Contacts of the helix formed by residues 22 - 31 (chain G) in PDB entry 5T0G
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 LEU 22 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G THR* 6.2 1.6 - - - -
15G ILE 4.0 15.9 - - - +
16G PHE* 6.0 3.1 - - + -
20G GLY 5.3 2.2 - - - +
21G ARG* 1.3 75.0 - - - +
23G TYR* 1.3 63.0 + - - +
24G GLN* 4.9 2.2 - - + +
25G VAL* 3.4 42.8 - - + -
26G GLU* 3.0 23.3 - - + +
29G PHE* 5.7 3.4 - - + -
126G THR* 5.0 2.0 - - + -
79H MET* 5.4 14.4 - - + -
128H ARG* 4.6 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 23 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G SER 2.4 36.5 + - - -
6G SER* 3.7 5.7 - - - -
10G ASP* 3.5 47.2 + - + +
11G ARG* 3.3 37.0 + - - -
15G ILE 5.2 0.9 + - - -
17G SER* 3.6 23.0 - - - -
21G ARG* 4.4 11.6 - - + -
22G LEU* 1.3 75.0 - - - +
24G GLN* 1.3 68.4 + - - +
26G GLU* 2.9 45.3 - - - +
27G TYR* 3.0 26.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ASP 3.4 4.0 + - - -
11G ARG* 2.3 34.9 + - - +
12G HIS 3.6 11.7 - - - +
13G ILE 2.9 32.0 + - - +
14G THR* 3.7 25.9 - - + +
22G LEU* 3.5 2.1 - - + +
23G TYR* 1.3 79.5 - - - +
25G VAL* 1.3 59.5 - - + +
27G TYR* 3.1 13.1 + - - +
28G ALA* 2.9 27.3 + - - +
133G PRO* 4.4 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G THR* 6.2 2.0 - - + -
22G LEU* 3.4 30.2 - - + +
23G TYR 3.4 0.4 - - - -
24G GLN* 1.3 79.7 - - + +
26G GLU* 1.3 59.5 + - - +
28G ALA* 3.3 8.3 + - + +
29G PHE* 2.9 52.9 + - + -
126G THR* 3.8 28.7 - - + +
133G PRO* 5.6 7.6 - - + -
156G PRO 3.5 22.7 - - - +
157G ALA* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ARG* 4.7 0.5 + - - -
21G ARG* 4.8 12.0 - - - +
22G LEU* 3.0 23.9 + - + +
23G TYR* 2.9 48.3 - - - +
25G VAL* 1.3 75.4 - - - +
27G TYR* 1.3 78.7 + - + +
29G PHE* 3.4 27.2 + - + +
30G LYS* 3.6 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 27 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ARG* 2.6 47.6 + - + -
23G TYR* 3.0 28.7 + - + -
24G GLN* 3.1 11.2 + - - +
26G GLU* 1.3 86.6 - - + +
28G ALA* 1.3 64.4 + - - +
29G PHE 3.2 0.3 + - - -
30G LYS* 3.2 35.5 + - - +
31G ALA* 3.0 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G GLN 2.9 13.3 + - - +
25G VAL* 3.3 11.4 + - - +
27G TYR* 1.3 77.1 - - - +
29G PHE* 1.3 64.9 + - - +
31G ALA* 3.0 24.6 + - + +
32G ILE* 3.4 10.9 - - - +
133G PRO* 5.2 10.1 - - + -
135G GLY* 3.8 27.4 - - - +
156G PRO* 4.6 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G LEU* 5.7 3.6 - - + -
25G VAL* 2.9 41.9 + - + -
26G GLU* 3.5 18.8 - - + +
27G TYR 3.1 0.4 - - - -
28G ALA* 1.3 77.6 - - - +
30G LYS* 1.3 58.5 + - - +
32G ILE* 3.2 25.9 + - + +
33G ASN* 5.1 1.0 - - - +
155G ASP* 4.5 12.3 - - + -
156G PRO* 4.4 23.1 - - + -
157G ALA* 4.3 13.9 - - + -
159G TYR* 6.0 0.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G GLU 3.6 6.3 + - - +
27G TYR* 3.2 47.9 + - - +
29G PHE* 1.3 74.5 - - - +
31G ALA* 1.3 61.4 + - - +
32G ILE 3.1 3.5 + - - -
33G ASN* 3.2 31.2 + - - +
34G GLN* 2.9 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G TYR 3.0 7.7 + - - +
28G ALA* 3.0 28.1 + - + +
30G LYS* 1.3 78.0 - - - +
32G ILE* 1.3 61.8 + - + +
34G GLN* 3.1 24.3 + - - +
35G GLY 4.3 1.2 + - - -
82G GLY* 4.8 1.7 - - - -
83G MET* 4.0 22.1 - - + +
132G ARG* 5.6 5.4 - - - +
135G GLY* 5.0 7.4 - - - +
----------------------------------------------------------
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