Contacts of the helix formed by residues 31 - 49 (chain F) in PDB entry 4JCQ
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 ASN 31 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F GLU* 3.3 36.2 + - - +
30F ILE* 1.3 74.8 - - - +
32F GLN* 1.3 59.7 + - - +
33F GLU* 3.4 21.7 + - - +
34F LEU* 2.9 35.1 + - - +
35F ALA 2.9 23.9 + - - -
63F HIS* 4.0 11.9 - - + +
66F ALA* 3.4 13.9 - - - +
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Residues in contact with GLN 32 (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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31F ASN* 1.3 75.7 - - - +
33F GLU* 1.3 65.6 + - - +
35F ALA* 3.4 7.7 + - - +
36F GLU* 2.9 29.9 + - - +
63F HIS* 5.5 1.0 - - + +
65F GLU* 4.4 15.8 - - + +
66F ALA* 3.8 6.5 - - + +
27G TYR* 3.8 9.0 - - + +
28G GLY* 3.5 26.2 - - - +
58G ASN* 3.2 39.3 + - - +
60G GLN* 3.1 31.1 + - - +
88G TRP* 3.4 10.7 - - - +
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Residues in contact with GLU 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F ASN* 3.4 26.1 + - - +
32F GLN* 1.3 84.8 + - - +
34F LEU* 1.3 59.7 + - - +
36F GLU* 3.4 9.6 + - - +
37F ASP* 3.1 22.7 + - - +
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Residues in contact with LEU 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F LEU 4.9 9.2 - - - +
26F ILE* 3.7 25.1 - - + -
27F TYR 5.0 11.9 - - - +
28F GLY 5.7 0.4 - - - +
29F GLU 4.0 15.0 - - - +
30F ILE* 4.1 10.8 - - + -
31F ASN* 2.9 20.8 + - - +
33F GLU* 1.3 73.1 - - - +
35F ALA* 1.3 61.1 + - - +
37F ASP* 3.2 13.2 + - - +
38F VAL* 2.8 47.4 + - + +
70F ILE* 3.7 23.8 - - + -
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Residues in contact with ALA 35 (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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31F ASN 2.9 16.3 + - - +
32F GLN* 3.6 10.1 - - - +
33F GLU 3.3 0.2 - - - -
34F LEU* 1.3 77.7 - - - +
36F GLU* 1.3 53.9 + - - +
38F VAL* 3.9 0.9 - - - +
39F SER* 2.7 38.3 + - - -
66F ALA* 3.9 25.8 - - + +
69F THR* 4.5 4.5 - - + -
70F ILE* 3.8 17.3 - - + +
27G TYR* 3.6 14.1 - - + -
58G ASN* 5.4 0.9 - - - +
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Residues in contact with GLU 36 (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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32F GLN 2.9 17.1 + - - +
33F GLU* 3.6 8.6 - - - +
34F LEU 3.2 0.2 - - - -
35F ALA* 1.3 74.3 - - - +
37F ASP* 1.3 59.3 + - - +
40F LYS* 3.0 58.2 + - + +
25G LEU* 3.6 31.6 - - + +
27G TYR* 3.5 34.5 + - + +
37G ASP* 5.5 2.8 - - - +
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Residues in contact with ASP 37 (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 GLU* 5.6 1.9 - - - +
33F GLU 3.1 15.1 + - - +
34F LEU* 3.6 18.3 - - + +
36F GLU* 1.3 77.9 - - - +
38F VAL* 1.3 57.1 + - - +
40F LYS* 3.5 9.8 + - - +
41F GLN* 3.1 48.5 + - - +
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Residues in contact with VAL 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F VAL* 4.4 13.0 - - + -
25F LEU 4.8 2.2 - - - +
26F ILE* 3.8 28.9 - - + -
34F LEU* 2.8 43.2 + - + +
35F ALA 4.0 2.9 - - - +
37F ASP* 1.3 68.9 - - - +
39F SER* 1.3 61.8 + - - +
41F GLN* 3.3 10.3 + - - +
42F LEU* 2.9 49.4 + - + +
55F ILE* 5.5 0.9 - - + -
70F ILE* 4.0 25.4 - - + -
73F MET* 6.3 0.2 - - + -
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Residues in contact with SER 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F ALA 2.7 24.4 + - - -
36F GLU 3.6 4.5 - - - -
38F VAL* 1.3 76.8 - - - +
40F LYS* 1.3 56.6 + - - +
42F LEU* 3.9 5.6 - - - +
43F LEU* 3.0 37.4 + - - +
69F THR* 3.9 2.9 - - - +
70F ILE* 5.5 1.2 - - - +
73F MET* 3.7 23.9 - - - +
25G LEU* 3.7 12.8 - - - -
27G TYR* 2.9 26.6 + - - -
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Residues in contact with LYS 40 (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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36F GLU* 3.0 49.5 + - + +
37F ASP* 3.7 9.9 - - - +
39F SER* 1.3 77.1 - - - +
41F GLN* 1.3 57.0 + - + +
43F LEU* 3.9 5.0 - - + -
44F LEU* 3.0 31.1 + - - +
18G LEU* 3.8 31.6 - - + +
25G LEU* 3.5 19.1 - - + -
37G ASP* 6.0 0.4 + - - -
41G GLN* 5.9 3.9 - - - +
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Residues in contact with GLN 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F THR 4.3 4.2 - - - +
24F VAL* 3.6 40.0 - - + +
25F LEU 4.6 5.9 + - - -
37F ASP* 3.1 49.6 + - - +
38F VAL* 3.3 9.1 + - - +
40F LYS* 1.3 77.5 - - + +
42F LEU* 1.3 56.1 + - - +
44F LEU* 3.4 6.8 + - - +
45F LEU* 3.0 38.2 + - + +
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Residues in contact with LEU 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F VAL* 4.2 15.3 - - + -
38F VAL* 2.9 37.6 + - + +
39F SER* 3.9 3.8 - - - +
41F GLN* 1.3 76.2 - - - +
43F LEU* 1.3 58.8 + - - +
45F LEU* 3.5 4.4 + - - +
46F GLU* 3.0 29.3 + - - +
53F ILE* 4.3 12.3 - - + -
55F ILE* 4.2 19.3 - - + -
70F ILE 4.9 0.7 - - - +
73F MET* 4.2 22.7 - - + +
74F ILE* 4.1 25.1 - - + +
77F ILE* 3.9 31.6 - - + +
81F VAL* 5.0 2.0 - - + -
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Residues in contact with LEU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F SER 3.0 22.2 + - - +
40F LYS* 4.0 6.1 - - + +
42F LEU* 1.3 74.3 - - - +
44F LEU* 1.3 64.8 + - - +
46F GLU* 3.5 10.6 + - - +
47F SER* 3.1 23.9 + - - -
73F MET* 3.9 26.2 - - + -
76F PHE* 5.1 0.9 - - + -
77F ILE* 4.6 2.5 - - + -
18G LEU* 5.3 4.7 - - + -
21G THR* 4.2 12.5 - - + +
23G THR* 3.7 30.7 - - + +
25G LEU* 4.1 16.4 - - + -
56G PHE* 4.3 11.2 - - + -
186G ARG* 3.5 27.8 - - - +
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Residues in contact with LEU 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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19F ILE* 3.8 27.4 - - + -
40F LYS 3.0 19.7 + - - +
41F GLN* 3.7 7.6 - - - +
43F LEU* 1.3 76.7 - - - +
45F LEU* 1.3 63.6 + - + +
47F SER* 2.7 26.3 + - - +
48F ILE* 3.3 33.8 + - + +
14G LEU* 3.6 33.0 - - + +
17G LYS* 4.2 9.0 - - + -
18G LEU* 4.0 26.4 - - + +
21G THR* 5.3 0.7 - - - -
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Residues in contact with LEU 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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19F ILE* 3.5 42.4 - - + +
22F ARG* 2.8 52.5 + - - +
23F THR 4.6 2.2 - - - +
24F VAL* 3.8 26.9 - - + -
41F GLN* 3.0 22.8 + - + +
42F LEU* 3.9 0.7 - - - +
44F LEU* 1.3 77.6 - - + +
46F GLU* 1.3 62.8 + - - +
48F ILE* 3.3 4.1 + - + +
49F SER 3.2 8.7 + - - +
53F ILE* 3.8 32.5 - - + -
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Residues in contact with GLU 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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22F ARG* 4.6 0.2 - - - +
42F LEU 3.0 17.5 + - - +
43F LEU* 3.7 9.3 - - - +
45F LEU* 1.3 77.4 - - - +
47F SER* 1.3 60.8 + - - +
49F SER 3.2 20.0 + - - +
50F ASN* 4.8 4.2 + - - +
77F ILE* 3.4 19.3 - - + +
78F LYS* 3.0 29.5 + - + +
79F PRO* 3.7 23.0 - - + +
186G ARG* 2.9 50.7 + - - +
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Residues in contact with SER 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 LEU 3.1 7.8 + - - -
44F LEU* 2.7 30.5 + - - +
46F GLU* 1.3 77.5 - - - +
48F ILE* 1.3 60.5 + - - +
17G LYS* 3.9 22.1 - - - +
20G ASP* 6.4 0.2 - - - -
21G THR* 3.5 29.7 - - - +
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Residues in contact with ILE 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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19F ILE* 3.7 29.8 - - + -
22F ARG* 4.1 9.0 - - - +
44F LEU* 3.3 34.7 + - + +
45F LEU* 3.6 12.1 - - + +
46F GLU 3.2 0.6 - - - -
47F SER* 1.3 80.8 - - - +
49F SER* 1.3 65.4 + - - +
14G LEU* 5.8 0.9 - - + -
17G LYS* 3.9 35.0 + - + +
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Residues in contact with SER 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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22F ARG* 3.3 23.6 + - - -
45F LEU 3.2 10.6 + - - +
46F GLU 3.2 17.0 + - - +
48F ILE* 1.3 85.1 - - - +
50F ASN* 1.3 60.9 + - - +
51F ASP* 3.3 27.0 + - - +
79F PRO* 3.7 5.0 - - - +
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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