Contacts of the helix formed by residues 43 - 55 (chain B) in PDB entry 2Z9A
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 LEU 43 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A VAL* 4.0 28.0 - - + -
6A GLU* 4.3 15.7 - - - +
7A VAL* 4.3 11.8 - - + +
39B LEU* 4.2 18.4 - - + -
40B PRO* 2.8 38.7 + - + +
42B SER* 1.3 89.0 - - - +
44B SER* 1.3 63.3 + - - +
45B GLU 3.3 2.9 - - - -
46B GLU* 3.2 20.7 + - + +
47B CYS* 2.9 24.5 + - - +
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Residues in contact with SER 44 (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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36B CYS* 4.3 16.6 + - - +
37B SER* 5.8 0.9 - - - -
39B LEU* 4.9 1.8 + - - +
40B PRO 3.5 4.6 + - - -
41B LYS* 4.0 38.8 + - - +
42B SER 3.7 0.8 - - - -
43B LEU* 1.3 76.2 - - - +
45B GLU* 1.3 65.0 + - - +
47B CYS* 3.2 7.6 + - - +
48B GLN* 3.0 33.8 + - - +
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Residues in contact with GLU 45 (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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41B LYS 5.4 0.2 + - - -
42B SER 5.4 0.4 - - - -
43B LEU 3.3 0.4 - - - -
44B SER* 1.3 77.8 - - - +
46B GLU* 1.3 67.7 + - - +
48B GLN* 3.1 15.2 + - + +
49B GLU* 2.9 51.4 + - + +
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Residues in contact with GLU 46 (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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3A VAL* 4.6 14.9 - - + +
4A TYR* 3.4 30.6 + - + +
7A VAL* 4.1 9.0 - - + -
42B SER 3.1 23.9 - - - +
43B LEU* 3.4 32.1 - - + +
45B GLU* 1.3 87.9 + - - +
47B CYS* 1.3 57.9 + - - +
49B GLU* 3.7 9.9 - - - -
50B VAL* 3.0 32.6 + - - +
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Residues in contact with CYS 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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7A VAL* 3.7 10.2 - - + +
11A LEU* 4.1 22.7 - - - -
35B MET 4.9 0.2 - - - -
36B CYS* 2.1 53.2 - - + -
39B LEU* 3.9 22.0 - - + -
43B LEU 2.9 16.8 + - - +
44B SER* 3.6 5.4 - - - +
46B GLU* 1.3 75.6 - - - +
48B GLN* 1.3 58.3 + - - +
50B VAL* 3.2 2.8 + - - +
51B VAL* 2.8 33.3 + - - +
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Residues in contact with GLN 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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36B CYS* 4.5 11.4 - - + -
44B SER* 3.0 26.6 + - - +
45B GLU* 3.6 16.6 + - + +
47B CYS* 1.3 73.0 - - - +
49B GLU* 1.3 61.8 + - - +
51B VAL* 4.4 6.1 - - - -
52B ASP* 2.9 43.9 + - - +
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Residues in contact with GLU 49 (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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4A TYR* 3.0 30.3 + - + -
45B GLU* 2.9 40.3 + - + +
46B GLU* 3.7 10.3 - - - +
47B CYS 3.3 0.2 - - - -
48B GLN* 1.3 76.4 - - - +
50B VAL* 1.3 57.7 + - - +
52B ASP* 3.7 3.1 - - - -
53B THR* 2.4 35.0 + - - +
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Residues in contact with VAL 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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4A TYR* 3.6 28.7 - - + +
7A VAL* 3.9 12.8 - - + -
8A CYS* 4.5 12.1 - - + -
11A LEU* 3.9 17.3 - - + -
75A LEU* 6.4 0.2 - - + -
77A LEU* 4.4 22.7 - - + -
46B GLU 3.0 19.9 + - - +
47B CYS 3.6 3.8 - - - +
48B GLN 3.2 0.4 - - - -
49B GLU* 1.3 75.0 - - - +
51B VAL* 1.3 61.2 + - - +
53B THR* 3.1 3.3 + - - -
54B TYR* 2.8 37.8 + - + +
55B GLY 3.6 1.6 + - - -
58B ILE* 5.6 5.4 - - + -
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Residues in contact with VAL 51 (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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11A LEU* 3.9 19.5 - - + -
32B PHE* 3.7 46.4 - - + -
36B CYS* 3.9 15.5 - - - -
47B CYS 2.8 23.2 + - - +
48B GLN* 3.9 4.9 - - - +
50B VAL* 1.3 72.3 - - - +
52B ASP* 1.3 71.9 + - - +
53B THR 3.1 1.4 + - - -
55B GLY* 2.8 28.9 + - - +
56B SER 4.6 0.3 + - - -
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Residues in contact with ASP 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 GLN* 2.9 31.4 + - - +
49B GLU* 3.7 2.7 - - - +
50B VAL 3.3 0.2 - - - -
51B VAL* 1.3 84.8 - - - +
53B THR* 1.3 61.7 + - - +
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Residues in contact with THR 53 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B GLU* 2.4 24.6 + - - +
50B VAL 3.1 1.4 + - - -
51B VAL 4.2 0.2 - - - -
52B ASP* 1.3 80.3 + - - +
54B TYR* 1.3 98.5 + - + +
55B GLY 3.8 0.9 - - - -
56B SER* 5.6 1.1 + - - -
57B SER* 5.4 1.0 + - - -
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Residues in contact with TYR 54 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LEU* 3.6 51.0 + - + -
76A HIS* 5.4 6.0 - + - +
77A LEU* 3.7 36.2 - - + +
50B VAL* 2.8 19.5 + - + +
53B THR* 1.3 108.5 - - + +
55B GLY* 1.3 64.4 + - - +
56B SER* 3.2 3.6 - - - -
57B SER* 3.0 20.2 + - - -
58B ILE* 3.4 15.2 + - + +
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Residues in contact with GLY 55 (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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25B GLU* 4.7 3.1 - - - +
28B ILE* 4.8 1.4 - - - +
29B LEU* 4.6 3.7 - - - +
32B PHE* 3.4 41.2 - - - -
50B VAL 3.6 2.2 + - - -
51B VAL* 2.8 24.4 + - - -
53B THR 3.8 0.6 - - - -
54B TYR* 1.3 77.2 - - - +
56B SER* 1.3 59.3 + - - +
57B SER 3.2 1.3 + - - -
58B ILE* 3.6 14.5 + - - +
59B LEU 5.0 0.5 + - - -
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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
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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