Contacts of the helix formed by residues 35 - 55 (chain A) in PDB entry 2Z3Q
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 CYS 35 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 4.5 1.1 - - + -
32A HIS* 2.7 25.6 + - + +
34A SER* 1.3 81.1 + - - +
36A LYS* 1.3 59.7 + - - +
37A VAL 3.3 3.0 + - - -
38A THR* 3.4 2.5 + - - -
39A ALA* 3.0 28.0 + - + +
82A GLU* 3.3 9.0 - - - -
83A SER 4.7 1.8 - - - -
84A GLY 4.6 3.6 - - - -
85A CYS* 2.1 52.3 - - + -
86A LYS 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 3.6 24.2 - - + -
32A HIS 3.2 1.7 + - - +
33A PRO* 3.4 21.9 + - + +
35A CYS* 1.3 79.1 - - - +
37A VAL* 1.3 63.0 + - + +
39A ALA* 4.2 0.2 - - - -
40A MET* 2.8 29.6 + - - +
82A GLU* 3.5 2.6 + - - +
106A ILE* 3.8 2.4 - - + +
109A MET* 3.8 24.7 - - + -
110A PHE* 3.4 36.1 - - + -
114A SER* 3.0 48.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LYS* 1.3 79.7 - - + +
38A THR* 1.3 65.2 + - - +
40A MET* 3.3 2.3 + - - +
41A LYS* 2.9 58.5 + - - +
74A LEU* 4.6 12.1 - - + -
75A SER 6.3 0.2 - - - +
81A THR* 4.6 17.7 - - + -
82A GLU* 3.1 22.6 + - + +
110A PHE* 4.2 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A CYS* 3.7 5.4 - - - -
37A VAL* 1.3 71.6 - - - +
39A ALA* 1.3 62.7 + - - +
41A LYS* 3.3 12.1 + - - +
42A CYS* 3.1 29.0 + - - -
82A GLU* 2.8 31.1 + - - +
85A CYS* 3.8 22.4 - - + +
86A LYS 3.6 22.9 - - - +
87A GLU* 5.5 1.3 - - - -
88A CYS* 5.8 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
28A GLU* 4.5 14.8 - - + +
31A VAL* 3.7 19.5 - - + -
35A CYS* 3.0 18.2 + - + +
36A LYS 3.8 0.7 - - - +
38A THR* 1.3 73.2 - - - +
40A MET* 1.3 68.0 + - - +
42A CYS* 3.2 10.3 + - - +
43A PHE* 3.1 26.4 + - + -
91A LEU* 6.0 0.7 - - - -
106A ILE* 3.6 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A TRP* 3.6 37.5 - - + -
36A LYS 2.8 19.8 + - - +
37A VAL* 3.7 4.3 - - - +
39A ALA* 1.3 74.9 - - - +
41A LYS* 1.3 65.7 + - - +
43A PHE* 3.2 5.0 + - - +
44A LEU* 2.9 44.6 + - + +
74A LEU* 4.1 9.6 - - + -
103A PHE* 3.9 22.0 - - - -
106A ILE* 3.6 25.7 - - + +
107A VAL* 4.1 8.3 - - + +
110A PHE* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 2.9 39.2 + - + +
38A THR* 3.4 12.3 - - - +
40A MET* 1.3 77.1 - - - +
42A CYS* 1.3 61.0 + - - +
44A LEU* 3.3 10.3 + - + +
45A LEU* 3.1 31.9 + - + +
71A ASN* 5.6 1.0 + - - -
74A LEU* 3.8 26.3 - - + +
75A SER 5.5 1.2 - - - +
81A THR* 6.4 0.2 - - - -
88A CYS* 5.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 5.3 2.9 - - + +
38A THR* 3.1 28.5 + - - -
39A ALA* 3.2 8.5 + - - +
41A LYS* 1.3 73.2 - - - +
43A PHE* 1.3 65.7 - - + +
45A LEU* 3.4 4.0 + - - +
46A GLU* 3.0 30.7 + - + +
86A LYS 5.2 0.7 - - - -
87A GLU 4.8 0.9 - - - -
88A CYS* 2.1 60.8 - - + -
91A LEU* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR 4.9 1.3 + - - -
27A THR* 4.3 4.0 - - + -
28A GLU* 3.3 43.5 - - + -
31A VAL* 4.5 0.2 - - + -
39A ALA 3.1 27.3 + - - -
40A MET* 3.6 5.6 - - - +
42A CYS* 1.3 78.8 - - + +
44A LEU* 1.4 57.4 + - - +
46A GLU 3.4 0.3 + - - -
47A LEU* 2.9 30.0 + - - +
91A LEU* 6.3 0.4 - - + -
99A PHE* 3.4 41.3 - + - -
102A SER* 3.8 16.2 - - - -
103A PHE* 3.5 50.2 - + + -
106A ILE* 4.0 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 2.9 43.9 + - + +
41A LYS* 3.7 9.4 - - + +
43A PHE* 1.4 68.7 - - - +
45A LEU* 1.3 66.3 + - + +
47A LEU* 3.4 14.8 + - + +
48A GLN* 3.5 14.9 - - - +
66A LEU* 3.7 29.6 - - + -
67A ILE* 4.1 21.8 - - + +
70A ALA* 3.8 15.9 - - + -
71A ASN* 4.1 13.9 - - - +
74A LEU* 4.0 18.2 - - + -
103A PHE* 4.0 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 3.1 20.3 + - + +
42A CYS 3.6 6.5 - - - +
44A LEU* 1.3 75.2 - - + +
46A GLU* 1.3 63.2 + - - +
48A GLN* 3.1 38.8 + - - +
49A VAL 3.9 0.3 + - - -
88A CYS* 4.4 11.2 - - - -
37B ALA* 4.1 29.6 - - + +
38B GLY* 3.3 25.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.2 16.7 - - + +
26A TYR* 2.7 49.1 + - + +
42A CYS* 3.0 20.6 + - - +
45A LEU* 1.3 75.6 - - - +
47A LEU* 1.3 66.7 - - - +
49A VAL* 3.0 23.0 + - - +
50A ILE 3.6 2.9 + - - -
99A PHE* 3.7 22.0 - - + -
35B ARG* 2.7 40.0 + - - -
37B ALA* 3.4 6.3 - - + -
38B GLY 2.9 19.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 4.7 0.7 - - + -
12A ILE* 4.3 10.3 - - + -
43A PHE 2.9 17.2 + - - +
44A LEU* 3.5 8.1 - - + +
45A LEU 3.1 0.2 - - - -
46A GLU* 1.3 78.0 - - - +
48A GLN* 1.3 61.7 + - - +
50A ILE* 3.2 32.4 + - + +
51A SER 3.3 8.1 + - - -
63A VAL* 3.9 35.6 - - + +
66A LEU* 3.6 41.7 - - + -
67A ILE* 4.6 4.0 - - + -
99A PHE* 3.8 8.7 - - + -
100A LEU* 4.4 8.1 - - + -
103A PHE* 3.7 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU 3.5 10.5 - - - +
45A LEU* 3.1 42.6 + - - +
47A LEU* 1.3 76.2 - - - +
49A VAL* 1.3 58.0 + - - +
51A SER* 3.4 4.4 + - - +
52A LEU* 2.9 35.0 + - + +
63A VAL* 4.5 0.9 - - - -
67A ILE* 3.9 15.5 - - + -
38B GLY* 4.6 11.0 + - - +
-3D MET 2.9 27.3 - - - +
-2D ALA* 3.0 15.2 + - + +
-1D ILE* 3.3 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 4.3 5.8 - - + -
25A LEU* 3.9 17.3 - - + -
46A GLU* 3.0 26.8 + - - +
48A GLN* 1.3 74.1 - - - +
50A ILE* 1.3 67.9 + - - +
52A LEU* 4.4 7.0 - - - +
53A GLU* 2.9 50.2 + - + +
35B ARG* 4.0 4.3 - - - +
38B GLY* 3.7 20.9 - - - +
39B THR 3.5 23.8 - - - +
40B SER* 4.3 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 4.6 7.0 - - + -
16A ILE* 4.3 13.0 - - + -
21A ILE* 4.0 24.6 - - + +
23A ALA* 6.3 0.4 - - + -
25A LEU* 3.7 30.7 - - + -
46A GLU 3.6 1.1 + - - +
47A LEU* 3.2 31.6 + - + +
49A VAL* 1.3 79.4 - - + +
51A SER* 1.3 56.4 + - - +
53A GLU* 4.0 0.3 - - - +
54A SER* 3.0 29.6 + - - -
59A ILE* 4.5 9.6 - - + -
63A VAL* 5.2 1.3 - - + -
96A ILE* 3.9 26.7 - - + -
99A PHE* 4.0 9.0 - - + -
100A LEU* 4.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU 3.3 2.4 + - - -
48A GLN 3.7 7.2 - - - -
49A VAL 3.2 0.6 - - - -
50A ILE* 1.3 77.4 - - - +
52A LEU* 1.3 65.7 + - - +
54A SER* 2.7 23.2 + - - -
55A GLY 3.2 5.9 + - - -
59A ILE* 4.1 4.7 - - - -
60A HIS* 3.4 35.4 + - - +
63A VAL* 4.0 30.9 - - - +
-1D ILE* 4.2 7.5 - - - +
22D TYR* 3.8 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN* 2.9 25.6 + - + +
49A VAL* 3.3 5.4 + - - +
51A SER* 1.3 78.8 + - - +
53A GLU* 1.3 65.5 + - + +
55A GLY* 3.6 7.3 + - - -
38B GLY 4.4 12.8 - - - +
40B SER* 4.0 13.0 - - - -
42B LEU* 5.2 1.4 - - - +
60B SER* 3.6 26.7 - - - +
-2D ALA* 5.2 11.4 - - + +
-1D ILE* 6.0 3.1 - - + -
21D LEU* 5.8 0.7 - - + -
22D TYR* 3.6 22.4 + - - +
47D LEU* 4.0 23.3 - - + -
49D LYS* 4.1 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 4.3 14.1 - - + +
23A ALA* 3.3 13.8 + - - +
49A VAL* 2.9 31.5 + - - +
50A ILE 4.4 1.6 - - - +
52A LEU* 1.3 80.6 - - - +
54A SER* 1.3 60.9 + - - +
55A GLY* 3.5 0.3 + - - -
24B ARG* 3.4 29.0 + - - +
26B ARG* 2.7 44.8 + - - -
40B SER* 2.5 34.7 + - - +
41B SER 4.0 0.2 + - - -
42B LEU* 3.7 19.9 - - + +
44B GLU* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A MET* 4.2 8.7 - - - +
21A ILE* 3.8 21.9 - - - +
50A ILE 3.0 16.4 + - - -
51A SER 2.7 17.7 + - - -
53A GLU* 1.3 79.0 - - - +
55A GLY* 1.3 63.3 + - - +
56A ASP* 3.2 17.0 + - - +
59A ILE* 3.4 32.3 - - - +
24B ARG* 5.7 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A SER 3.2 5.7 + - - -
52A LEU 3.6 4.1 + - - -
53A GLU 3.4 3.4 - - - -
54A SER* 1.3 78.5 + - - +
56A ASP* 1.3 56.3 + - - +
22D TYR* 3.5 42.6 - - - +
44D GLU* 5.3 5.0 - - - +
----------------------------------------------------------
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