Contacts of the helix formed by residues 39 - 56 (chain A) in PDB entry 3JQL
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A TYR* 2.6 34.4 + - - -
37A PRO 3.4 1.2 - - - -
38A VAL* 1.3 79.0 - - - +
40A ASP* 1.3 60.4 + - - +
41A LEU 3.3 4.1 + - - -
42A ASP* 3.0 20.8 + - - +
43A ARG* 2.9 35.8 + - - +
105A PRO* 4.6 4.1 - - - +
107A ASN* 4.1 6.5 - - - +
110A ASN* 3.1 15.5 - - - +
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Residues in contact with ASP 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASP* 1.3 76.9 - - - +
41A LEU* 1.3 61.9 + - - +
43A ARG* 3.1 14.4 + - - +
44A CYS* 3.1 25.1 + - - -
100A CYS* 5.0 2.6 - - - +
103A GLY 4.3 2.4 - - - +
104A ALA* 3.2 32.1 + - - +
105A PRO* 3.6 17.6 - - + +
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.8 22.0 - - + -
25A TYR* 3.6 31.9 - - + -
29A CYS* 4.3 4.7 - - - -
39A ASP* 3.3 3.5 + - - +
40A ASP* 1.3 78.3 + - - +
42A ASP* 1.3 62.8 + - - +
44A CYS* 3.0 20.5 + - - +
45A CYS* 3.2 6.6 + - - -
101A PHE* 3.4 31.0 - - + -
104A ALA* 3.8 18.5 - - + +
105A PRO 3.7 18.7 + - - +
106A TYR* 3.5 33.4 - - + -
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Residues in contact with ASP 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TYR* 3.6 3.8 - - + +
26A GLY* 3.7 6.1 - - - -
27A CYS* 2.7 25.0 + - - +
28A TYR* 2.8 28.4 + - - +
29A CYS* 3.6 10.7 + - - -
37A PRO* 3.3 10.6 - - - +
38A VAL* 2.9 32.1 + - + +
39A ASP* 3.0 21.7 + - - +
41A LEU* 1.3 76.4 - - - +
43A ARG* 1.3 57.9 + - - +
45A CYS* 3.1 2.4 + - - +
46A GLN* 2.8 27.0 + - - +
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Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A THR* 5.0 6.9 - - - +
37A PRO* 3.6 33.7 + - + +
39A ASP* 2.9 20.6 + - - +
40A ASP* 3.1 14.8 + - - +
42A ASP* 1.3 74.3 - - - +
44A CYS* 1.3 64.1 + - - +
46A GLN* 3.7 18.6 + - - +
47A THR* 3.1 28.1 + - - -
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Residues in contact with CYS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASP* 3.1 21.2 + - - -
41A LEU* 3.0 15.5 + - - +
43A ARG* 1.3 74.8 - - - +
45A CYS* 1.3 59.5 + - - +
47A THR* 3.5 5.3 + - - -
48A HIS* 3.1 25.6 + - - +
97A ALA* 4.7 5.2 - - - +
100A CYS* 2.0 68.4 - - + -
101A PHE* 3.7 16.6 - - + -
104A ALA* 4.3 4.0 - - - -
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Residues in contact with CYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TYR* 3.5 4.0 - - - +
29A CYS* 2.0 67.3 - - - +
41A LEU 3.2 2.2 + - - -
42A ASP 3.1 5.9 + - - +
44A CYS* 1.3 76.0 - - - +
46A GLN* 1.3 59.4 + - - +
48A HIS* 3.3 7.9 + - - +
49A ASP* 2.9 33.4 + - - +
101A PHE* 3.4 30.5 - - - -
1B LYS* 4.1 4.3 - - - -
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Residues in contact with GLN 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TYR* 3.5 47.5 + - + +
35A GLY 4.3 0.8 + - - -
37A PRO* 3.4 28.4 - - + +
42A ASP 2.8 18.7 + - - +
43A ARG* 3.3 17.4 + - - +
45A CYS* 1.3 70.7 - - - +
47A THR* 1.3 67.1 + - - +
49A ASP* 3.3 1.7 + - - +
50A ASN* 3.0 37.5 + - - +
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Residues in contact with THR 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ARG 3.1 16.5 + - - -
44A CYS* 3.8 6.0 - - - -
46A GLN* 1.3 77.5 + - - +
48A HIS* 1.3 57.8 + - - +
50A ASN* 3.3 8.5 + - - +
51A CYS* 2.9 31.2 + - + +
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Residues in contact with HIS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 3.4 25.0 - + - -
44A CYS 3.1 15.7 + - - +
45A CYS* 3.5 11.0 - - - +
47A THR* 1.3 78.4 - - - +
49A ASP* 1.3 61.6 + - - +
51A CYS* 3.2 6.8 + - - +
52A TYR* 2.9 61.2 + + - +
93A CYS* 3.4 30.3 - - + -
94A ASP* 2.7 23.1 + - - -
97A ALA* 3.5 18.8 - - + -
101A PHE* 5.9 0.7 - + + -
1B LYS* 4.2 14.6 - - - -
2B LEU* 4.6 2.0 - - + -
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Residues in contact with ASP 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TYR* 3.5 12.7 - - + -
32A GLY 3.1 9.0 - - - +
33A GLY* 3.3 15.0 - - - -
45A CYS 2.9 17.8 + - - +
46A GLN 3.6 4.7 - - - +
48A HIS* 1.3 78.7 + - - +
50A ASN* 1.3 65.5 + - - +
52A TYR* 3.3 10.6 + - - +
53A ASN* 3.0 29.1 + - - +
121A CA 2.2 30.9 - - - -
1B LYS* 3.3 15.2 + - - -
2B LEU* 5.0 2.1 - - - +
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Residues in contact with ASN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TYR* 5.3 2.9 - - - -
46A GLN* 3.0 34.3 + - - +
47A THR* 3.6 7.3 - - - +
49A ASP* 1.3 77.7 - - - +
51A CYS* 1.3 62.1 + - - +
53A ASN* 3.2 15.3 + - - +
54A GLU* 3.0 23.8 + - - +
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Residues in contact with CYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A THR* 2.9 21.7 + - + +
48A HIS* 3.2 8.0 + - - +
50A ASN* 1.3 77.0 - - - +
52A TYR* 1.3 56.0 + - - +
54A GLU* 3.3 7.4 + - - +
55A ALA* 3.0 28.1 + - - +
89A SER 4.5 0.7 - - - -
92A ASP* 5.1 0.9 - - - -
93A CYS* 2.0 55.5 - - + -
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Residues in contact with TYR 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ASN 5.2 2.4 + - - -
2A LEU* 5.5 1.4 + - + +
5A PHE* 4.2 8.1 - - - +
48A HIS* 2.9 37.7 + + - +
49A ASP* 3.5 12.3 - - - +
51A CYS* 1.3 76.4 - - - +
53A ASN* 1.3 56.5 + - - +
55A ALA* 3.2 3.0 + - - +
56A GLU* 2.9 44.2 + - - +
63A PRO* 3.5 37.1 + - + +
64A TYR* 3.7 35.7 - + - -
90A VAL* 4.1 7.6 - - + -
93A CYS* 3.9 17.0 - - + -
94A ASP* 2.6 37.3 + - - -
2B LEU* 4.8 6.2 - - + +
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Residues in contact with ASN 53 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ASP* 3.0 19.4 + - - +
50A ASN* 3.2 18.5 + - - +
52A TYR* 1.3 76.6 - - - +
54A GLU* 1.3 60.1 + - - +
56A GLU* 2.9 29.8 - - - +
57A ASN* 3.0 20.3 - - - +
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASN 3.0 13.1 + - - +
51A CYS* 3.6 9.6 - - - +
53A ASN* 1.3 74.4 - - - +
55A ALA* 1.3 64.8 + - - +
57A ASN* 3.0 38.6 + - - +
58A ILE* 4.3 2.8 + - - +
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A CYS 3.0 17.3 + - - +
52A TYR* 3.2 6.5 + - - +
54A GLU* 1.3 76.3 - - - +
56A GLU* 1.3 56.7 + - - +
57A ASN 3.1 0.2 - - - -
58A ILE* 3.0 36.2 + - - +
61A CYS* 3.4 11.0 - - - +
63A PRO* 4.2 3.8 - - + -
89A SER* 4.3 17.7 - - - -
90A VAL* 4.1 26.7 - - + +
93A CYS* 4.9 2.7 - - - -
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TYR* 2.9 38.5 + - - +
53A ASN* 2.9 29.8 - - - +
54A GLU 3.2 0.6 - - - -
55A ALA* 1.3 74.8 - - - +
57A ASN* 1.3 63.6 + - - +
58A ILE 3.2 8.1 + - - +
61A CYS 3.7 14.0 - - - +
62A ARG* 5.5 0.4 - - - -
63A PRO* 3.6 22.0 - - + +
64A TYR* 5.5 4.2 - - - -
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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