Contacts of the helix formed by residues 4 - 15 (chain G) in PDB entry 2Q9Q
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 GLU 4 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET* 3.6 30.3 + - - +
2G PHE 3.1 6.2 + - - +
3G CYS* 1.3 77.5 - - - +
5G LYS* 1.3 66.7 + - - +
6G ALA 3.3 1.3 - - - -
7G MET* 3.3 12.6 + - - +
8G GLU* 3.3 10.4 + - - +
11G ARG* 3.7 19.0 + - - +
35G GLU* 5.0 0.8 + - - -
29H HIS* 3.4 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 5 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G CYS* 4.5 0.2 - - - +
4G GLU* 1.3 76.8 - - - +
6G ALA* 1.3 66.6 + - - +
8G GLU* 2.8 57.1 + - - +
9G LEU* 3.5 8.0 + - - +
25G ASN* 5.8 0.2 + - - -
27G ASP* 5.6 1.4 - - - +
28G GLY* 3.6 22.8 - - - +
31G GLN* 3.4 52.3 + - + +
32G VAL* 4.0 13.0 - - + +
35G GLU* 4.6 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 6 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G CYS* 4.1 8.9 - - + +
4G GLU 3.3 0.2 - - - -
5G LYS* 1.3 80.2 - - - +
7G MET* 1.3 61.7 + - - +
9G LEU* 3.2 22.4 + - + +
10G ILE* 3.4 11.1 + - - +
32G VAL* 3.6 20.3 - - + +
72G ASN* 3.4 26.1 + - - +
75G CYS* 3.7 29.1 - - + +
76G THR 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 7 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G CYS 3.5 14.6 + - - +
4G GLU* 3.3 13.7 + - - +
5G LYS 3.1 0.8 - - - -
6G ALA* 1.3 76.3 - - - +
8G GLU* 1.3 60.6 + - - +
9G LEU 3.2 0.2 - - - -
10G ILE* 3.4 4.3 + - + +
11G ARG* 2.9 58.4 + - - +
71G ARG* 3.5 23.6 - - - +
75G CYS* 4.5 5.2 - - - -
25H ILE* 4.0 16.6 - - - +
26H LEU* 3.9 26.5 - - + -
29H HIS* 3.5 42.6 - - + +
71H TRP* 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 8 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G GLU 3.3 6.6 + - - +
5G LYS* 2.8 53.3 + - - +
7G MET* 1.3 79.1 - - - +
9G LEU* 1.3 61.2 + - + +
11G ARG* 3.8 10.7 - - - +
12G GLU* 3.1 24.2 + - + +
15G ARG* 4.8 3.6 + - - +
25G ASN* 3.9 19.2 + - - +
28G GLY* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LYS 3.5 6.5 + - - +
6G ALA* 3.2 12.9 + - + +
7G MET 3.2 0.4 - - - -
8G GLU* 1.3 79.5 - - + +
10G ILE* 1.3 64.0 + - + +
12G GLU* 3.4 7.9 + - - +
13G LEU* 3.3 16.1 + - - +
25G ASN* 3.6 43.3 - - + +
28G GLY* 4.3 4.5 - - - -
29G LEU* 4.2 17.0 - - + +
32G VAL* 4.3 19.5 - - + -
75G CYS 5.1 1.1 - - - +
76G THR* 4.8 14.4 - - - +
79G TYR* 3.6 50.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 10 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ALA 3.4 12.8 + - - +
7G MET* 3.4 10.9 + - - +
9G LEU* 1.3 73.2 - - - +
11G ARG* 1.3 65.7 + - - +
13G LEU* 3.5 4.0 + - - +
14G HIS* 3.1 21.5 + - - +
75G CYS* 3.5 34.5 - - - +
79G TYR* 4.1 10.3 - - + +
22H LEU* 3.7 51.6 - - + +
25H ILE* 3.9 27.6 - - + -
26H LEU* 4.1 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 11 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G GLU* 3.7 22.6 + - - +
7G MET* 2.9 47.3 + - - +
8G GLU* 3.8 9.2 - - - +
9G LEU 3.3 0.2 - - - -
10G ILE* 1.3 78.2 - - - +
12G GLU* 1.3 63.0 + - - +
14G HIS* 3.2 16.0 + - + +
15G ARG* 3.2 42.7 + - + +
26H LEU* 4.3 17.0 - - + +
29H HIS* 3.8 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 12 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G GLU* 3.1 17.3 + - + +
9G LEU* 3.5 4.5 - - - +
10G ILE 3.3 0.2 - - - -
11G ARG* 1.3 75.7 - - - +
13G LEU* 1.3 62.7 + - - +
15G ARG* 3.3 34.4 + - - +
16G ALA* 3.5 10.7 + - - +
22G PRO* 4.3 21.3 - - + +
23G ALA* 3.7 17.5 + - - +
25G ASN* 3.2 36.0 + - - +
79G TYR* 4.1 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G LEU 3.3 4.1 + - - +
10G ILE 4.0 6.3 - - - +
12G GLU* 1.3 79.3 - - + +
14G HIS* 1.3 62.2 + - - +
16G ALA* 3.2 12.6 + - - +
22G PRO* 3.8 30.1 - - + -
79G TYR* 3.4 55.4 - - + +
82G ASP* 3.5 20.4 - - + +
83G ARG* 3.8 18.4 - - + +
86G ARG* 2.9 38.0 + - - +
22H LEU* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 14 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ILE* 3.1 18.4 + - + +
11G ARG* 3.2 8.0 + - + +
13G LEU* 1.3 77.6 - - - +
15G ARG* 1.3 64.4 + - + +
16G ALA 3.6 2.9 + - - +
17G PRO* 5.8 0.2 - - - +
86G ARG* 5.0 0.4 - - - +
7H ARG* 4.6 13.0 + - - +
22H LEU* 4.5 9.0 - - + +
23H ASP* 3.5 24.1 + - - -
26H LEU* 3.5 30.7 - - + +
170H GLU* 4.3 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 15 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LYS* 4.3 22.2 - - - +
194B TYR* 5.8 0.2 - - - -
196B ILE* 5.2 11.2 - - + +
199B GLU* 5.2 2.6 + - - -
8G GLU* 4.8 4.6 + - - +
11G ARG* 3.2 31.5 + - + +
12G GLU* 3.3 37.0 + - - +
13G LEU 3.2 0.6 - - - -
14G HIS* 1.3 84.3 - - + +
16G ALA* 1.3 59.3 + - - +
17G PRO* 2.9 15.8 - - - +
----------------------------------------------------------
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