
63A VAL* 3.9 25.8 - - + -
65A ASP* 4.8 5.8 - - + -
161A PHE* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 2.8 41.8 + - + +
25A THR* 3.9 5.2 - - - +
27A VAL* 1.3 73.2 - - + +
29A ARG* 1.3 56.9 + - - +
31A LEU* 3.8 15.3 - - + -
32A THR* 3.3 17.9 + - - +
34A GLU* 3.4 39.7 + - + +
36A GLU* 4.9 22.0 + - + -
46A GLU* 5.4 2.5 - - - +
48A HIS* 4.5 23.8 - - + +
58B LYS* 5.3 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 3.2 14.8 + - + +
26A PHE* 3.1 7.5 + - - +
27A VAL 2.9 1.0 - - - -
28A LYS* 1.3 75.6 - - - +
30A HIS* 1.3 60.9 + - - +
31A LEU 2.9 5.4 - - - -
33A GLY* 2.7 40.6 + - - +
34A GLU 3.3 21.7 + - - +
35A PHE* 3.7 19.5 - - - +
151A ALA* 3.2 29.4 + - + +
152A LYS* 3.4 21.2 + - - +
154A ASN* 3.1 33.1 + - - +
157A PHE* 4.3 14.9 - - + -
59B GLU* 2.3 40.1 + - - -
82B ARG* 4.6 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.3 23.0 + + - +
27A VAL* 3.0 5.9 + - - +
29A ARG* 1.3 76.4 - - - +
31A LEU* 1.3 57.5 + - - +
50A LEU* 3.6 26.2 - - + +
52A PHE* 3.9 17.8 - + + -
157A PHE* 2.5 73.5 + + + -
158A GLU* 4.2 2.1 + - + +
161A PHE* 3.0 29.1 - + - -
82B ARG* 4.7 8.0 + - - +
85B VAL* 5.9 2.5 - - + -
87B LYS* 5.2 8.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 3.1 14.2 + - + +
28A LYS* 4.2 14.1 - - + +
29A ARG 2.9 0.8 - - - -
30A HIS* 1.3 81.7 - - - +
32A THR* 1.3 66.9 + - - +
48A HIS* 4.0 31.2 - - + +
49A PRO* 3.9 24.9 - - + +
50A LEU* 4.3 6.1 - - + -
60B ARG* 5.2 3.1 + - - -
82B ARG* 5.0 5.3 + - - -
119B ASP* 4.9 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LYS* 3.3 5.0 + - - +
31A LEU* 1.3 87.6 + - - +
33A GLY* 1.3 61.1 + - - +
34A GLU* 3.0 43.8 + - + -
49B ARG* 3.8 33.8 + - - +
58B LYS* 5.1 2.2 - - + -
59B GLU 3.6 1.2 - - - +
60B ARG* 3.1 15.5 - - - +
82B ARG* 3.1 18.9 + - - +
----------------------------------------------------------
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