Contacts of the helix formed by residues 30 - 45 (chain G) in PDB entry 1RZR
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 30 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G VAL* 1.3 76.6 - - - +
31G PRO* 1.3 68.7 - - + -
32G SER* 2.9 24.7 - - - +
33G THR* 2.8 11.4 + - - +
34G ARG 2.8 25.5 + - - -
700H C 3.6 15.7 + - - +
701H T 3.1 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 31 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G VAL 3.4 3.7 - - - +
30G LYS* 1.3 95.2 - - + +
32G SER* 1.3 57.0 + - - +
34G ARG* 4.2 12.3 - - + +
35G LYS* 3.0 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 32 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G LYS* 3.6 28.3 - - - +
31G PRO* 1.3 79.7 - - - +
33G THR* 1.3 64.0 + - - +
35G LYS* 3.7 3.4 - - - +
36G LYS* 3.3 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 33 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G VAL* 3.7 29.8 - - + -
18G THR* 3.8 17.3 - - + -
29G VAL* 4.2 6.1 - - - -
30G LYS* 2.8 6.7 + - - +
32G SER* 1.3 76.2 + - - +
34G ARG* 1.3 56.2 + - - -
35G LYS 2.5 17.3 + - - -
36G LYS* 2.8 19.9 + - + +
37G VAL* 3.0 14.4 + - + +
701H T 2.7 28.4 + - - +
702H G 5.8 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 34 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ARG 4.8 0.8 + - - -
22G VAL* 4.1 24.1 + - + +
25G GLY* 3.8 22.8 - - - -
26G ASN 2.7 30.7 + - - +
27G PRO* 4.7 0.4 - - - +
28G ASN 4.5 8.1 - - - +
29G VAL* 3.5 40.4 + - + +
30G LYS 2.8 11.4 + - - +
31G PRO* 4.3 9.8 - - + +
33G THR* 1.3 72.2 - - - +
35G LYS* 1.3 58.3 + - + +
37G VAL* 4.2 1.0 - - - +
38G LEU* 2.9 47.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 35 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G PRO* 3.0 25.8 + - + +
32G SER* 3.7 4.5 - - - +
33G THR 2.5 5.3 + - - -
34G ARG* 1.3 75.8 - - + +
36G LYS* 1.3 69.9 + - - +
38G LEU* 3.1 22.0 + - + +
39G GLU* 3.2 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G GLU 5.2 1.6 - - - -
12G ALA* 2.9 36.5 + - - +
13G SER* 4.1 12.2 + - - -
14G VAL* 4.5 10.4 - - + +
32G SER 3.3 11.8 + - - +
33G THR* 2.8 15.8 + - + +
35G LYS* 1.3 75.6 - - - +
37G VAL* 1.3 63.8 + - - +
39G GLU* 3.1 25.6 + - - +
40G THR* 3.2 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G VAL* 4.4 3.4 - - + -
12G ALA* 4.1 9.2 - - + -
14G VAL* 3.9 33.2 - - + -
18G THR* 4.0 18.4 - - + -
19G VAL* 4.1 13.9 - - + -
22G VAL* 3.3 38.1 - - + -
33G THR* 3.0 16.4 + - + +
34G ARG 4.2 0.4 - - - +
36G LYS* 1.3 76.8 - - - +
38G LEU* 1.3 55.4 + - - +
39G GLU 3.1 0.2 + - - -
40G THR* 3.1 5.2 + - - -
41G ILE* 2.9 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G VAL* 4.7 20.9 - - + +
23G VAL* 6.2 0.9 - - - -
34G ARG* 2.9 41.7 + - + +
35G LYS* 3.1 17.3 + - + +
37G VAL* 1.3 77.9 - - - +
39G GLU* 1.3 57.2 + - + +
41G ILE* 3.3 15.9 - - + +
42G GLU* 3.0 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G LYS* 3.2 16.6 - - + +
36G LYS* 3.5 22.6 + - - +
37G VAL 3.1 0.6 - - - -
38G LEU* 1.3 72.7 - - + +
40G THR* 1.3 68.4 + - - +
41G ILE 2.6 6.0 + - - -
42G GLU* 3.2 1.2 + - - +
43G ARG* 2.9 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 40 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G VAL* 3.2 32.5 - - + +
11G GLU* 3.0 47.5 + - + +
12G ALA* 3.2 13.0 - - - +
36G LYS* 3.2 8.6 + - - +
37G VAL 3.1 8.5 + - - -
39G GLU* 1.3 78.3 - - - +
41G ILE* 1.3 56.4 + - - +
43G ARG* 3.5 9.3 + - - +
44G LEU* 2.9 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G VAL* 3.5 23.1 - - + -
19G VAL* 4.4 2.7 - - + -
22G VAL* 3.8 15.0 - - + -
23G VAL* 4.2 15.5 - - + -
37G VAL* 2.9 41.1 + - + +
38G LEU* 3.3 19.3 - - + +
39G GLU 2.6 0.8 + - - -
40G THR* 1.3 75.3 - - - +
42G GLU* 1.3 89.4 + - + +
43G ARG 3.2 1.3 - - - -
44G LEU 3.5 0.3 + - - -
45G GLY 3.1 15.1 + - - -
46G TYR* 3.2 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G LEU* 3.0 19.6 + - + +
39G GLU* 3.2 1.1 + - - -
41G ILE* 1.3 101.3 - - + +
43G ARG* 1.3 60.8 + - - +
45G GLY* 3.6 11.1 + - - -
46G TYR 3.5 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G GLU* 2.9 34.4 + - - +
39G GLU* 2.9 29.3 + - + +
40G THR* 3.5 8.0 + - - +
42G GLU* 1.3 75.0 - - - +
44G LEU* 1.3 123.0 + - - +
45G GLY* 3.0 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G VAL* 4.0 29.6 - - + +
7G ASP* 4.2 22.0 - - + -
8G VAL* 4.3 10.8 - - + +
11G GLU* 4.0 16.4 - - + -
40G THR 2.9 17.1 + - - +
41G ILE* 4.1 2.7 - - - +
43G ARG* 1.3 113.2 - - - +
45G GLY* 1.3 63.1 + - - +
46G TYR* 4.6 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 45 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G VAL* 5.1 4.3 - - - +
41G ILE 3.1 6.2 + - - -
42G GLU* 3.6 11.4 + - - -
43G ARG 3.0 5.9 - - - -
44G LEU* 1.3 80.9 - - - +
46G TYR* 1.3 67.8 + - - +
47G ARG* 3.6 14.4 - - - +
----------------------------------------------------------
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