Contacts of the helix formed by residues 49 - 63 (chain A) in PDB entry 5JKC
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 HIS 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A LEU* 3.8 25.1 - - + -
46A ASP* 2.9 35.1 + - + +
48A LYS* 1.3 103.0 + - + +
50A HIS* 1.3 65.3 + - - +
51A LYS 3.3 2.6 + - - -
52A ALA* 3.4 8.4 + - - +
53A MET* 2.9 23.1 + - + +
105A ASP* 5.9 2.6 + - - -
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Residues in contact with HIS 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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37A GLU* 5.3 3.7 + - + +
41A LEU* 3.0 48.1 + - + +
42A PRO* 3.6 16.7 - - + +
45A LEU* 2.8 29.3 + - + -
46A ASP 3.2 14.6 - - - -
47A ALA* 3.2 25.5 + - + +
49A HIS* 1.3 76.5 - - - +
51A LYS* 1.3 67.2 + - + +
53A MET* 3.3 3.4 + - - +
54A MET* 3.1 28.3 + - - +
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Residues in contact with LYS 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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37A GLU* 5.9 1.1 - - - -
47A ALA 5.0 8.2 + - - -
48A LYS* 5.5 9.7 - - - +
49A HIS 3.3 0.4 - - - -
50A HIS* 1.3 83.9 - - + +
52A ALA* 1.3 63.2 + - + +
54A MET* 3.3 4.4 + - - +
55A GLU* 3.1 32.8 + - - +
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Residues in contact with ALA 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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48A LYS 5.5 2.0 + - - +
49A HIS* 3.4 10.5 + - - +
50A HIS 3.3 0.4 - - - -
51A LYS* 1.3 77.8 - - - +
53A MET* 1.3 66.4 + - - +
55A GLU* 3.4 16.4 + - - +
56A ARG* 3.0 23.9 + - - +
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Residues in contact with MET 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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36A LEU* 6.3 0.4 - - + -
41A LEU* 4.2 14.1 - - + -
45A LEU* 3.8 22.2 - - + -
49A HIS* 2.9 18.4 + - + +
50A HIS 3.3 4.5 + - - +
52A ALA* 1.3 77.9 - - - +
54A MET* 1.3 61.1 + - + +
56A ARG* 3.1 9.1 + - - +
57A VAL* 2.8 31.2 + - + +
107A PHE* 3.2 42.0 - - + -
108A VAL* 3.9 18.6 - - + -
111A LEU* 3.8 13.2 - - + -
112A PHE* 3.7 27.6 - - - -
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Residues in contact with MET 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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33A LEU* 4.4 14.4 - - + +
34A LYS* 5.9 0.4 - - - -
36A LEU* 5.1 6.7 - - - -
37A GLU* 3.5 61.2 - - + +
41A LEU* 3.8 11.9 - - + -
50A HIS 3.1 14.8 + - - +
51A LYS* 3.8 4.0 - - - +
53A MET* 1.3 77.3 - - - +
55A GLU* 1.3 61.8 - - - +
57A VAL* 3.1 21.0 + - + +
58A GLU* 2.8 57.9 + - + +
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Residues in contact with GLU 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 LYS* 3.1 26.6 + - - +
52A ALA* 3.6 16.5 - - - +
53A MET 3.3 0.2 - - - -
54A MET* 1.3 74.7 - - - +
56A ARG* 1.3 62.1 + - - +
58A GLU* 3.6 9.2 + - - +
59A ASN* 3.1 34.4 + - - +
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Residues in contact with ARG 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 ALA 3.0 14.1 + - - +
53A MET* 3.3 11.9 - - - +
55A GLU* 1.3 78.2 - - - +
57A VAL* 1.3 55.9 + - - +
59A ASN* 3.4 7.2 + - - +
60A ALA* 3.0 26.3 + - - +
108A VAL* 3.8 15.8 - - - +
112A PHE* 3.4 54.8 - - + +
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Residues in contact with VAL 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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33A LEU* 4.5 25.4 - - + -
36A LEU* 5.2 6.1 - - + -
53A MET* 2.8 29.5 + - + +
54A MET* 3.7 22.2 - - + +
56A ARG* 1.3 69.2 - - - +
58A GLU* 1.3 67.5 + - - +
60A ALA* 3.0 14.0 + - - +
61A VAL* 3.2 18.8 + - + +
111A LEU* 4.1 19.1 - - + -
112A PHE* 3.6 23.1 - - + -
115A LEU* 4.7 11.2 - - + -
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Residues in contact with GLU 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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33A LEU* 6.5 0.2 - - - -
37A GLU* 5.0 3.8 - - - +
54A MET* 2.8 57.8 + - + +
55A GLU* 3.8 8.5 - - - +
57A VAL* 1.3 70.8 - - - +
59A ASN* 1.3 59.2 + - - +
61A VAL* 3.2 8.9 + - - +
62A LYS* 2.8 57.0 + - - +
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Residues in contact with ASN 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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18A ARG* 5.7 6.6 + - - +
55A GLU* 3.1 24.3 + - - +
56A ARG* 3.7 6.6 - - - +
58A GLU* 1.3 75.3 - - - +
60A ALA* 1.3 62.8 + - - +
62A LYS* 3.3 29.5 + - - +
63A ASP* 3.4 15.2 + - - +
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Residues in contact with ALA 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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21A TRP* 5.1 0.7 - - + -
56A ARG 3.0 13.9 + - - +
57A VAL* 3.0 14.3 + - - +
59A ASN* 1.3 75.4 - - - +
61A VAL* 1.3 60.9 + - + +
63A ASP 3.1 3.5 - - - +
112A PHE* 4.6 8.1 - - + -
115A LEU* 4.5 22.2 - - + -
119A LYS* 2.7 41.6 + - - +
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Residues in contact with VAL 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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20A PRO* 3.6 2.6 - - - +
21A TRP* 2.9 56.3 + - + +
24A ILE* 2.6 45.7 - - + +
29A VAL* 6.2 0.2 - - + -
33A LEU* 4.2 21.8 - - + -
57A VAL* 3.2 16.7 + - + +
58A GLU* 3.7 8.1 - - - +
59A ASN 3.2 0.2 - - - -
60A ALA* 1.3 80.9 - - + +
62A LYS* 1.3 60.0 + - + +
63A ASP 3.3 0.4 - - - -
115A LEU* 5.7 3.6 - - + -
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Residues in contact with LYS 62 (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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18A ARG* 5.1 11.3 + - - +
19A SER* 3.5 4.7 + - - +
20A PRO* 3.5 24.9 - - + +
24A ILE* 5.1 5.6 - - + -
58A GLU* 2.8 48.6 + - - +
59A ASN* 3.3 20.2 + - - +
61A VAL* 1.3 77.3 - - + +
63A ASP* 1.3 59.1 + - - +
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Residues in contact with ASP 63 (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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18A ARG* 3.2 43.2 + - - +
19A SER 3.2 21.2 + - - -
21A TRP 4.7 1.3 - - - -
59A ASN 3.4 11.1 + - - +
60A ALA 3.1 2.6 - - - +
61A VAL 3.3 0.4 - - - -
62A LYS* 1.3 78.5 - - - +
64A PHE* 1.3 62.7 + - - +
65A GLN* 3.0 36.3 + - - +
119A LYS* 2.2 33.2 + - - -
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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