Contacts of the helix formed by residues 33 - 55 (chain B) in PDB entry 2Z3X
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 THR 33 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA 3.8 10.5 - - - -
31A GLU* 3.4 37.8 + - - +
32A THR 3.5 7.6 - - - +
33A THR* 4.0 4.9 - - + +
31B GLU 3.9 1.2 + - - +
32B THR* 1.3 79.2 - - - +
34B SER* 1.3 60.8 + - - +
35B ARG* 4.0 2.3 - - - +
36B ALA* 3.0 27.0 + - - +
37B ASN* 3.0 26.5 + - - -
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Residues in contact with SER 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 3.5 4.7 + - - -
32A THR 3.0 9.0 + - - -
34A SER* 3.4 14.8 - - - +
37A ASN* 3.1 27.8 + - - -
32B THR 3.6 1.0 + - - -
33B THR* 1.3 74.0 - - - +
35B ARG* 1.3 57.6 + - - +
37B ASN* 4.5 3.4 - - - +
38B GLY* 2.8 25.3 + - - -
7D G 4.1 0.5 + - - -
8D G 3.0 48.8 + - - +
9D G 3.4 6.3 + - - -
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Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 3.1 38.5 + - - +
31A GLU* 2.8 44.4 + - - +
33B THR* 3.1 2.9 - - - +
34B SER* 1.3 76.4 - - - +
36B ALA* 1.3 62.0 + - - +
38B GLY 3.7 0.3 - - - -
39B SER* 2.8 31.5 + - - -
9D G 3.9 12.5 + - - +
10D G 2.7 37.1 + - - +
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Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 4.1 21.8 - - + +
32B THR* 3.5 17.9 - - + -
33B THR* 3.0 22.1 + - - +
35B ARG* 1.3 78.6 - - - +
37B ASN* 1.3 61.5 + - - +
39B SER* 2.6 25.8 + - - -
40B VAL* 3.8 7.4 + - - +
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Residues in contact with ASN 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER* 3.8 9.5 + - - -
28B LEU* 3.5 15.0 - - - +
29B GLY 3.0 42.3 + - - -
32B THR* 3.0 26.4 + - - +
33B THR 3.0 11.6 + - - +
34B SER 4.0 2.9 - - - +
36B ALA* 1.3 76.4 - - - +
38B GLY* 1.3 63.3 + - - +
40B VAL* 3.4 15.1 + - - +
8D G 4.4 2.2 - - - +
14E C 3.4 19.4 + - - +
15E C 3.2 33.1 + - - +
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Residues in contact with GLY 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B SER 2.8 20.3 + - - -
35B ARG 3.7 0.4 - - - -
37B ASN* 1.3 73.2 - - - +
39B SER* 1.3 64.4 + - - +
41B GLY 2.9 12.3 + - - -
42B GLY 3.1 9.0 + - - -
9D G 3.1 24.2 + - - -
10D G 3.4 9.2 - - - +
14E C 3.3 15.7 + - - -
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Residues in contact with SER 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.7 29.5 - - - -
26B VAL* 4.2 4.7 - - - +
35B ARG* 2.8 20.5 + - - -
36B ALA* 2.6 23.1 + - - -
38B GLY* 1.3 71.5 - - - +
40B VAL* 1.3 62.7 + - - +
42B GLY* 3.2 10.0 + - - -
43B GLU* 3.2 9.5 + - - +
10D G 3.5 19.6 + - - +
11D A 5.7 1.2 - - - +
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LYS* 4.0 32.5 - - + +
20B ILE* 4.1 20.6 - - + -
21B ALA* 4.2 6.5 - - - -
24B PHE* 4.6 1.8 - - + -
26B VAL* 3.3 34.1 - - + -
28B LEU* 3.8 14.8 - - + -
36B ALA 4.0 4.9 - - - +
37B ASN 3.4 8.0 + - - +
38B GLY 3.1 0.4 - - - -
39B SER* 1.3 81.5 + - - +
41B GLY* 1.3 66.0 + - - +
43B GLU* 3.3 3.6 + - - +
44B ILE* 3.1 27.5 + - + +
14E C 4.5 4.7 - - - +
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Residues in contact with GLY 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN 3.7 0.2 + - - -
38B GLY 2.9 7.6 + - - -
40B VAL* 1.3 79.3 - - - +
42B GLY* 1.3 61.5 + - - +
44B ILE* 3.4 5.2 + - - +
45B THR* 3.1 19.8 + - - -
9D G 3.9 0.2 - - - -
10D G 3.5 3.5 + - - -
13E C 3.2 33.4 + - - +
14E C 3.2 21.1 + - - -
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Residues in contact with GLY 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY 3.1 9.1 + - - -
39B SER 3.2 4.5 + - - -
40B VAL 3.1 0.4 - - - -
41B GLY* 1.3 75.3 - - - +
43B GLU* 1.3 63.8 + - - +
45B THR* 3.4 1.6 + - - -
46B LYS* 3.1 18.2 + - - +
10D G 3.3 21.2 + - - -
11D A 3.2 35.5 + - - +
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Residues in contact with GLU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 3.7 19.3 - - + -
24B PHE* 3.0 36.5 - - + -
39B SER 3.2 6.5 + - - +
40B VAL 3.7 7.0 - - - +
42B GLY* 1.3 72.5 - - - +
44B ILE* 1.3 56.4 + - - +
46B LYS* 3.0 36.6 + - - +
47B ARG* 2.7 75.8 + - - +
50B ARG* 5.5 0.9 + - - -
11D A 4.6 4.1 - - - +
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Residues in contact with ILE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 4.9 11.7 - - + +
16B MET* 4.2 15.4 - - - +
17B LYS* 3.9 24.2 - - + +
20B ILE* 3.5 20.2 - - + -
40B VAL* 3.1 18.0 + - + +
41B GLY* 3.5 7.4 - - - +
43B GLU* 1.3 77.8 - - - +
45B THR* 1.3 63.9 + - - +
47B ARG* 3.4 1.0 + - - +
48B LEU* 3.0 41.8 + - + +
13E C 3.9 17.7 - - - +
14E C 3.5 31.9 - - - +
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Residues in contact with THR 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLY 3.1 3.8 + - - -
42B GLY 3.9 3.4 - - - -
43B GLU 3.2 0.2 - - - -
44B ILE* 1.3 79.1 - - - +
46B LYS* 1.3 58.1 + - - +
48B LEU* 3.4 7.5 + - + +
49B VAL* 2.9 43.2 + - + +
10D G 3.2 14.6 + - - -
11D A 3.9 14.8 - - + +
12E C 2.7 37.2 + - - +
13E C 3.3 15.1 + - - -
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Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLY 3.1 14.6 + - - +
43B GLU* 3.0 33.1 + - - +
45B THR* 1.3 79.5 - - - +
47B ARG* 1.3 63.9 + - + +
49B VAL* 3.4 5.6 + - - +
50B ARG* 3.1 50.0 + - + +
11D A 3.6 30.2 + - + +
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Residues in contact with ARG 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B MET* 4.0 25.5 - - + +
19B GLU* 2.7 28.7 + - - +
20B ILE* 3.5 28.3 - - - +
23B GLU* 3.1 27.9 + - - -
24B PHE* 5.2 2.0 - - - -
43B GLU* 2.7 43.8 + - - +
44B ILE 4.1 1.3 - - - +
46B LYS* 1.3 72.6 - - + +
48B LEU* 1.3 57.9 + - - +
50B ARG* 3.1 28.0 + - - +
51B LEU* 2.9 37.9 + - + +
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 4.9 16.6 - - + -
16B MET* 4.4 17.9 - - + -
44B ILE* 3.0 39.9 + - + +
45B THR* 3.7 7.2 - - + +
47B ARG* 1.3 77.0 - - - +
49B VAL* 1.3 57.3 - - + +
51B LEU* 3.4 13.4 + - + +
52B ALA* 3.0 28.2 + - - +
12E C 6.3 1.1 - - - +
13E C 4.7 13.9 - - - -
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Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR* 2.9 32.9 + - + +
46B LYS* 3.8 6.1 - - - +
48B LEU* 1.3 74.5 - - + +
50B ARG* 1.3 65.9 + - - +
52B ALA* 3.5 6.2 + - - +
53B GLN* 3.1 44.8 + - + +
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Residues in contact with ARG 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B GLU* 5.5 1.2 + - - -
46B LYS* 3.1 49.8 + - - +
47B ARG* 3.3 32.3 - - - +
49B VAL* 1.3 77.2 - - - +
51B LEU* 1.3 70.3 + - - +
53B GLN* 3.1 11.1 + - - +
54B GLN* 3.0 44.5 + - + +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B MET* 4.3 21.8 - - + -
47B ARG* 2.9 24.9 + - + +
48B LEU* 3.7 14.1 - - + +
50B ARG* 1.3 81.7 - - + +
52B ALA* 1.3 61.9 + - - +
54B GLN* 3.3 19.8 + - - +
55B ASN* 2.9 39.2 + - - +
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU 3.0 17.2 + - - +
49B VAL* 3.8 7.0 - - - +
50B ARG 3.2 0.2 - - - -
51B LEU* 1.3 79.1 - - - +
53B GLN* 1.3 59.2 + - + +
54B GLN 3.4 0.2 + - - -
55B ASN* 3.7 4.4 + - - +
56B MET* 2.9 32.6 + - + +
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Residues in contact with GLN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 3.1 38.6 + - + +
50B ARG* 3.1 9.2 + - - +
52B ALA* 1.3 77.6 - - + +
54B GLN* 1.3 64.4 + - + +
56B MET* 3.6 21.3 + - + +
57B GLY 3.6 20.8 + - - +
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Residues in contact with GLN 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ARG* 3.0 37.6 + - + +
51B LEU* 3.7 24.8 - - - +
53B GLN* 1.3 75.1 - - + +
55B ASN* 1.3 60.6 + - - +
56B MET 2.7 16.3 + - - -
57B GLY* 3.0 15.7 + - - +
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Residues in contact with ASN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 2.9 33.8 + - - +
52B ALA* 3.8 4.6 - - - +
53B GLN 3.6 0.2 - - - -
54B GLN* 1.3 77.8 + - - +
56B MET* 1.3 58.5 + - - +
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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
------------------------------------------------------------
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