Contacts of the helix formed by residues 27 - 46 (chain A) in PDB entry 2HZA
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 ASN 27 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER* 5.9 2.5 - - - -
25A TYR* 3.5 5.7 - - - +
26A ASN* 1.3 82.0 - - + +
28A ARG* 1.3 62.0 + - - +
29A SER* 3.3 11.0 + - - -
30A GLU* 3.1 31.1 + - - +
31A ALA* 3.6 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.8 34.8 - - - +
16A LEU* 4.3 17.5 - - + -
17A ASP* 3.0 42.5 + - - +
20A SER* 5.7 1.8 - - - +
27A ASN* 1.3 72.9 - - - +
29A SER* 1.3 59.4 + - - +
31A ALA* 3.3 6.5 + - - +
32A ILE* 2.8 35.8 + - + +
2B GLN* 5.1 7.5 + - - +
3B ARG 5.8 0.4 + - - -
4B VAL* 4.3 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASN* 3.3 11.7 + - - -
28A ARG* 1.3 77.7 - - - +
30A GLU* 1.3 62.1 + - - +
32A ILE* 3.4 1.7 + - - +
33A ARG* 2.8 45.0 + - - +
4B VAL* 5.1 1.7 - - - +
5B THR 4.7 3.8 - - - -
6B ILE* 3.8 39.9 - - - +
7B THR 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 4.0 16.4 - - + -
27A ASN* 3.1 20.2 + - - +
29A SER* 1.3 78.3 + - - +
31A ALA* 1.3 67.6 + - - +
33A ARG* 3.2 21.5 + - - +
34A ASP* 2.9 34.4 + - - +
37A ARG* 3.6 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.3 7.6 - - + -
20A SER* 3.5 24.5 - - - +
25A TYR* 3.4 28.0 - - + -
27A ASN 3.6 7.9 + - - +
28A ARG* 3.3 10.0 + - - +
29A SER 3.3 0.4 - - - -
30A GLU* 1.3 79.9 - - - +
32A ILE* 1.3 62.2 + - - +
34A ASP* 3.3 2.6 + - - +
35A ILE* 3.2 28.3 + - - +
201B 3CM 4.1 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.4 3.4 - - + -
8A LEU* 4.6 6.5 - - + -
16A LEU* 3.7 29.6 - - + -
28A ARG 2.8 25.7 + - - +
31A ALA* 1.3 73.0 - - - +
33A ARG* 1.3 57.2 + - - +
35A ILE* 3.4 2.9 + - - +
36A LEU* 3.0 33.9 + - + +
4B VAL* 4.3 12.3 - - + -
6B ILE* 3.4 35.2 - - + -
8B LEU* 6.4 0.2 - - + -
32B ILE* 4.2 17.9 - - + -
36B LEU* 3.9 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER* 2.8 35.8 + - - +
30A GLU* 3.2 31.5 + - - +
32A ILE* 1.3 74.5 - - - +
34A ASP* 1.3 56.8 + - - +
36A LEU* 3.3 5.9 + - - +
37A ARG* 2.9 64.7 + - + +
6B ILE* 3.9 7.5 - - + +
7B THR* 3.1 35.5 + - - +
8B LEU* 4.2 19.6 - - + +
9B ASP* 5.4 5.4 + - - -
12B LEU* 5.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 2.5 38.8 + - - +
30A GLU* 2.9 24.2 + - - +
31A ALA 3.7 3.8 - - - +
33A ARG* 1.3 75.4 - - - +
35A ILE* 1.3 63.1 + - - +
37A ARG* 3.0 29.7 + - - +
38A SER* 3.0 26.2 + - - -
201B 3CM 4.3 14.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.5 5.2 - - + -
31A ALA 3.2 14.7 + - - +
32A ILE 3.6 5.8 - - - +
34A ASP* 1.3 77.2 - - - +
36A LEU* 1.3 59.6 + - + +
38A SER* 3.6 3.4 - - - -
39A ALA* 2.9 29.8 + - + +
35B ILE* 3.9 17.0 - - + -
36B LEU* 3.6 28.0 - - + -
39B ALA* 3.4 34.5 - - + -
40B LEU* 4.2 14.8 - - + -
201B 3CM 3.9 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 3.0 23.5 + - + +
33A ARG* 3.6 4.9 - - - +
35A ILE* 1.3 79.6 - - + +
37A ARG* 1.3 56.6 + - - +
39A ALA* 3.9 2.0 - - - +
40A LEU* 2.8 48.3 + - + +
8B LEU* 3.8 32.8 - - + -
12B LEU* 4.1 15.0 - - + -
16B LEU* 4.5 4.0 - - + -
32B ILE* 4.0 35.7 - - + -
35B ILE* 3.7 35.0 - - + -
36B LEU* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 3.6 10.5 + - - -
33A ARG* 2.9 46.3 + - - +
34A ASP* 3.0 27.8 + - - +
36A LEU* 1.3 75.5 - - - +
38A SER* 1.3 63.8 + - - +
40A LEU* 4.1 2.6 - - - +
41A ALA* 2.9 27.1 + - - +
9B ASP* 5.6 2.9 - - - -
12B LEU* 3.6 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP 3.0 19.5 + - - -
35A ILE* 3.6 5.4 - - - -
37A ARG* 1.3 77.5 - - - +
39A ALA* 1.3 63.0 + - - +
41A ALA* 3.2 7.1 + - - +
42A GLN* 3.1 28.8 + - - +
201B 3CM 3.7 43.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 2.9 22.2 + - + +
36A LEU 3.9 2.0 - - - +
38A SER* 1.3 72.1 + - - +
40A LEU* 1.3 66.6 + - - +
42A GLN* 3.3 9.6 + - - +
43A GLU* 3.1 24.5 + - - +
35B ILE* 3.6 30.1 - - + -
39B ALA* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 2.8 32.0 + - + +
37A ARG* 4.1 2.9 - - - +
39A ALA* 1.3 73.2 - - - +
41A ALA* 1.3 63.2 + - - +
43A GLU* 3.4 6.8 + - + +
44A ALA* 3.0 24.8 + - - +
12B LEU* 3.9 40.8 - - + +
15B THR* 4.3 21.0 - - + +
16B LEU* 4.0 23.6 - - + +
19B LEU* 4.1 26.9 - - + -
35B ILE* 4.5 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG 2.9 20.4 + - - +
38A SER* 3.2 8.5 - - - +
39A ALA 3.1 0.2 - - - -
40A LEU* 1.3 79.0 - - - +
42A GLN* 1.3 62.8 + - + +
44A ALA* 3.5 7.1 + - - +
45A THR* 3.2 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A SER* 3.1 18.5 + - - +
39A ALA* 3.3 10.4 + - - +
41A ALA* 1.3 74.3 - - + +
43A GLU* 1.3 60.2 + - - +
45A THR* 2.8 39.6 + - + +
46A GLN* 3.1 18.8 + - - +
125A HIS* 4.2 14.6 + - - -
126A LEU 3.3 24.4 + - - -
127A GLN* 4.8 6.3 - - - +
128A CYS 5.6 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA 3.1 12.6 + - - +
40A LEU* 3.7 11.7 - - + +
42A GLN* 1.3 77.7 - - - +
44A ALA* 1.3 58.9 + - - +
46A GLN* 2.8 31.7 + - - +
47A GLN* 2.8 43.7 + - - +
109A GLN* 5.1 4.2 - - - +
19B LEU* 4.7 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU 3.0 17.2 + - - +
41A ALA* 3.7 7.2 - - - +
43A GLU* 1.3 76.2 - - - +
45A THR* 1.3 59.8 + - - +
46A GLN 3.6 0.2 + - - -
47A GLN* 3.9 22.5 - - - +
130A PRO* 5.2 1.7 - - - +
15B THR* 5.5 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ALA 3.2 13.1 + - - -
42A GLN* 2.8 25.1 + - + +
44A ALA* 1.3 80.4 - - - +
46A GLN* 1.3 59.6 + - + +
47A GLN 3.5 2.8 + - - -
105A MSE 3.7 5.7 - - - +
128A CYS* 3.1 47.4 + - + +
130A PRO* 3.3 31.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 3.2 32.6 + - - +
43A GLU* 2.8 24.5 + - - +
45A THR* 1.3 86.5 - - + +
47A GLN* 1.3 68.8 + - - +
48A HIS* 5.4 1.4 - - - -
105A MSE 4.3 6.7 - - - -
106A GLY* 3.7 12.0 - - - -
109A GLN* 3.1 44.4 + - + +
126A LEU* 4.2 16.5 - - - +
128A CYS* 3.8 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