Contacts of the helix formed by residues 34 - 46 (chain B) in PDB entry 2ZPB
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 HIS 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A TRP* 4.2 9.6 - + - -
40A VAL* 3.7 31.4 + - + +
41A GLU* 5.1 3.1 - - + -
44A LYS* 3.7 38.0 - - + +
47A PHE* 4.3 5.4 - - + -
28B PHE* 3.7 34.9 - + + -
30B ALA 5.3 0.7 - - - -
31B GLU 3.1 28.9 + - - -
32B TRP 3.9 1.3 - - - -
33B GLU* 1.3 76.0 - - - +
35B LEU* 1.3 88.7 + - + +
36B PRO 3.6 0.4 - - - -
37B TYR* 3.7 2.9 + - - +
38B SER* 2.8 25.1 + - - -
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Residues in contact with LEU 35 (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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22A ALA* 3.7 26.2 - - + +
23A TRP* 3.6 39.5 - - + -
25A LEU* 6.4 0.2 - - + -
26A PHE* 4.1 19.3 - - + -
40A VAL* 4.0 18.8 - - + -
32B TRP* 2.9 22.9 + - - +
34B HIS* 1.3 99.7 - - + +
36B PRO* 1.4 68.5 - - + +
38B SER* 3.0 3.2 + - - +
39B LEU* 2.8 36.9 + - + +
77B VAL* 5.6 0.4 - - + -
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Residues in contact with PRO 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 5.8 2.2 - - + -
32B TRP* 3.5 6.7 - - + +
33B GLU* 3.3 19.3 - - - +
35B LEU* 1.4 91.8 - - + +
37B TYR* 1.3 57.9 + - + +
39B LEU* 3.8 2.2 - - + -
40B MET* 2.9 29.9 + - - +
73B TYR* 3.6 31.2 - - + +
76B TYR* 3.6 30.0 - - + +
77B VAL* 3.8 22.7 - - + +
80B VAL* 4.0 7.3 - - + +
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Residues in contact with TYR 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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47A PHE* 3.6 25.8 - + + -
113A SER* 3.9 3.5 + - - -
117A TRP* 3.4 40.1 + + + -
122A LEU* 3.9 22.0 - - + -
123A PRO* 4.5 7.4 - - - +
128A LYS* 4.9 0.2 - - - +
301A NO 5.3 0.2 + - - -
28B PHE* 5.4 1.3 - + - -
33B GLU 5.0 0.2 + - - -
34B HIS* 3.7 3.4 + - - +
35B LEU 3.3 0.2 - - - -
36B PRO* 1.3 82.3 - - + +
38B SER* 1.3 66.1 + - - +
40B MET* 3.3 19.6 + - + +
41B PHE* 3.0 30.6 + - + -
72B TYR* 2.5 40.5 + + - -
73B TYR* 3.8 30.7 + + - -
76B TYR* 4.8 12.8 - + - -
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Residues in contact with SER 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 3.4 12.7 - - - -
40A VAL* 3.4 30.9 - - - +
43A TRP* 3.7 34.8 - - - -
47A PHE* 4.2 0.8 - - - -
34B HIS 2.8 22.5 + - - -
35B LEU* 3.0 13.2 + - - -
37B TYR* 1.3 79.0 - - - +
39B LEU* 1.3 58.3 + - - +
41B PHE* 3.3 2.4 + - - +
42B ALA 3.0 21.5 + - - -
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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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22A ALA 4.8 0.7 - - - +
25A LEU* 3.8 31.0 - - + -
26A PHE* 3.9 26.7 - - + +
29A LEU* 4.0 18.8 - - + -
35A VAL* 4.1 16.8 - - + -
40A VAL* 3.9 22.0 - - + -
35B LEU* 2.8 33.6 + - + +
36B PRO* 4.2 2.0 - - + +
38B SER* 1.3 71.3 - - - +
40B MET* 1.3 64.5 + - - +
42B ALA* 3.3 8.4 + - + +
43B GLY* 2.9 19.6 + - - -
50B PHE* 4.5 0.2 - - - -
80B VAL* 4.3 18.8 - - + +
84B MET* 4.3 3.5 - - - +
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Residues in contact with MET 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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90A GLN* 6.1 1.6 - - - +
117A TRP* 4.4 6.3 - - + -
36B PRO 2.9 18.3 + - - +
37B TYR* 3.3 24.4 + - + +
39B LEU* 1.3 76.4 - - - +
41B PHE* 1.3 89.6 - - + +
43B GLY* 3.1 3.6 + - - -
44B VAL* 2.9 35.1 + - + +
50B PHE* 3.7 4.5 - - - -
52B VAL* 4.6 19.1 - - + -
55B VAL* 3.8 40.8 - - + -
76B TYR* 5.4 3.6 - - - -
80B VAL* 4.1 14.5 - - + +
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Residues in contact with PHE 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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39A TYR* 3.3 14.3 + - - +
43A TRP* 3.6 41.7 - + + +
47A PHE* 4.2 4.5 - + - -
89A PRO* 4.2 17.0 - - + -
90A GLN* 5.2 6.7 - - + -
117A TRP* 3.6 36.1 - + - -
37B TYR 3.0 26.6 + - - -
38B SER 3.7 1.8 - - - +
39B LEU 3.3 0.2 - - - -
40B MET* 1.3 89.7 - - + +
42B ALA* 1.3 60.8 + - - +
44B VAL* 4.3 11.2 - - + +
45B ALA* 2.7 39.2 + - + +
52B VAL* 4.9 11.0 - - + -
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Residues in contact with ALA 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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29A LEU* 6.0 1.3 - - + -
34A LEU 4.9 5.4 - - - +
35A VAL* 5.1 5.2 - - + -
36A PRO* 5.6 0.2 - - + -
39A TYR* 3.4 27.0 + - + -
38B SER 3.0 10.7 + - - +
39B LEU* 3.5 20.0 - - + +
40B MET 3.3 0.2 - - - -
41B PHE* 1.3 76.4 - - - +
43B GLY* 1.3 57.1 + - - +
46B GLU* 3.0 13.9 + - + +
47B LEU* 2.8 41.7 + - + +
84B MET* 5.8 1.3 - - + -
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Residues in contact with GLY 43 (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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39B LEU 2.9 12.6 + - - -
40B MET 3.1 4.0 + - - -
42B ALA* 1.3 77.7 - - - +
44B VAL* 1.3 56.6 + - - +
47B LEU* 3.7 7.1 - - - +
48B GLY 3.1 6.4 + - - -
49B ALA* 2.8 29.7 + - - -
50B PHE* 3.6 26.8 + - - -
84B MET* 4.1 9.1 - - - +
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Residues in contact with VAL 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 MET* 2.9 25.7 + - + +
41B PHE* 4.1 10.5 - - + +
43B GLY* 1.3 76.4 - - - +
45B ALA* 1.3 65.2 + - + +
48B GLY* 3.5 16.8 - - - -
50B PHE* 3.4 34.3 - - + +
51B SER* 3.9 1.8 - - - -
52B VAL* 3.9 35.2 - - + +
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 4.5 4.3 - - - +
43A TRP* 6.4 1.1 - - + -
41B PHE* 2.7 25.8 + - + +
44B VAL* 1.3 78.5 - - + +
46B GLU* 1.3 73.2 + - - +
48B GLY* 4.5 1.1 + - - -
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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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34A LEU 4.9 5.4 - - - +
36A PRO* 4.0 19.2 - - + +
39A TYR* 3.6 43.3 + - + +
42B ALA* 3.0 14.6 + - + +
45B ALA* 1.3 88.1 - - - +
47B LEU* 1.3 69.7 + - + +
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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