Contacts of the helix formed by residues 37 - 59 (chain F) in PDB entry 3ZP0
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 ASP 37 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F TYR 2.8 13.8 + - - +
23F GLY* 3.5 3.0 - - - -
24F TYR* 3.0 36.7 + - + -
35F ALA 3.7 0.2 + - - -
36F ALA* 1.3 68.4 - - - +
38F LYS* 1.3 59.5 + - - +
39F GLU* 3.8 8.5 - - - +
40F SER* 2.4 41.5 + - - +
41F THR* 2.7 31.7 + - - -
118F LEU* 4.0 17.0 - - + +
121F LYS* 4.5 4.6 + - - -
153F ARG 4.3 5.7 - - - +
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Residues in contact with LYS 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F ALA* 4.0 15.9 - - + +
37F ASP* 1.3 71.3 - - - +
39F GLU* 1.3 57.1 + - - +
41F THR* 3.6 3.8 - - - -
42F GLN* 2.8 39.4 + - - +
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Residues in contact with GLU 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ASP* 3.8 9.6 - - - +
38F LYS* 1.3 79.3 - - - +
40F SER* 1.3 58.4 + - - +
42F GLN* 3.3 5.0 + - - +
43F LYS* 3.0 64.4 + - - +
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Residues in contact with SER 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F TYR* 3.7 18.6 - - - -
37F ASP* 2.4 33.0 + - - +
39F GLU* 1.3 77.0 - - - +
41F THR* 1.3 65.9 + - - +
43F LYS* 3.4 12.0 + - - +
44F ALA* 2.9 24.4 + - - +
114F ASN* 5.0 13.1 + - - -
118F LEU* 4.0 12.3 - - - +
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Residues in contact with THR 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ASP 5.1 1.6 - - - +
20F GLY* 4.0 10.9 - - - -
21F TRP* 3.4 36.9 + - + +
22F TYR* 3.6 19.6 + - - -
36F ALA* 5.9 0.2 - - - -
37F ASP 2.7 23.2 + - - -
38F LYS* 3.4 5.8 + - - -
39F GLU 3.3 0.6 - - - -
40F SER* 1.3 77.0 - - - +
42F GLN* 1.3 57.4 + - - +
44F ALA* 3.1 5.1 + - - +
45F ILE* 2.8 45.5 + - + +
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Residues in contact with GLN 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F LYS* 2.8 22.1 + - + +
39F GLU* 3.7 4.5 - - - +
41F THR* 1.3 73.7 - - - +
43F LYS* 1.3 61.7 + - - +
45F ILE* 3.2 22.9 + - - +
46F ASP* 3.0 56.7 + - - +
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Residues in contact with LYS 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F GLU* 3.0 43.4 + - - +
40F SER* 3.7 13.7 - - - +
41F THR 3.4 0.2 - - - -
42F GLN* 1.3 75.9 - - - +
44F ALA* 1.3 57.2 + - - +
46F ASP* 3.5 9.1 + - - +
47F GLY* 3.0 24.3 + - - -
110F PHE* 4.3 6.1 - - + -
114F ASN* 5.9 2.2 - - - +
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Residues in contact with ALA 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F TRP* 3.9 11.9 - - + -
22F TYR* 3.3 29.4 - - + +
40F SER 2.9 17.0 + - - +
41F THR 3.1 5.1 + - - +
43F LYS* 1.3 73.1 - - - +
45F ILE* 1.3 67.2 + - - +
47F GLY* 3.3 0.7 + - - -
48F VAL* 3.0 29.5 + - - +
110F PHE* 3.7 13.4 - - + -
111F HIS* 4.5 0.9 - - + -
114F ASN* 3.7 8.9 - - - +
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Residues in contact with ILE 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F TRP* 3.6 26.7 - - + -
41F THR* 2.8 32.8 + - + +
42F GLN* 3.2 28.7 + - - +
44F ALA* 1.3 76.8 - - - +
46F ASP* 1.3 57.4 + - - +
48F VAL* 3.4 1.4 + - - +
49F THR* 2.7 47.1 + - - +
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Residues in contact with ASP 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F GLN* 3.0 40.6 + - - +
43F LYS* 3.7 8.1 - - - +
45F ILE* 1.3 77.0 - - - +
47F GLY* 1.3 62.9 + - - +
49F THR* 3.3 5.2 + - - -
50F ASN* 3.0 39.3 + - - +
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Residues in contact with GLY 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F LYS 3.0 15.4 + - - -
44F ALA 3.3 3.3 + - - -
46F ASP* 1.3 76.8 - - - +
48F VAL* 1.3 56.6 + - - +
50F ASN* 3.5 6.9 + - - +
51F LYS* 3.1 28.7 + - - +
110F PHE* 4.6 13.0 - - - -
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Residues in contact with VAL 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318E ALA 4.5 3.1 - - - +
319E THR* 3.7 52.9 - - + +
21F TRP* 4.7 7.4 - - + -
44F ALA 3.0 17.0 + - - +
45F ILE 4.1 2.2 - - - +
47F GLY* 1.3 72.6 - - - +
49F THR* 1.3 65.2 + - - +
51F LYS* 3.4 9.8 + - + +
52F VAL* 3.1 27.0 + - + +
107F THR* 4.4 11.0 - - + +
110F PHE* 4.2 14.6 - - + -
111F HIS* 4.2 12.8 - - + +
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Residues in contact with THR 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F ILE* 2.7 33.6 + - - +
46F ASP* 3.7 4.9 - - - -
48F VAL* 1.3 76.1 - - - +
50F ASN* 1.3 68.9 + - - +
52F VAL* 3.4 4.8 + - - +
53F ASN* 3.2 40.4 + - - +
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Residues in contact with ASN 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F ASP* 3.0 31.4 + - - +
47F GLY* 3.8 5.8 - - - +
49F THR* 1.3 79.7 - - - +
51F LYS* 1.3 57.3 + - - +
53F ASN* 3.3 10.7 + - - +
54F SER* 2.8 33.3 + - - +
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Residues in contact with LYS 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E LEU* 5.8 2.0 - - + -
318E ALA 5.6 1.3 - - - +
47F GLY 3.1 18.1 + - - +
48F VAL* 3.6 12.8 - - + +
49F THR 3.2 0.2 - - - -
50F ASN* 1.3 75.5 - - - +
52F VAL* 1.3 57.4 + - + +
54F SER* 3.0 8.2 + - - -
55F ILE* 2.7 55.3 + - + +
103F GLU* 2.8 43.2 + - + +
106F ARG* 4.0 5.3 - - - +
107F THR* 2.8 37.9 + - - +
110F PHE* 6.0 1.1 - - - +
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Residues in contact with VAL 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E GLN* 3.8 26.0 - - - +
36E ILE* 5.3 0.4 - - + -
317E LEU* 4.2 23.6 - - + -
318E ALA 5.5 1.3 - - - +
319E THR* 4.3 23.3 - - + -
48F VAL* 3.1 19.1 + - + +
49F THR* 3.4 6.0 + - - +
51F LYS* 1.3 80.0 - - + +
53F ASN* 1.3 61.5 + - - +
55F ILE* 3.3 6.7 + - - +
56F ILE* 2.8 50.5 + - + +
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Residues in contact with ASN 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F THR* 3.2 30.3 + - - +
50F ASN* 3.6 11.1 + - - +
52F VAL* 1.3 81.7 - - - +
54F SER* 1.3 55.7 + - - +
56F ILE* 3.3 10.1 + - - +
57F ASP* 2.9 44.1 + - - +
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Residues in contact with SER 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F ASN* 2.8 19.6 + - - +
51F LYS* 3.4 11.2 - - - -
53F ASN* 1.3 72.0 - - - +
55F ILE* 1.3 64.2 - - - +
57F ASP* 4.0 3.1 - - - +
58F LYS* 3.0 33.4 + - - +
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Residues in contact with ILE 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E ILE* 4.9 11.0 - - + -
295E PHE* 5.6 1.8 - - + -
317E LEU* 3.7 42.4 - - + -
51F LYS* 2.7 37.5 + - + +
52F VAL* 3.5 8.3 - - - +
54F SER* 1.3 74.8 - - - +
56F ILE* 1.3 66.3 + - + +
58F LYS* 3.9 2.6 - - - +
59F MET* 3.3 24.2 + - + +
99F LEU* 4.0 33.1 - - + +
100F VAL* 5.2 4.0 - - + -
103F GLU* 3.9 19.7 - - + -
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Residues in contact with ILE 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E GLN* 4.7 9.2 - - - +
36E ILE* 5.1 6.1 - - + -
294E PRO* 3.6 42.5 - - + +
295E PHE* 5.7 2.0 - - - -
317E LEU* 5.9 0.4 - - + -
52F VAL* 2.8 42.4 + - + +
53F ASN* 3.7 11.7 - - - +
55F ILE* 1.3 76.7 - - + +
57F ASP* 1.3 66.5 + - - +
59F MET* 3.0 22.2 + - - +
60F ASN* 3.3 12.2 + - + -
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Residues in contact with ASP 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F ASN* 2.9 35.0 + - - +
54F SER* 4.3 3.1 - - - +
56F ILE* 1.3 77.6 - - - +
58F LYS* 1.3 63.5 + - - +
59F MET 3.0 5.3 + - - -
60F ASN* 3.0 36.4 + - - +
61F THR* 5.3 0.3 + - - -
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Residues in contact with LYS 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F SER* 3.0 21.2 + - - +
55F ILE* 3.9 6.1 - - - +
56F ILE 3.3 0.4 - - - -
57F ASP* 1.3 78.0 - - - +
59F MET* 1.3 63.6 + - + +
60F ASN 3.6 0.4 - - - -
61F THR* 4.3 12.7 + - - +
92F TRP* 5.0 5.4 - - - -
99F LEU* 5.3 7.6 - - + -
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Residues in contact with MET 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294E PRO* 6.2 0.4 - - + -
295E PHE* 3.5 29.2 - - + -
308E LYS* 3.4 10.5 - - + +
55F ILE* 3.3 15.9 - - + +
56F ILE 3.0 11.3 + - - +
58F LYS* 1.3 81.6 - - + +
60F ASN* 1.3 61.2 + - - +
61F THR 3.2 3.4 - - - -
62F GLN* 3.2 38.3 - - - +
92F TRP* 4.3 16.2 - - + -
95F ASN* 3.7 9.6 - - + +
96F ALA* 3.4 36.6 - - + +
99F LEU* 3.7 25.6 - - + -
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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
------------------------------------------------------------
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