Contacts of the helix formed by residues 48 - 65 (chain J) in PDB entry 5JGH
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 SER 48 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H T 2.4 31.2 + - - -
16H T 3.8 25.4 - - - -
7I A 4.2 10.4 + - - -
8I A 3.7 5.4 - - - -
46J PRO 4.0 0.8 + - - -
47J THR* 1.3 85.6 - - - +
49J ALA* 1.3 65.5 + - - +
50J TYR* 3.9 8.2 + - - +
51J PHE* 3.2 13.5 + - - +
52J LEU* 3.8 4.3 + - - +
96J ARG* 3.1 14.3 - - - +
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Residues in contact with ALA 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H T 6.3 2.1 - - - -
47J THR 3.8 0.4 + - - -
48J SER* 1.3 74.5 - - - +
50J TYR* 1.3 63.2 + - - +
51J PHE 3.1 1.0 + - - -
52J LEU* 3.2 23.7 + - - +
53J TYR* 3.3 11.3 + - - +
81J TRP* 3.9 16.8 - - + -
92J TYR* 3.7 29.3 - - - +
93J ILE* 4.0 11.7 - - + -
96J ARG* 3.8 16.1 - - + +
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Residues in contact with TYR 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H A 3.1 52.0 + + + +
15H T 3.1 37.9 - + - +
16H T 6.1 1.4 - - - -
48J SER* 3.2 2.5 + - - +
49J ALA* 1.3 78.9 - - - +
51J PHE* 1.3 82.3 + + - +
53J TYR* 3.3 8.6 + + - +
54J LEU* 2.8 38.4 + - + +
74J SER* 3.5 7.6 + - - -
77J ALA* 3.5 35.2 - - + +
78J GLY* 4.0 1.6 - - - -
81J TRP* 3.6 40.7 - + + -
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Residues in contact with PHE 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H A 3.5 22.0 - + - -
15H T 4.0 3.4 - - - -
8I A 3.2 66.6 - + + -
9I T 3.4 52.9 - + - -
47J THR* 3.1 21.8 - - + -
48J SER* 3.2 1.6 + - - +
49J ALA 3.1 0.8 - - - -
50J TYR* 1.3 96.4 - + - +
52J LEU* 1.3 57.6 + - - +
54J LEU* 3.5 11.1 - - + +
55J GLN* 2.6 37.0 + - + +
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Residues in contact with LEU 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J THR* 4.9 11.2 - - - +
48J SER 4.0 6.1 - - - +
49J ALA* 3.2 17.2 + - - +
51J PHE* 1.3 75.4 - - - +
53J TYR* 1.3 65.1 + - - +
55J GLN* 3.2 10.6 + - - +
56J ASP* 3.0 29.5 + - - +
92J TYR* 3.5 39.3 - - + +
95J GLU* 3.8 25.6 - - + +
96J ARG* 4.0 16.6 - - + +
99J LEU* 4.1 15.5 - - + -
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Residues in contact with TYR 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J ALA 3.3 3.0 + - - +
50J TYR* 3.3 12.3 - + - +
52J LEU* 1.3 79.8 - - - +
54J LEU* 1.3 63.9 + - - +
56J ASP 3.5 0.3 + - - -
57J HIS* 3.3 56.8 + + - +
61J PHE* 3.5 18.1 - + - -
77J ALA* 3.9 20.4 - - + -
80J LYS* 3.2 24.8 + - + +
81J TRP* 3.6 40.6 - + + -
84J LEU* 3.5 33.9 - - + +
88J ILE* 5.3 1.1 - - + -
92J TYR* 3.4 23.1 - + + -
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Residues in contact with LEU 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H A 4.2 9.0 - - + +
9I T 4.1 20.0 - - - +
50J TYR* 2.8 49.3 + - + +
51J PHE* 3.3 16.8 + - + +
52J LEU 3.1 0.2 - - - -
53J TYR* 1.3 76.2 - - + +
55J GLN* 1.3 66.6 + - - +
57J HIS* 4.4 2.0 - - - +
58J ARG* 3.0 49.9 + - + +
61J PHE* 4.4 6.5 - - + -
73J ILE* 5.4 6.1 - - + -
74J SER* 5.4 3.8 - - - +
77J ALA* 3.9 21.8 - - + -
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Residues in contact with GLN 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I A 5.2 2.9 - - - +
9I T 4.5 15.2 + - - +
51J PHE* 2.6 25.0 + - + +
52J LEU* 3.2 12.6 + - - +
54J LEU* 1.3 73.8 - - - +
56J ASP* 1.3 66.6 + - - +
57J HIS 3.5 0.2 + - - -
58J ARG* 3.5 33.7 + - - +
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Residues in contact with ASP 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J LEU 3.0 15.2 + - - +
53J TYR 3.7 0.7 - - - +
55J GLN* 1.3 84.1 - - - +
57J HIS* 1.3 76.5 + - + +
58J ARG 3.5 0.6 + - - -
59J SER* 4.7 5.0 + - - -
60J GLN* 4.6 9.4 + - - +
91J LYS* 4.5 4.5 + - - -
92J TYR* 2.3 37.9 + - - +
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Residues in contact with HIS 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J TYR* 3.3 44.1 + + - +
54J LEU 3.3 3.8 + - - -
56J ASP* 1.3 99.6 + - + +
58J ARG* 1.3 58.3 + - - +
59J SER 3.6 1.1 - - - -
60J GLN* 3.8 25.7 + - + -
61J PHE* 3.0 55.9 + + + -
88J ILE* 6.1 1.2 - - - +
92J TYR* 3.8 12.5 + + - -
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Residues in contact with ARG 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I T 3.7 36.7 + - - -
10I A 3.3 44.2 + - - +
54J LEU* 3.0 31.0 + - + +
55J GLN* 3.5 41.4 + - - +
56J ASP 3.5 2.4 - - - -
57J HIS* 1.3 74.5 - - - +
59J SER* 1.3 70.1 + - - +
60J GLN 3.2 0.5 + - - -
61J PHE* 3.3 2.2 + - - +
62J VAL* 3.0 39.5 + - + +
73J ILE* 5.6 2.9 - - + -
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Residues in contact with SER 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J ASP 4.7 6.6 + - - -
58J ARG* 1.3 79.3 - - - +
60J GLN* 1.3 73.5 + - - +
62J VAL* 3.9 8.3 - - - -
63J LYS* 2.9 47.2 + - - +
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Residues in contact with GLN 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J ASP 4.6 5.1 + - - +
57J HIS* 3.4 36.1 + - + +
58J ARG 3.1 0.4 - - - -
59J SER* 1.3 82.7 + - - +
61J PHE* 1.3 69.9 + - + +
63J LYS* 4.1 0.8 - - - +
64J GLU* 2.7 47.2 + - - +
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Residues in contact with PHE 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53J TYR* 3.5 29.4 - + - -
54J LEU* 4.4 9.0 - - + -
57J HIS* 3.0 49.3 + + + +
58J ARG* 3.9 2.7 - - - +
60J GLN* 1.3 75.3 - - + +
62J VAL* 1.3 53.2 + - - +
64J GLU* 3.5 9.4 - - - +
65J ASN* 2.6 41.1 + - - +
73J ILE* 4.0 20.0 - - + -
76J ILE* 4.8 14.6 - - + -
77J ALA* 3.7 30.3 - - + -
80J LYS* 4.3 22.0 - - + -
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Residues in contact with VAL 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I A 6.1 0.9 - - - +
11I T 4.9 14.8 - - - +
58J ARG* 3.0 29.4 + - + +
59J SER* 3.6 9.6 - - - +
61J PHE* 1.3 76.4 - - - +
63J LYS* 1.3 73.9 + - + +
65J ASN 3.1 25.6 - - - +
66J PRO* 3.4 8.7 - - - +
70J PRO* 6.3 0.4 - - + -
73J ILE* 3.6 33.4 - - + -
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Residues in contact with LYS 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I T 6.1 0.4 - - - -
59J SER* 2.9 39.8 + - - +
60J GLN* 4.1 0.9 - - - +
62J VAL* 1.3 85.1 - - + +
64J GLU* 1.3 66.1 + - + +
65J ASN 3.2 0.6 + - - -
66J PRO* 4.3 10.9 - - - +
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Residues in contact with GLU 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60J GLN* 2.7 39.3 + - - +
61J PHE* 4.1 8.3 + - - +
63J LYS* 1.3 78.3 - - + +
65J ASN* 1.3 67.7 + - + +
66J PRO* 3.8 6.1 - - - +
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Residues in contact with ASN 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61J PHE* 2.6 18.2 + - + +
62J VAL* 3.1 9.8 - - - +
64J GLU* 1.3 84.4 - - - +
66J PRO* 1.3 63.9 - - - +
67J THR* 3.5 5.3 + - - -
68J LEU* 3.5 27.8 + - + +
73J ILE* 3.7 24.3 - - + +
76J ILE* 4.6 17.0 - - - +
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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