Contacts of the helix formed by residues 45 - 61 (chain A) in PDB entry 3J8B
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 LYS 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A TRP 4.0 0.2 + - - -
44A GLN* 1.3 71.7 - - - +
46A ILE* 1.3 57.5 + - - +
47A HIS 3.2 0.4 - - - -
48A GLU* 2.7 34.7 - - - +
49A PRO 3.8 0.7 - - - -
81A VAL* 5.8 1.0 - - - +
82A ASN* 1.9 48.5 - - + +
85A SER* 4.3 5.0 - - - -
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Residues in contact with ILE 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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44A GLN* 3.0 11.1 - - + +
45A LYS* 1.3 79.6 - - - +
47A HIS* 1.3 52.9 + - - +
49A PRO* 2.5 39.1 - - + +
50A ILE 3.8 0.2 + - - -
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Residues in contact with HIS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 6.2 5.2 - - + -
35A MET* 6.4 1.8 - - + -
40A HIS* 6.3 2.0 - - + -
43A TRP* 5.1 10.5 - - + -
44A GLN 3.3 12.3 + - - +
45A LYS 3.2 0.6 - - - -
46A ILE* 1.3 72.4 - - - +
48A GLU* 1.3 58.1 + - - +
49A PRO 2.8 1.6 - - - -
50A ILE* 2.3 40.1 + - + +
51A MET* 2.8 11.8 + - - -
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Residues in contact with GLU 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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44A GLN 4.5 0.4 + - - -
45A LYS* 2.7 20.6 + - - +
47A HIS* 1.3 74.6 - - - +
49A PRO* 1.3 62.1 - - - +
51A MET* 3.7 12.5 - - - +
52A LEU* 2.9 23.0 + - - +
85A SER* 3.5 32.1 - - - +
89A VAL* 4.9 6.0 - - + +
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Residues in contact with PRO 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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45A LYS 3.8 0.4 - - - -
46A ILE* 2.5 26.7 - - + +
47A HIS 2.7 0.2 - - - -
48A GLU* 1.3 75.2 - - - +
50A ILE* 1.3 54.8 + - - +
52A LEU* 3.1 8.2 + - + +
53A LYS* 3.0 25.5 + - - +
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Residues in contact with ILE 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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8A PRO* 5.8 4.5 - - + +
11A ALA* 6.0 6.5 - - + -
12A LEU* 5.9 8.7 - - + -
31A LEU* 5.6 0.2 - - - +
34A VAL* 6.6 0.7 - - + -
35A MET* 5.6 0.7 - - + -
46A ILE 3.8 0.2 + - - -
47A HIS* 2.3 32.5 + - + +
49A PRO* 1.3 69.7 - - - +
51A MET* 1.3 63.2 + - - +
53A LYS* 3.2 8.8 + - - +
54A TYR* 2.9 22.7 + - - +
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Residues in contact with MET 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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35A MET* 3.8 30.0 - - + +
47A HIS 2.8 9.7 + - - +
48A GLU* 3.7 18.6 - - - +
50A ILE* 1.3 73.1 - - - +
52A LEU* 1.3 58.2 + - - +
54A TYR* 3.2 6.6 + - - +
55A LEU* 2.9 29.2 + - - +
74A TYR* 5.1 10.5 - - + -
89A VAL* 5.4 6.5 - - + -
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLU 2.9 14.0 + - - +
49A PRO* 3.3 11.9 - - + +
51A MET* 1.3 75.6 - - - +
53A LYS* 1.3 57.6 - - - +
55A LEU* 3.2 9.0 + - - +
56A GLU* 2.9 28.5 + - - +
88A ASP 5.9 0.2 - - - -
89A VAL* 4.4 14.5 - - + +
92A ALA* 4.2 26.6 - - + +
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Residues in contact with LYS 53 (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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12A LEU* 6.1 4.9 - - + -
49A PRO 3.0 12.8 + - - +
50A ILE* 3.2 11.2 + - - +
52A LEU* 1.3 76.6 - - - +
54A TYR* 1.3 60.8 + - - +
56A GLU* 3.1 10.0 + - - +
57A LEU* 3.0 21.3 + - - +
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Residues in contact with TYR 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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28A LEU* 5.4 3.8 - - - +
31A LEU* 3.4 39.0 - - + +
32A TYR* 4.9 1.8 - - - +
35A MET* 5.7 2.0 - - + -
50A ILE 2.9 12.1 + - - +
51A MET* 3.5 11.9 - - - +
53A LYS* 1.3 76.0 - - - +
55A LEU* 1.3 62.3 + - - +
57A LEU* 3.2 16.0 + - - +
58A CYS* 3.3 13.0 + - - +
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Residues in contact with LEU 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 MET 2.9 13.4 + - - +
52A LEU* 3.2 12.8 + - - +
54A TYR* 1.3 76.6 - - - +
56A GLU* 1.3 58.7 + - - +
58A CYS* 2.9 26.3 - - - +
59A VAL* 3.3 7.3 + - - +
67A ALA* 5.2 9.5 - - + +
71A LEU* 6.5 1.3 - - + -
89A VAL* 5.5 4.5 - - + +
92A ALA* 6.4 0.2 - - + -
93A TYR* 5.0 20.0 - - + +
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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 LEU 2.9 13.7 + - - +
53A LYS* 3.3 13.7 - - - +
55A LEU* 1.3 78.6 - - - +
57A LEU* 1.3 62.7 + - - +
59A VAL* 3.0 22.9 + - - +
60A ASP* 3.6 3.1 + - - +
93A TYR* 6.2 0.9 - - - +
96A MET* 4.8 15.4 - - + +
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Residues in contact with LEU 57 (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 LEU* 5.2 13.5 - - + -
53A LYS 3.0 11.9 + - - +
54A TYR* 3.2 9.8 + - - +
56A GLU* 1.3 75.2 - - - +
58A CYS* 1.3 54.8 + - - +
59A VAL 3.0 0.2 - - - -
60A ASP* 2.8 31.2 + - - +
61A LEU* 3.2 11.1 + - - +
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Residues in contact with CYS 58 (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 LEU* 5.2 8.7 - - + +
54A TYR 3.3 10.3 + - - +
55A LEU* 2.9 21.3 - - - +
57A LEU* 1.3 74.3 - - - +
59A VAL* 1.3 55.1 + - - +
61A LEU* 3.5 4.1 + - - +
62A ARG* 3.0 22.0 + - - -
63A LYS* 3.0 25.6 + - + +
66A LEU* 5.8 1.6 - - + -
67A ALA* 4.2 24.2 - - + +
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Residues in contact with VAL 59 (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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55A LEU 3.3 4.6 + - - +
56A GLU* 3.0 18.9 + - - +
57A LEU 3.0 1.2 - - - -
58A CYS* 1.3 77.7 - - - +
60A ASP* 1.3 63.9 + - - +
62A ARG* 3.0 15.1 + - - +
96A MET* 4.5 22.4 - - + +
97A ALA* 5.1 7.0 - - + +
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Residues in contact with ASP 60 (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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56A GLU 3.6 3.6 + - - +
57A LEU* 2.8 18.1 + - - +
59A VAL* 1.3 75.9 - - - +
61A LEU* 1.3 57.5 + - - +
62A ARG* 3.4 2.3 + - - +
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Residues in contact with LEU 61 (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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24A LYS* 6.1 5.2 - - + -
25A GLN* 6.3 4.0 - - + -
28A LEU* 5.9 6.3 - - + -
57A LEU 3.2 8.4 + - - +
58A CYS* 3.5 7.6 + - - +
60A ASP* 1.3 76.9 - - - +
62A ARG* 1.3 69.9 + - - +
63A LYS* 3.1 12.7 + - + +
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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