Contacts of the helix formed by residues 69 - 84 (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 ARG 69 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12I A 4.7 7.4 - - - +
13I A 3.6 38.8 + - - +
14I A 3.7 26.0 + - - -
67J THR 4.0 1.3 + - - +
68J LEU* 1.3 78.6 - - - +
70J PRO* 1.3 75.4 - - + +
71J ALA* 3.4 6.1 - - + +
72J GLU* 3.0 23.0 + - + +
73J ILE* 3.0 18.2 + - - +
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Residues in contact with PRO 70 (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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12H A 4.5 2.7 - - + -
13H T 4.5 0.9 - - - -
10I A 4.0 22.1 - - + +
11I T 3.3 46.7 - - - +
12I A 3.6 28.0 - - + +
62J VAL* 6.3 0.4 - - + -
68J LEU 4.5 0.7 - - - +
69J ARG* 1.3 88.4 - - + +
71J ALA* 1.3 54.8 + - - +
73J ILE* 2.7 32.2 + - + +
74J SER* 3.0 14.1 + - - -
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Residues in contact with ALA 71 (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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12H A 3.6 34.5 + - - +
13H T 3.3 37.3 + - - +
69J ARG* 3.4 4.8 - - + +
70J PRO* 1.3 79.3 - - - +
72J GLU* 1.3 60.2 + - + +
74J SER* 3.5 2.9 + - - -
75J LYS* 3.0 30.2 + - - +
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Residues in contact with GLU 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H T 5.3 1.6 + - - -
68J LEU* 3.6 29.4 - - + +
69J ARG* 3.2 35.5 - - + +
70J PRO 3.0 0.8 + - - -
71J ALA* 1.3 77.5 - - + +
73J ILE* 1.3 65.5 + - - +
75J LYS* 3.2 30.4 + - - +
76J ILE* 3.2 24.9 + - - +
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Residues in contact with ILE 73 (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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54J LEU* 5.4 6.1 - - + -
58J ARG* 5.2 3.1 - - + +
61J PHE* 4.0 27.1 - - + +
62J VAL* 3.6 31.6 - - + -
65J ASN* 3.7 30.3 - - + +
68J LEU* 3.9 27.1 - - + +
69J ARG 3.0 14.9 + - - +
70J PRO* 2.7 18.0 + - + +
72J GLU* 1.3 71.0 - - - +
74J SER* 1.3 57.7 + - - +
76J ILE* 3.1 8.7 + - + +
77J ALA* 2.8 27.9 + - + +
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Residues in contact with SER 74 (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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13H T 2.3 32.1 + - - -
14H A 2.9 45.5 + - - +
9I T 5.2 0.2 + - - -
10I A 4.3 4.5 + - - -
50J TYR* 3.5 4.3 + - - -
54J LEU* 5.4 4.1 - - - +
70J PRO 3.0 7.8 + - - -
71J ALA 3.8 5.6 - - - -
72J GLU 3.3 0.2 - - - -
73J ILE* 1.3 77.4 - - - +
75J LYS* 1.3 57.4 + - - +
77J ALA* 3.3 2.4 + - - +
78J GLY 2.8 25.3 + - - -
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Residues in contact with LYS 75 (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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13H T 3.3 45.1 + - - +
14H A 3.9 19.6 - - - +
71J ALA 3.0 17.5 - - - +
72J GLU* 3.5 26.4 + - - +
73J ILE 3.2 0.6 - - - -
74J SER* 1.3 77.5 - - - +
76J ILE* 1.3 63.5 + - + +
78J GLY* 3.1 2.6 + - - -
79J GLU* 2.9 37.8 + - - +
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Residues in contact with ILE 76 (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* 4.8 15.9 - - + -
65J ASN* 4.6 13.7 - - - +
68J LEU* 4.3 19.7 - - + -
72J GLU 3.2 11.4 + - - +
73J ILE* 3.1 12.7 + - + +
75J LYS* 1.3 75.8 - - + +
77J ALA* 1.3 58.8 + - - +
79J GLU* 3.0 26.7 + - - +
80J LYS* 2.8 50.6 + - + +
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Residues in contact with ALA 77 (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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50J TYR* 3.5 21.2 - - + +
53J TYR* 3.9 3.8 - - + -
54J LEU* 3.9 15.0 - - + -
61J PHE* 3.7 34.1 - - + -
73J ILE 2.8 19.8 + - - +
74J SER* 4.4 0.9 - - - -
76J ILE* 1.3 73.3 - - - +
78J GLY* 1.3 57.4 + - - +
80J LYS* 3.8 3.3 - - - +
81J TRP* 3.0 28.1 + - - +
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Residues in contact with GLY 78 (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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14H A 3.3 32.1 - - - -
15H T 4.3 2.5 - - - -
50J TYR* 3.8 5.3 + - - -
74J SER 2.8 13.1 + - - -
75J LYS 3.5 2.7 - - - -
77J ALA* 1.3 74.6 - - - +
79J GLU* 1.3 64.0 + - - +
81J TRP* 3.2 3.7 + - - +
82J GLN* 3.0 29.9 + - - +
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Residues in contact with GLU 79 (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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75J LYS* 2.9 29.7 + - - +
76J ILE* 3.5 26.4 - - - +
78J GLY* 1.3 75.5 - - - +
80J LYS* 1.3 66.0 + - + +
82J GLN* 3.3 6.9 + - - +
83J ASN* 3.2 32.1 + - - +
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Residues in contact with LYS 80 (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* 3.2 23.0 + - + +
61J PHE* 4.3 17.0 - - + -
76J ILE* 2.8 33.6 + - + +
77J ALA* 3.8 5.6 - - - +
78J GLY 3.2 0.2 - - - -
79J GLU* 1.3 81.2 - - + +
81J TRP* 1.3 56.9 + - - +
83J ASN* 3.4 5.8 + - + +
84J LEU* 3.0 31.2 + - - +
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Residues in contact with TRP 81 (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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15H T 3.3 15.2 + - - -
16H T 2.9 25.5 + - - -
49J ALA* 3.9 17.7 - - + -
50J TYR* 3.6 36.1 - + + +
53J TYR* 3.6 43.7 - + + -
77J ALA 3.0 17.7 + - - +
78J GLY 3.2 4.0 + - - +
80J LYS* 1.3 78.8 - - - +
82J GLN* 1.3 87.0 + - - +
84J LEU* 3.6 25.2 + - + +
89J LYS* 3.1 48.1 + - + +
92J TYR* 4.2 14.1 - + + -
93J ILE* 4.5 7.6 - - + -
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Residues in contact with GLN 82 (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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15H T 3.5 24.4 + - - +
16H T 3.4 24.1 + - - -
78J GLY 3.0 13.9 + - - +
79J GLU* 3.9 7.0 - - - +
80J LYS 3.3 0.2 - - - -
81J TRP* 1.3 105.2 - - - +
83J ASN* 1.3 66.4 + - - +
84J LEU 3.5 1.7 + - - +
89J LYS* 4.0 13.5 + - - +
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Residues in contact with ASN 83 (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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79J GLU* 3.2 19.7 + - - +
80J LYS* 3.7 6.4 - - + +
82J GLN* 1.3 79.9 - - - +
84J LEU* 1.3 65.8 + - - +
85J GLU* 3.6 4.2 + - - +
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Residues in contact with LEU 84 (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 41.5 - - + +
80J LYS 3.0 14.7 + - - +
81J TRP* 3.6 24.7 + - + +
82J GLN 3.3 3.8 - - - +
83J ASN* 1.3 81.0 - - - +
85J GLU* 1.3 87.9 + - - +
86J ALA* 3.3 2.3 + - - -
88J ILE* 3.7 31.0 - - + -
89J LYS* 3.6 31.1 - - + +
92J TYR* 5.0 0.2 - - + -
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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