Contacts of the helix formed by residues 29 - 45 (chain E) in PDB entry 2GZJ
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 SER 29 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E THR* 2.9 17.8 + - - -
28E SER* 1.3 80.5 - - - +
30E GLU* 1.3 64.0 + - - +
31E GLU* 3.7 6.7 + - - +
32E GLU* 2.6 37.1 + - - +
33E LEU 3.3 5.2 + - - -
83F TYR* 3.2 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E SER* 1.3 73.6 - - - +
31E GLU* 1.3 59.3 + - - +
33E LEU* 3.0 8.1 + - + +
34E VAL* 2.9 37.7 + - + +
54F ARG* 2.6 46.9 + - - +
83F TYR* 3.4 34.5 - - + -
84F SER* 2.8 25.5 + - - +
86F PHE* 6.3 0.4 - - + -
98F VAL* 3.6 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E SER* 3.3 7.6 + - - +
30E GLU* 1.3 80.0 - - - +
32E GLU* 1.3 57.2 + - + +
34E VAL* 3.4 20.7 + - - +
35E LYS* 3.0 51.7 + - - +
95F GLY* 4.7 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E THR* 4.2 12.3 - - + -
28E SER* 3.7 16.7 + - - -
29E SER* 2.6 39.3 + - - +
30E GLU 3.2 0.6 - - - -
31E GLU* 1.3 75.1 - - + +
33E LEU* 1.3 66.3 + - - +
35E LYS* 3.3 11.9 + - + +
36E LEU* 3.0 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E THR 4.6 0.2 - - - +
22E ILE* 3.9 40.8 - - + +
25E ALA* 3.9 30.5 - - + -
27E THR* 3.5 24.1 + - + +
29E SER 3.3 3.7 + - - +
30E GLU* 3.0 12.6 + - + +
32E GLU* 1.3 79.6 - - - +
34E VAL* 1.3 62.9 + - - +
36E LEU* 3.2 5.7 + - + +
37E VAL* 3.0 25.8 + - - +
54E TYR* 4.5 3.1 - - - +
78F SER* 4.2 8.5 - - - +
83F TYR* 4.0 15.0 - - + -
86F PHE* 4.0 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E GLU* 2.9 24.9 + - + +
31E GLU* 3.8 19.1 - - - +
33E LEU* 1.3 73.7 - - - +
35E LYS* 1.3 58.3 + - - +
37E VAL* 3.2 3.8 + - - +
38E THR* 2.9 29.9 + - - +
86F PHE* 3.8 24.7 - - + -
95F GLY* 3.5 26.7 - - - +
97F LYS* 4.0 22.7 - - + +
98F VAL* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 35 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E GLU* 3.0 48.1 + - - +
32E GLU* 3.7 10.8 - - + +
33E LEU 3.2 0.2 - - - -
34E VAL* 1.3 76.0 - - - +
36E LEU* 1.3 59.3 + - + +
38E THR* 3.4 7.8 + - - -
39E HIS* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E LYS* 5.4 8.5 - - - +
18E LEU* 4.0 19.8 - - + +
21E THR* 3.9 20.2 - - + -
22E ILE* 3.8 23.4 - - + +
27E THR* 3.7 29.2 - - + -
32E GLU 3.0 14.3 + - - +
33E LEU* 3.2 7.8 + - + +
35E LYS* 1.3 79.1 - - + +
37E VAL* 1.3 56.9 + - - +
39E HIS* 3.3 11.5 + - + +
40E PHE* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E ILE* 3.7 29.4 - - + -
33E LEU* 3.0 15.2 + - + +
34E VAL 3.2 6.5 + - - +
36E LEU* 1.3 72.3 - - - +
38E THR* 1.3 66.7 + - - +
40E PHE* 3.2 8.3 + - - +
41E GLU* 3.0 23.7 + - + +
50E SER* 3.6 31.4 - - - -
53E ILE* 4.6 4.7 - - + -
54E TYR* 3.8 8.5 - - + +
86F PHE* 3.7 30.7 - - + -
97F LYS* 4.6 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E VAL* 2.9 16.0 + - - +
35E LYS* 3.6 12.2 - - - -
37E VAL* 1.3 74.7 - - - +
39E HIS* 1.3 63.4 + - - +
41E GLU* 3.1 7.3 + - - +
42E GLU* 3.1 44.4 + - + +
94F GLY 6.3 0.9 - - - -
95F GLY* 4.8 6.8 - - - -
97F LYS* 3.2 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 39 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E LYS* 2.7 51.7 + - - +
10E TYR* 2.6 32.4 + + - -
18E LEU* 4.0 15.1 - - + +
35E LYS 3.0 17.0 + - - +
36E LEU* 3.4 11.3 + - + +
38E THR* 1.3 77.2 - - - +
40E PHE* 1.3 56.8 + - - +
42E GLU* 3.2 12.8 + - - +
43E MET* 2.8 64.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E PHE* 3.7 33.2 - + - -
18E LEU* 5.0 7.1 - - + +
19E VAL* 3.9 20.0 - - + -
22E ILE* 4.1 12.3 - - + -
36E LEU 2.8 17.6 + - - +
37E VAL* 3.2 11.6 + - - +
39E HIS* 1.3 72.5 + - - +
41E GLU* 1.3 70.1 + - + +
43E MET* 4.0 4.6 - - - +
44E THR* 3.0 47.4 + - + +
49E GLY 3.8 22.0 - - - -
50E SER* 4.9 0.4 - - - -
52E LEU* 4.2 7.0 - - + -
53E ILE* 3.6 27.4 - - + -
67E ILE* 3.9 21.8 - - + -
71E VAL* 4.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E VAL 3.0 18.0 + - - +
38E THR* 3.1 8.7 + - + +
40E PHE* 1.3 78.2 - - + +
42E GLU* 1.3 63.7 + - + +
44E THR* 3.5 6.3 + - - -
45E GLU* 3.3 21.8 + - - -
46E HIS 4.6 2.4 + - - +
49E GLY* 3.6 11.6 - - - -
50E SER* 2.7 50.1 + - - +
89F LYS* 4.1 13.5 - - - +
92F GLN* 4.0 1.6 - - - +
97F LYS* 3.0 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E THR* 3.1 32.9 + - + +
39E HIS* 3.2 14.4 + - - +
41E GLU* 1.3 78.4 - - + +
43E MET* 1.3 74.4 + - + +
45E GLU* 4.0 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 43 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E LYS 3.5 3.8 - - - +
5E HIS* 3.2 22.7 - - - +
6E SER* 3.4 33.0 - - - +
7E ILE* 3.8 27.6 + - + +
10E TYR* 4.0 8.7 - - + -
15E PHE* 4.7 7.2 - - + -
18E LEU* 5.4 0.9 - - + -
39E HIS* 2.8 65.0 + - + +
40E PHE* 4.0 5.2 - - - +
42E GLU* 1.3 85.7 - - + +
44E THR* 1.3 61.3 + - - +
45E GLU* 3.6 2.9 + - - +
75E ARG* 3.4 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 44 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E ILE* 4.4 4.9 - - - -
15E PHE* 3.8 17.9 - - + -
40E PHE* 3.0 51.5 + - + +
41E GLU* 3.5 6.9 + - - -
43E MET* 1.3 74.4 - - - +
45E GLU* 1.3 66.5 + - - +
46E HIS* 3.1 23.6 + - - +
49E GLY* 5.3 1.0 - - - -
71E VAL* 3.9 16.4 - - + -
74E TRP* 3.8 8.8 - - - -
75E ARG* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E GLU 3.3 12.3 + - - -
42E GLU 4.0 13.5 - - - +
43E MET 3.5 2.1 - - - +
44E THR* 1.3 78.1 + - - +
46E HIS* 1.3 63.7 + - - +
47E PRO* 3.5 2.4 - - - +
74E TRP* 3.3 19.4 - - + -
75E ARG* 2.9 28.1 + - - +
80E LYS* 3.2 31.2 + - - +
----------------------------------------------------------
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