Contacts of the helix formed by residues 15 - 25 (chain G) in PDB entry 3ZWG
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 GLY 15 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G GLY 3.3 6.9 + - - -
14G LEU* 1.3 76.7 - - - +
16G PHE* 1.3 67.1 + - - -
17G ASP* 3.1 4.6 + - - -
18G VAL* 3.4 11.2 + - - +
19G LEU* 3.4 17.0 + - - +
173G GLU* 4.1 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 16 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G GLY* 1.3 73.9 - - - -
17G ASP* 1.3 85.5 + - + +
19G LEU* 3.4 7.5 + - - +
20G LYS* 2.7 41.0 + - + +
171G ILE* 4.7 10.7 - - + +
173G GLU* 4.1 10.3 + - - +
2H ALA* 5.4 1.3 - - + -
4H VAL* 3.0 36.8 - - + -
5H ALA* 4.1 6.5 - - + -
6H GLY* 3.1 52.5 - - - +
7H ALA* 3.7 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 17 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G GLY 3.1 1.2 - - - -
16G PHE* 1.3 110.7 - - + +
18G VAL* 1.3 67.4 + - + +
20G LYS* 3.8 7.4 - - - +
21G THR* 3.1 36.4 + - - +
2H ALA* 4.3 9.1 - - + +
4H VAL* 3.8 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 18 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G ASP* 3.7 19.7 - - + +
9G ILE* 4.6 6.5 - - + -
13G GLY 3.2 26.7 - - - +
14G LEU* 4.8 1.8 - - + -
15G GLY* 3.4 10.3 + - - +
16G PHE 3.3 0.2 - - - -
17G ASP* 1.3 78.5 - - + +
19G LEU* 1.3 59.9 + - + +
21G THR* 3.1 8.8 + - - -
22G VAL* 3.1 30.0 + - - +
72G LEU* 3.5 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LEU* 4.0 18.6 - - + -
15G GLY 3.4 15.5 + - - +
16G PHE* 3.4 6.2 + - - +
17G ASP 3.3 0.4 - - - -
18G VAL* 1.3 76.3 - - - +
20G LYS* 1.3 66.3 + - - +
22G VAL* 3.1 7.4 + - + +
23G LEU* 3.0 23.9 + - - +
34G ALA* 3.6 13.3 - - + +
35G VAL 3.8 24.2 - - - +
36G GLY* 3.8 7.2 - - - +
72G LEU* 4.7 9.2 - - + -
171G ILE* 3.7 33.0 - - + -
172G LEU 3.9 6.5 - - - +
173G GLU* 3.8 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 20 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G PHE* 2.7 31.6 + - + +
17G ASP* 3.8 12.8 - - - +
19G LEU* 1.3 73.8 - - - +
21G THR* 1.3 65.6 + - + +
23G LEU* 3.2 17.6 + - + +
24G GLU* 3.2 42.0 + - + +
171G ILE* 4.1 18.9 - - + +
5H ALA* 6.2 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 21 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G ASP* 4.3 12.8 + - - +
17G ASP* 3.1 23.2 + - - +
18G VAL* 3.1 10.8 + - - -
19G LEU 3.2 0.2 - - - -
20G LYS* 1.3 75.5 - - + +
22G VAL* 1.3 70.0 + - - +
23G LEU 3.0 1.7 + - - -
24G GLU* 3.1 12.3 + - - +
25G ALA* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 22 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G ASP 3.8 17.3 - - - +
4G VAL* 4.3 15.5 - - - +
5G ALA* 4.3 7.4 - - + +
18G VAL 3.1 21.8 + - - +
19G LEU* 3.1 12.8 + - + +
21G THR* 1.3 82.0 + - - +
23G LEU* 1.3 59.6 + - - +
25G ALA* 3.7 14.7 + - - +
26G LEU* 3.9 11.1 + - - +
34G ALA* 3.5 20.0 - - + -
35G VAL 5.6 0.2 - - - +
72G LEU* 4.4 14.4 - - + -
73G TYR 3.9 15.5 - - - +
74G ASN* 4.1 17.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G LEU 3.0 11.0 + - - +
20G LYS* 3.3 17.3 - - + +
21G THR 3.0 0.2 - - - -
22G VAL* 1.3 77.7 - - - +
24G GLU* 1.3 63.6 + - + +
26G LEU* 3.4 15.6 - - + +
32G LYS* 2.9 47.4 + - + +
33G ILE 3.8 6.3 - - - -
34G ALA* 3.6 28.9 - - + +
169G HIS* 3.8 32.5 - - + +
170G ALA 3.6 9.2 - - - +
171G ILE* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G LYS* 3.2 43.6 + - + +
21G THR* 3.1 13.0 + - - +
23G LEU* 1.3 75.2 - - + +
25G ALA* 1.3 61.5 - - - +
26G LEU 3.0 5.2 - - - -
27G GLY* 3.0 17.3 + - - +
32G LYS* 4.0 8.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G THR 3.0 16.6 + - - +
22G VAL* 3.8 9.6 - - - +
23G LEU 3.3 0.4 - - - -
24G GLU* 1.3 76.3 - - - +
26G LEU* 1.3 59.9 + - - +
27G GLY* 3.1 2.6 + - - -
----------------------------------------------------------
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