Contacts of the helix formed by residues 33 - 45 (chain B) in PDB entry 2Z9O
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 ARG 33 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU 4.0 0.6 + - - -
32B SER* 1.3 72.2 - - - +
34B ASP* 1.3 90.6 + - - +
36B LYS* 2.9 13.3 + - - +
37B ARG* 2.5 90.9 + - + +
73B LEU* 5.7 3.4 - - - +
81B ASP* 3.6 12.7 + - - -
156B GLU* 3.6 9.5 + - - +
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Residues in contact with ASP 34 (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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32B SER* 4.0 6.0 - - - +
33B ARG* 1.3 112.6 + - - +
35B GLN* 1.3 64.1 + - - +
37B ARG* 3.1 16.5 + - - +
38B MET* 2.9 21.7 + - - +
67B TYR* 4.1 5.2 + - - +
81B ASP* 3.1 35.8 - - - +
84B GLN* 5.0 6.8 - - + +
85B ALA* 3.9 17.9 - - + -
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Residues in contact with GLN 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.1 26.5 - - + +
32B SER* 2.8 35.8 + - - +
34B ASP* 1.3 75.5 - - - +
36B LYS* 1.3 51.8 + - - +
38B MET* 2.6 8.9 + - - +
39B LEU* 2.5 34.5 + - - +
85B ALA* 3.0 22.7 + - + -
88B SER* 3.2 14.7 + - - -
89B PHE* 3.0 65.4 - - + +
92B LYS* 3.8 9.7 + - - +
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Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA 3.5 9.0 + - - +
29B TYR* 3.2 22.8 + - - +
31B LEU* 3.1 30.9 + - + +
32B SER 2.6 14.6 + - - +
33B ARG* 3.0 15.9 - - + +
35B GLN* 1.3 71.2 - - - +
37B ARG* 1.3 65.8 + - + +
38B MET 2.9 1.2 + - - -
39B LEU* 3.0 18.8 + - - +
40B TYR* 3.1 13.3 + - - +
146B PHE* 4.5 10.4 - - + -
151B LEU* 3.7 31.4 - - + +
152B SER* 5.2 7.6 + - - +
154B THR* 2.8 32.5 - - - +
155B LYS 3.5 7.7 + - - -
156B GLU* 5.8 0.4 - - + -
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Residues in contact with ARG 37 (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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33B ARG* 2.5 90.8 + - + +
34B ASP* 3.2 10.3 + - - +
36B LYS* 1.3 73.4 - - + +
38B MET* 1.3 60.4 + - - +
40B TYR* 3.9 9.1 + - - +
41B LEU* 3.8 17.7 - - - +
67B TYR* 3.4 23.9 + - + +
71B PHE* 2.7 63.6 + - + +
73B LEU* 3.7 22.0 - - - +
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Residues in contact with MET 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASP 2.9 9.8 + - - +
35B GLN* 2.6 19.3 + - - +
37B ARG* 1.3 70.3 - - - +
39B LEU* 1.3 53.8 + - - +
40B TYR 2.8 15.6 + - - -
41B LEU* 3.1 15.4 + - + +
42B PHE* 3.2 39.7 + - + -
62B ILE* 3.3 22.2 - - + -
67B TYR* 4.1 12.3 - - + +
82B ILE* 3.3 53.4 - - + +
85B ALA* 5.8 3.1 - - + -
86B LEU* 4.3 18.2 - - - -
89B PHE* 4.4 7.2 - - + -
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Residues in contact with LEU 39 (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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28B ALA* 4.1 13.9 - - + -
31B LEU* 3.4 27.6 - - + -
35B GLN 2.5 14.7 + - - +
36B LYS* 3.0 12.3 + - - +
38B MET* 1.3 72.3 - - - +
40B TYR* 1.3 56.3 + - - +
42B PHE* 3.5 13.6 - - + +
43B VAL* 3.0 37.3 + - + +
89B PHE* 4.5 8.2 - - + -
114B TRP* 4.1 26.7 - - + -
139B PHE* 4.3 10.5 - - + -
142B LEU* 4.1 19.5 - - + -
146B PHE* 3.7 26.2 - - + -
151B LEU* 4.6 0.9 - - + -
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Residues in contact with TYR 40 (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 LYS 3.1 12.7 + - - +
37B ARG* 3.9 7.4 - - - +
38B MET 2.8 2.0 + - - -
39B LEU* 1.3 75.7 - - - +
41B LEU* 1.3 67.7 + - + +
42B PHE 2.7 14.7 + - - -
43B VAL* 3.0 8.7 + - + +
44B ASP* 2.9 30.4 + - + +
146B PHE* 3.5 38.1 - + + -
152B SER* 3.6 19.5 - - - +
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Residues in contact with LEU 41 (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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37B ARG 3.8 14.8 - - - +
38B MET* 3.1 7.9 + - - +
40B TYR* 1.3 87.6 - - + +
42B PHE* 1.3 68.0 + - + +
44B ASP* 3.8 12.5 - - - +
45B GLN* 3.5 20.2 + - - +
61B GLU 5.9 1.1 - - - +
62B ILE* 4.5 18.4 - - + -
67B TYR* 4.1 31.9 - - + -
70B ILE* 6.0 7.6 - - + -
71B PHE* 5.2 9.9 - - + -
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Residues in contact with PHE 42 (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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38B MET* 3.3 35.4 - - + -
39B LEU* 3.5 21.5 - - + +
40B TYR 2.7 0.6 + - - -
41B LEU* 1.3 78.1 - - + +
43B VAL* 1.3 68.3 + - - +
44B ASP 2.9 1.8 - - - -
45B GLN* 2.7 20.1 + - - +
46B ILE* 3.1 11.8 + - - -
60B CYS* 3.8 33.4 - - + -
62B ILE* 3.3 28.7 - - + -
89B PHE* 4.8 4.5 - + - -
114B TRP* 6.4 1.1 - + - -
115B PHE* 3.7 32.5 - + - -
129B VAL* 4.2 21.8 - - + -
131B ILE* 5.0 8.7 - - + -
139B PHE* 4.8 9.9 - + + -
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Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.0 28.9 + - + +
40B TYR* 3.6 10.8 - - + +
42B PHE* 1.3 78.6 - - - +
44B ASP* 1.3 67.9 + - - +
46B ILE 3.1 23.7 - - - +
139B PHE* 4.3 18.1 - - + -
142B LEU* 4.6 8.5 - - + -
143B GLN* 3.2 41.3 + - + +
146B PHE* 4.2 24.0 - - + -
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Residues in contact with ASP 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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40B TYR* 2.9 25.8 + - + +
41B LEU* 3.8 10.9 - - - +
42B PHE 2.7 4.2 + - - -
43B VAL* 1.3 76.2 - - - +
45B GLN* 1.3 84.0 + - - +
46B ILE 4.3 0.7 - - - +
143B GLN* 6.1 0.9 - - - +
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Residues in contact with GLN 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 LEU* 3.5 17.7 + - - +
42B PHE* 2.7 9.7 + - - +
44B ASP* 1.3 93.9 - - - +
46B ILE* 1.3 61.9 + - + +
59B ILE 3.9 12.8 - - - +
60B CYS* 4.1 22.3 - - - +
61B GLU* 3.9 23.5 + - - +
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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