Contacts of the helix formed by residues 50 - 64 (chain B) in PDB entry 4ZGK
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 MET 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B GLU 3.9 14.6 - - - +
24B GLN 3.3 11.3 + - - +
26B THR* 3.1 19.7 + - - +
28B VAL* 3.8 24.5 - - + -
49B THR* 1.3 71.9 - - - +
51B LYS* 1.3 60.4 + - - +
53B VAL* 3.3 7.5 + - - +
54B LEU* 3.0 30.1 + - + +
100B TYR* 3.6 43.3 - - + +
103B ILE* 3.6 35.7 - - + -
104B TYR* 3.9 18.4 - - + +
107B LEU* 4.1 11.9 - - - -
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Residues in contact with LYS 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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201A 4NX 3.3 48.5 + - + +
24B GLN* 3.1 44.6 + - + +
25B GLU* 2.3 38.5 + - - +
49B THR* 3.2 8.7 - - - +
50B MET* 1.3 75.0 - - - +
52B GLU* 1.3 57.8 + - - +
54B LEU* 3.5 12.6 + - + +
55B PHE 3.0 21.1 + - - -
100B TYR* 5.5 0.4 - - - +
201B 4NX 4.7 2.1 + - - -
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Residues in contact with GLU 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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55A PHE* 4.0 12.6 - - + -
59A GLN* 2.8 30.5 + - - +
201A 4NX 4.3 8.4 - - + -
45B LYS* 3.0 28.5 + - - -
48B TYR* 3.4 15.2 - - + -
49B THR* 2.9 40.2 + - - +
51B LYS* 1.3 77.3 - - - +
53B VAL* 1.3 65.7 + - - +
55B PHE* 3.0 16.5 + - - +
56B TYR* 3.1 22.4 + - + -
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Residues in contact with VAL 53 (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 VAL* 3.9 18.4 - - + -
30B PRO* 4.9 3.1 - - + -
34B LEU* 4.8 6.3 - - + -
38B LEU* 4.0 22.7 - - + +
48B TYR* 3.7 19.9 - - + +
49B THR 3.1 13.7 + - - +
50B MET* 3.4 10.8 - - - +
52B GLU* 1.3 74.1 - - - +
54B LEU* 1.3 58.1 + - - +
56B TYR* 3.2 6.5 + - - +
57B LEU* 2.9 44.9 + - + +
103B ILE* 4.2 23.1 - - + -
107B LEU* 5.1 1.8 - - + -
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Residues in contact with LEU 54 (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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24B GLN* 6.4 0.7 - - - -
50B MET* 3.0 18.0 + - + +
51B LYS* 3.6 12.1 - - + +
53B VAL* 1.3 74.9 - - - +
55B PHE* 1.3 64.4 + - - +
57B LEU* 3.3 2.6 + - + -
58B GLY 3.0 18.5 + - - -
99B ILE* 4.3 0.2 - - + -
100B TYR* 3.6 33.2 - - + +
103B ILE* 3.7 27.4 - - + -
201B 4NX 3.2 81.9 - - + +
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Residues in contact with PHE 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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52A GLU* 3.9 14.8 - - + -
55A PHE* 3.3 57.7 - + + -
56A TYR* 3.6 28.7 - + - -
201A 4NX 4.1 2.7 - - + -
51B LYS 3.0 13.4 + - - +
52B GLU 3.0 8.9 + - - +
54B LEU* 1.3 79.4 - - - +
56B TYR* 1.3 75.1 + + - +
58B GLY* 3.1 8.7 + - - -
59B GLN* 3.2 39.2 + - + +
201B 4NX 3.4 45.3 + + + -
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Residues in contact with TYR 56 (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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41A VAL 4.8 6.4 + - - -
55A PHE* 3.7 26.5 - + - -
56A TYR* 4.9 7.8 - + - -
59A GLN* 4.5 9.6 + - - +
38B LEU* 3.6 22.2 - - + +
41B VAL* 3.6 24.0 - - + +
42B GLY 4.1 5.4 + - - -
43B ALA* 3.6 46.7 - - + -
44B GLN 4.6 2.3 + - - -
45B LYS* 5.7 1.4 - - - +
48B TYR* 3.8 19.7 - + - -
52B GLU* 3.1 28.0 + - + -
53B VAL* 3.9 1.3 - - - +
55B PHE* 1.3 88.8 - + - +
57B LEU* 1.3 61.2 + - - +
59B GLN* 3.1 6.0 + - + +
60B TYR* 2.8 28.6 + - - +
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Residues in contact with LEU 57 (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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34B LEU* 4.5 12.8 - - + -
37B LEU* 4.0 22.0 - - + -
38B LEU* 4.3 4.7 - - + +
53B VAL* 2.9 28.5 + - + +
54B LEU* 3.7 6.3 - - - +
56B TYR* 1.3 75.6 - - - +
58B GLY* 1.3 57.7 + - - +
60B TYR* 3.2 4.9 + - + +
61B ILE* 2.8 37.8 + - + +
82B LEU* 4.1 26.2 - - + -
86B PHE* 4.2 8.7 - - + -
103B ILE* 3.7 34.3 - - + -
201B 4NX 4.0 18.6 - - + -
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Residues in contact with GLY 58 (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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54B LEU 3.0 10.5 + - - -
55B PHE 3.1 4.2 + - - -
57B LEU* 1.3 75.0 - - - +
59B GLN* 1.3 67.2 + - - +
61B ILE* 3.5 2.9 + - - +
62B MET* 3.1 23.4 + - - +
67B TYR* 4.9 1.7 + - - -
201B 4NX 3.3 39.5 - - - +
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Residues in contact with GLN 59 (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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45A LYS* 3.1 29.7 + - - +
52A GLU* 2.7 30.1 + - - +
56A TYR* 4.4 8.4 + - - +
41B VAL* 4.1 16.4 - - + +
55B PHE* 3.2 42.7 + - + +
56B TYR* 3.1 10.6 + - + +
58B GLY* 1.3 76.4 - - - +
60B TYR* 1.3 66.6 + - - +
62B MET* 3.3 7.9 + - - +
63B THR* 3.0 34.7 + - + +
201B 4NX 5.7 2.4 - - - -
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Residues in contact with TYR 60 (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 LEU* 3.5 47.8 - - + -
40B SER* 4.1 18.4 - - - -
41B VAL* 3.7 16.0 - - + +
56B TYR 2.8 12.4 + - - +
57B LEU* 3.3 9.0 - - + +
59B GLN* 1.3 75.0 - - - +
61B ILE* 1.3 69.8 + - + +
63B THR* 3.1 2.0 + - - -
64B LYS* 2.9 62.7 + - + +
66B LEU* 4.0 5.8 - - + -
80B ASP* 2.7 35.9 + - - -
81B LEU* 4.1 13.0 - - + +
82B LEU* 4.0 14.8 - - + -
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Residues in contact with ILE 61 (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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57B LEU* 2.8 27.8 + - + +
58B GLY* 3.8 4.3 - - - +
60B TYR* 1.3 77.3 - - + +
62B MET* 1.3 61.1 + - - +
64B LYS 3.8 0.3 - - - -
65B ARG* 3.1 17.2 + - - -
66B LEU* 3.1 21.7 + - + -
67B TYR* 3.6 39.5 + - + -
75B VAL* 4.0 17.0 - - + -
82B LEU* 3.9 29.4 - - + -
91B PHE* 4.2 8.7 - - + -
201B 4NX 3.6 36.3 - - + -
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Residues in contact with MET 62 (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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45A LYS* 5.1 18.4 - - - +
58B GLY 3.1 16.9 + - - +
59B GLN* 3.7 8.1 - - - +
61B ILE* 1.3 76.9 - - - +
63B THR* 1.3 86.5 + - + +
65B ARG* 3.1 41.4 + - - +
67B TYR* 4.6 13.7 - - + -
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Residues in contact with THR 63 (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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44A GLN* 6.2 1.6 - - - +
45A LYS* 5.9 4.9 - - + -
41B VAL* 3.9 13.6 - - + +
59B GLN* 3.0 21.2 + - + +
60B TYR* 3.1 11.1 + - - -
62B MET* 1.3 100.7 - - + +
64B LYS* 1.3 75.0 + - - +
65B ARG* 3.2 10.8 + - - +
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Residues in contact with LYS 64 (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 SER* 5.4 4.0 + - - -
41B VAL* 6.0 0.2 - - + -
60B TYR* 2.9 52.8 + - + +
63B THR* 1.3 88.6 + - - +
65B ARG* 1.3 70.0 + - - +
66B LEU* 3.4 25.3 + - + +
80B ASP* 3.8 11.8 + - - +
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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