Contacts of the helix formed by residues 19 - 29 (chain G) in PDB entry 2QXU
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 PHE 19 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G MET* 3.4 44.9 - - + -
9G VAL 3.5 26.2 - - - -
10G HIS* 3.5 31.6 - - + -
15G ALA 4.4 3.6 - - - -
16G SER* 3.2 14.7 + - - +
17G PHE 3.0 1.8 - - - -
18G ASN* 1.3 80.5 - - + +
20G ALA* 1.3 57.0 + - - +
21G GLY 3.2 2.9 - - - -
22G ILE* 3.3 15.6 + - + -
23G LYS* 2.8 33.9 + - - +
38G ALA* 4.5 3.8 - - + -
39G VAL 5.9 0.2 - - - -
74G VAL* 4.0 24.0 - - + -
76G HIS* 4.1 12.8 - - + -
102G LEU* 4.8 1.1 - - + -
160G LEU* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G SER 4.5 0.2 + - - -
17G PHE* 3.2 18.1 + - - +
18G ASN 3.4 1.4 - - - -
19G PHE* 1.3 77.8 - - - +
21G GLY* 1.3 62.8 + - - +
23G LYS* 3.6 12.2 - - - +
24G SER* 3.1 27.4 + - - -
33G ARG* 5.2 0.3 + - - -
161G TYR* 5.4 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ASN 4.7 0.2 + - - -
19G PHE 3.2 0.4 - - - -
20G ALA* 1.3 76.7 - - - +
22G ILE* 1.3 66.2 + - - +
24G SER* 3.3 7.1 + - - -
25G TYR* 3.0 22.7 + - - +
160G LEU 4.5 1.1 - - - -
161G TYR* 4.1 26.7 - - - -
166G ASN* 5.0 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G MET* 4.4 11.2 - - - -
19G PHE* 3.3 27.0 + - + +
21G GLY* 1.3 75.2 - - - +
23G LYS* 1.3 63.9 + - - +
25G TYR* 3.2 5.5 + - + +
26G LEU* 2.9 44.2 + - + +
74G VAL* 4.9 5.2 - - + -
102G LEU* 5.1 1.6 - - + -
159G LEU 4.8 2.9 - - - +
160G LEU* 3.8 28.6 + - + +
165G VAL* 5.1 0.2 - - + -
166G ASN* 2.8 29.6 - - - +
169G ILE* 3.3 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G MET* 3.0 37.1 - - + +
16G SER 5.6 2.2 - - - -
19G PHE 2.8 17.9 + - - +
20G ALA* 3.6 11.4 - - - +
22G ILE* 1.3 80.1 - - - +
24G SER* 1.3 62.1 + - - +
26G LEU* 3.3 0.8 + - - -
27G VAL* 3.0 29.0 + - - +
33G ARG* 4.0 29.8 - - + +
36G LEU* 3.6 41.4 + - + +
38G ALA* 4.2 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 24 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ALA 3.1 16.0 + - - -
21G GLY* 3.7 5.8 - - - -
22G ILE 3.3 0.2 - - - -
23G LYS* 1.3 77.6 - - - +
25G TYR* 1.3 64.9 + - - +
27G VAL* 3.4 4.2 + - - +
28G SER* 3.1 23.2 + - - -
33G ARG* 3.7 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 25 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G GLY 3.0 14.0 + - - +
22G ILE* 3.2 8.0 + - + +
24G SER* 1.3 77.4 - - - +
26G LEU* 1.3 77.8 + - + +
28G SER* 2.5 25.9 + - - -
29G GLN* 3.1 40.9 + - + +
163G SER 5.6 0.2 - - - -
166G ASN* 3.1 66.2 + - + +
167G SER* 3.6 13.0 + - - -
169G ILE* 5.5 1.3 - - + -
170G LYS* 3.5 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G VAL* 4.9 4.7 - - + -
8G MET* 5.4 2.5 - - - -
22G ILE* 2.9 36.1 + - + +
23G LYS* 3.8 4.5 - - - +
25G TYR* 1.3 94.4 - - + +
27G VAL* 1.3 65.1 + - - +
29G GLN* 3.0 8.5 + - - -
30G GLY 3.2 0.7 + - - -
31G TRP* 3.0 55.1 + - + +
36G LEU* 4.0 22.7 - - + -
74G VAL* 5.2 1.1 - - + -
169G ILE* 4.2 8.5 - - + -
170G LYS* 4.8 2.0 - - - -
173G LEU* 3.7 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G LYS 3.0 20.6 + - - +
24G SER 3.7 5.2 - - - +
25G TYR 3.3 0.2 - - - -
26G LEU* 1.3 75.5 - - - +
28G SER* 1.3 64.8 + - - +
30G GLY* 3.1 12.8 + - - -
31G TRP 3.3 16.2 - - - +
33G ARG* 3.5 64.4 - - + +
36G LEU* 3.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G SER 3.1 12.6 + - - -
25G TYR* 2.5 28.1 + - - -
27G VAL* 1.3 78.8 - - - +
29G GLN* 1.3 75.8 + - - +
30G GLY 3.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 29 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G HIS* 4.8 2.4 - - - -
25G TYR* 3.1 47.2 + - + +
26G LEU* 3.0 12.3 + - - +
28G SER* 1.3 97.3 + - - +
30G GLY* 1.3 55.8 + - - +
31G TRP* 3.7 20.4 - - + -
170G LYS* 3.6 32.2 + - + +
----------------------------------------------------------
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