Contacts of the helix formed by residues 35 - 55 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C VAL* 4.6 0.9 - - - -
32C HIS* 2.6 41.4 + - + +
34C SER* 1.3 77.7 - - - +
36C LYS* 1.3 58.2 + - - +
37C VAL 3.3 3.1 + - - -
38C THR* 3.4 3.6 + - + -
39C ALA* 3.0 28.2 + - - +
82C GLU* 3.4 7.4 - - - -
84C GLY 5.0 0.7 - - - -
85C CYS* 2.0 52.9 - - + -
86C LYS 4.9 0.9 - - - +
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Residues in contact with LYS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C VAL* 3.4 24.4 - - + +
32C HIS 3.5 1.6 + - - -
33C PRO* 3.1 28.8 + - - +
34C SER 3.6 0.2 - - - -
35C CYS* 1.3 79.5 - - - +
37C VAL* 1.3 63.8 + - + +
39C ALA* 3.8 1.1 - - - -
40C MET* 3.0 26.5 + - - +
82C GLU* 3.6 3.6 + - - +
106C ILE* 3.7 3.3 - - + +
109C MET* 4.4 29.8 - - + +
110C PHE* 3.4 39.1 - - + -
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Residues in contact with VAL 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LYS* 1.3 76.6 - - + +
38C THR* 1.3 60.0 + - - +
40C MET* 3.4 3.1 + - - +
41C LYS* 2.9 54.2 + - - +
74C LEU* 4.3 14.8 - - + +
77C ASN* 6.0 2.2 - - - +
80C VAL 6.1 1.1 - - - +
82C GLU* 3.1 21.6 + - + +
110C PHE* 4.0 24.2 - - + -
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Residues in contact with THR 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C CYS* 3.6 6.7 - - + -
37C VAL* 1.3 75.6 - - - +
39C ALA* 1.3 62.4 + - - +
41C LYS* 3.2 9.9 + - - +
42C CYS* 3.0 32.8 + - - -
82C GLU* 2.7 28.0 + - - +
85C CYS* 3.9 20.1 - - + +
86C LYS 3.5 24.9 - - - +
87C GLU* 5.6 0.4 - - - -
88C CYS* 5.8 0.2 - - - -
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Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLU* 3.9 33.2 - - + -
31C VAL* 4.6 2.5 - - + -
35C CYS 3.0 17.7 + - - +
36C LYS* 3.8 7.0 - - - +
38C THR* 1.3 72.8 - - - +
40C MET* 1.3 66.6 + - - +
42C CYS* 2.9 18.7 + - - +
43C PHE* 2.9 19.5 + - + -
91C LEU* 5.7 1.3 - - - -
106C ILE* 3.8 13.7 - - + -
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Residues in contact with MET 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C TRP* 3.7 37.7 - - + -
36C LYS 3.0 17.5 + - - +
37C VAL* 3.6 6.3 - - - +
39C ALA* 1.3 75.0 - - - +
41C LYS* 1.3 64.3 + - - +
43C PHE* 3.1 6.8 + - - +
44C LEU* 2.9 31.7 + - + +
74C LEU* 4.0 15.9 - - + -
103C PHE* 3.9 27.6 - - - -
106C ILE* 3.7 14.1 - - + +
107C VAL* 3.8 17.5 - - + -
110C PHE* 3.3 38.6 - - + -
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Residues in contact with LYS 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C VAL* 2.9 38.5 + - - +
38C THR* 3.6 7.9 - - - +
39C ALA 3.2 0.2 - - - -
40C MET* 1.3 75.5 - - - +
42C CYS* 1.3 58.6 + - - +
44C LEU* 3.4 9.8 + - + +
45C LEU* 3.1 36.4 + - + +
71C ASN* 6.0 1.3 - - - +
74C LEU* 4.1 22.9 - - + -
88C CYS* 4.9 0.4 - - - -
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Residues in contact with CYS 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C TYR 5.2 4.7 - - - +
38C THR* 3.0 27.6 + - - -
39C ALA* 2.9 10.3 + - - +
41C LYS* 1.3 74.8 - - - +
43C PHE* 1.3 66.1 + - + +
45C LEU* 3.4 2.5 + - - +
46C GLU* 2.9 30.0 + - + +
86C LYS 5.1 0.4 - - - -
87C GLU 4.7 0.9 - - - -
88C CYS* 2.1 61.7 - - + -
91C LEU* 4.1 18.8 - - + -
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Residues in contact with PHE 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C TYR 4.9 1.1 + - - -
27C THR* 4.3 2.9 - - + -
28C GLU* 3.4 46.2 - - + -
39C ALA 2.9 24.2 + - - -
40C MET* 3.4 7.0 - - - +
42C CYS* 1.3 75.2 - - + +
44C LEU* 1.3 58.2 + - - +
46C GLU 3.3 0.5 + - - -
47C LEU* 3.0 30.1 + - - +
99C PHE* 3.4 52.8 - + - -
102C SER* 3.7 17.0 - - - -
103C PHE* 3.5 36.7 - + + -
106C ILE* 3.7 29.6 - - + -
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Residues in contact with LEU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C TRP* 5.7 0.2 - - + -
40C MET* 2.9 26.1 + - + +
41C LYS* 3.4 11.2 + - + +
42C CYS 3.2 0.2 - - - -
43C PHE* 1.3 76.4 - - - +
45C LEU* 1.3 62.4 + - + +
47C LEU* 3.5 13.3 + - - +
48C GLN* 3.6 13.5 - - - +
66C LEU* 3.6 32.1 - - + -
67C ILE* 3.8 24.5 - - + +
70C ALA* 3.6 26.5 - - + -
71C ASN* 4.2 10.8 - - - +
74C LEU* 3.8 23.6 - - + -
103C PHE* 3.8 10.8 - - + -
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LYS* 3.1 22.8 + - + +
42C CYS 3.7 3.6 - - - +
44C LEU* 1.3 72.3 - - + +
46C GLU* 1.3 67.1 + - - +
48C GLN* 3.0 37.8 + - - +
88C CYS* 4.2 13.5 - - - -
37D ALA* 4.1 27.1 - - + +
38D GLY* 3.3 20.6 - - - +
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LEU* 3.1 18.0 - - + +
26C TYR* 2.6 53.4 + - + +
42C CYS* 2.9 20.5 + - - +
45C LEU* 1.3 78.1 - - - +
47C LEU* 1.3 61.6 + - - +
49C VAL* 3.0 23.5 + - - +
50C ILE 3.7 2.4 + - - -
99C PHE* 3.5 23.1 - - + -
35D ARG* 2.9 35.7 + - - -
37D ALA* 3.5 6.5 - - + -
38D GLY 3.0 18.7 + - - -
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LEU* 4.5 0.9 - - + -
12C ILE* 4.2 16.4 - - + -
43C PHE 3.0 16.6 + - - +
44C LEU* 3.6 6.3 - - - +
45C LEU 3.1 0.4 + - - -
46C GLU* 1.3 78.1 - - - +
48C GLN* 1.3 61.4 + - - +
50C ILE* 3.2 33.8 + - + +
51C SER 3.2 8.8 + - - -
63C VAL* 3.9 31.3 - - + +
66C LEU* 3.8 38.4 - - + -
67C ILE* 4.4 6.7 - - + -
99C PHE* 3.9 7.4 - - + -
100C LEU* 4.4 7.2 - - + -
103C PHE* 4.0 17.9 - - + -
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Residues in contact with GLN 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-2B ALA* 4.2 30.0 + - - +
44C LEU 3.6 12.6 - - - +
45C LEU* 3.2 29.8 - - - +
47C LEU* 1.3 77.9 - - - +
49C VAL* 1.3 56.8 + - - +
51C SER* 3.4 9.4 + - - -
52C LEU* 3.0 37.7 + - + +
63C VAL* 4.5 4.2 - - + +
67C ILE* 4.0 21.3 - - + +
38D GLY* 4.3 13.2 - - - +
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Residues in contact with VAL 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ALA* 4.2 5.4 - - + -
25C LEU* 3.7 19.1 - - + -
46C GLU* 3.0 26.4 + - - +
48C GLN* 1.3 73.4 - - - +
50C ILE* 1.3 61.2 + - - +
52C LEU* 3.7 6.0 - - - +
53C GLU* 2.8 54.4 + - - +
35D ARG* 3.9 4.5 - - - +
38D GLY* 3.6 20.9 - - - +
39D THR 3.3 26.2 - - - +
40D SER* 4.0 7.0 - - - -
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Residues in contact with ILE 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ILE* 4.3 20.9 - - + -
16C ILE* 4.4 15.3 - - + -
21C ILE* 4.6 11.8 - - + +
25C LEU* 3.6 31.4 - - + -
46C GLU 4.2 1.1 - - - +
47C LEU* 3.2 21.5 + - + +
49C VAL* 1.3 77.4 - - + +
51C SER* 1.3 57.7 - - - +
53C GLU* 3.9 3.7 - - - +
54C SER* 2.9 32.7 + - - -
59C ILE* 4.4 6.1 - - + -
63C VAL* 5.3 0.7 - - + -
96C ILE* 3.9 25.4 - - + -
99C PHE* 3.9 22.4 - - + -
100C LEU* 4.3 7.2 - - + -
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Residues in contact with SER 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TYR* 3.7 7.8 + - - -
47C LEU 3.2 5.4 + - - -
48C GLN* 3.6 9.6 - - - -
50C ILE* 1.3 79.1 - - - +
52C LEU* 1.3 62.5 + - - +
54C SER* 2.6 24.0 + - - -
55C GLY 3.1 5.5 + - - -
59C ILE* 4.0 7.4 - - - +
60C HIS* 3.2 35.1 + - - +
63C VAL* 4.0 27.6 - - - -
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Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TYR* 3.6 19.8 + - - +
47B LEU* 5.0 3.4 - - + -
49B LYS* 3.8 37.2 - - + -
48C GLN* 3.0 31.4 + - + +
49C VAL* 3.7 9.2 - - - +
51C SER* 1.3 77.6 + - - +
53C GLU* 1.3 69.1 + - + +
54C SER 3.3 0.5 + - - -
55C GLY* 3.3 9.7 + - - -
38D GLY 4.3 10.3 - - - +
40D SER* 4.5 8.5 - - - -
42D LEU* 5.3 0.9 - - - +
44D GLU* 5.7 0.9 - - - +
60D SER* 3.9 21.1 - - - +
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Residues in contact with GLU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ILE* 4.2 15.9 - - + +
22C ASP* 4.7 0.2 - - - +
23C ALA* 3.4 18.3 + - - +
49C VAL* 2.8 26.5 + - - +
52C LEU* 1.3 77.9 - - - +
54C SER* 1.3 62.2 + - - +
55C GLY* 4.6 0.2 - - - -
24D ARG* 3.3 30.1 + - - +
26D ARG* 2.7 45.1 + - - -
40D SER* 2.5 33.9 + - - +
42D LEU* 3.8 23.1 - - + +
44D GLU* 5.2 1.0 - - - +
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Residues in contact with SER 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C MET* 3.4 19.1 - - - +
21C ILE* 4.0 15.6 - - - +
50C ILE 2.9 17.2 + - - -
51C SER 2.6 19.1 + - - -
53C GLU* 1.3 81.1 - - - +
55C GLY* 1.3 61.7 + - - +
56C ASP* 3.1 13.5 + - - +
59C ILE* 3.7 35.2 - - - +
24D ARG* 5.7 0.3 + - - -
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Residues in contact with GLY 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TYR* 3.3 42.2 - - - +
44B GLU* 5.5 2.3 - - - +
51C SER 3.1 5.3 + - - -
52C LEU 3.3 7.8 + - - -
54C SER* 1.3 80.8 + - - +
56C ASP* 1.3 56.7 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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