Contacts of the helix formed by residues 69 - 82 (chain J) in PDB entry 4J7X
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 ALA 69 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66J ASP* 3.2 22.2 + - + +
67J LEU 3.2 1.5 - - - +
68J GLY* 1.3 81.3 - - - +
70J GLU* 1.3 67.0 + - - +
71J ALA* 4.5 5.6 - - + +
72J GLY 4.6 2.7 - - - +
73J LEU* 3.1 25.4 + - - +
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Residues in contact with GLU 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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114F SER* 2.5 28.9 + - - -
115F THR* 4.2 17.7 - - + +
118F ASN* 4.0 14.0 + - - +
69J ALA* 1.3 71.0 - - - +
71J ALA* 1.3 67.6 + - - +
73J LEU* 3.3 7.4 + - - +
74J GLN* 3.0 57.6 + - - +
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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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69J ALA* 3.5 3.8 - - + +
70J GLU* 1.3 76.6 - - - +
72J GLY* 1.3 62.7 + - - +
74J GLN* 3.3 7.8 + - - +
75J GLN* 3.0 33.4 + - - +
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Residues in contact with GLY 72 (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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65J ALA* 3.4 14.0 - - - +
66J ASP* 3.2 31.9 + - - +
67J LEU* 4.2 2.3 - - - +
69J ALA* 3.6 4.9 + - - +
70J GLU 3.3 0.8 - - - -
71J ALA* 1.3 78.3 - - - +
73J LEU* 1.3 62.8 + - - +
75J GLN* 3.1 17.7 + - - +
76J LEU 3.2 9.5 + - - -
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Residues in contact with LEU 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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114F SER* 3.7 31.0 - - - +
66J ASP 3.8 2.2 + - - -
67J LEU* 4.1 20.9 - - + +
69J ALA 3.1 17.3 + - - +
70J GLU* 3.7 7.4 - - - +
72J GLY* 1.3 74.1 - - - +
74J GLN* 1.3 65.2 + - - +
76J LEU* 3.2 5.6 + - + +
77J LEU* 3.0 44.8 + - + +
122J ALA 5.6 0.4 - - - +
126J THR* 4.6 4.3 - - + -
127J SER* 4.1 39.5 - - - +
130J CYS* 4.5 9.2 - - + -
131J LEU* 4.8 4.3 - - + +
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Residues in contact with GLN 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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112F SER 5.7 1.4 + - - -
114F SER* 3.7 12.5 + - - +
70J GLU* 3.0 41.3 + - + +
71J ALA* 3.7 5.8 - - - +
73J LEU* 1.3 81.8 - - - +
75J GLN* 1.3 55.5 + - - +
77J LEU* 3.7 21.4 - - - +
78J GLY* 2.7 33.4 + - - -
81J ARG* 6.0 0.2 + - - -
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Residues in contact with GLN 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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63J VAL* 4.2 8.6 - - + +
64J PRO* 3.1 23.4 - - - +
65J ALA* 4.2 6.6 - - + +
71J ALA* 3.0 21.3 + - - +
72J GLY* 3.1 13.0 + - - +
74J GLN* 1.3 77.2 - - - +
76J LEU* 1.3 57.6 + - - +
78J GLY* 3.3 1.7 + - - -
79J ALA* 3.0 28.8 + - - +
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Residues in contact with LEU 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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8J LEU* 4.9 9.9 - - + -
10J THR* 4.2 9.0 - - + -
35J VAL* 4.5 11.4 - - + -
37J SER* 4.0 17.3 - - - +
63J VAL* 4.1 34.4 - - + +
65J ALA* 4.9 1.3 - - + -
67J LEU* 3.8 31.0 - - + -
72J GLY 3.2 6.9 + - - +
73J LEU* 3.2 10.7 + - + +
75J GLN* 1.3 77.8 - - - +
77J LEU* 1.3 64.0 + - - +
79J ALA* 3.3 2.2 + - + +
80J LEU* 3.1 21.3 + - + +
131J LEU* 4.1 30.3 - - + -
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Residues in contact with LEU 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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112F SER* 4.8 12.6 - - - +
114F SER* 6.5 0.2 - - - -
73J LEU* 3.0 32.0 + - + +
74J GLN* 3.7 29.2 - - - +
76J LEU* 1.3 75.4 - - - +
78J GLY* 1.3 61.7 + - - +
80J LEU* 3.2 20.6 - - + +
81J ARG* 3.3 24.0 + - - +
130J CYS* 4.2 5.2 - - + +
131J LEU* 4.0 27.8 - - + -
134J SER* 3.5 36.6 - - - +
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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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74J GLN 2.7 22.7 + - - -
75J GLN* 3.7 1.8 - - - -
77J LEU* 1.3 71.1 - - - +
79J ALA* 1.3 62.9 + - - +
81J ARG* 3.2 30.3 + - - +
82J GLU* 3.3 16.8 + - - +
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Residues in contact with ALA 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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35J VAL* 5.8 0.7 - - + -
61J VAL* 5.3 4.5 - - + -
63J VAL* 3.9 28.3 - - + -
75J GLN 3.0 15.9 + - - +
76J LEU* 3.3 6.7 + - + +
78J GLY* 1.3 75.2 - - - +
80J LEU* 1.3 62.6 + - - +
82J GLU* 3.3 18.5 + - - +
83J LEU* 3.1 25.0 + - + +
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Residues in contact with LEU 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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8J LEU* 3.3 35.4 - - + -
76J LEU* 3.1 12.8 + - + +
77J LEU* 3.2 18.4 - - + +
79J ALA* 1.3 76.9 - - - +
81J ARG* 1.3 61.3 + - + +
83J LEU* 3.5 28.5 + - + +
85J ARG* 4.8 7.8 + - - -
131J LEU* 4.5 5.8 - - + -
134J SER* 3.6 44.6 - - - +
135J VAL* 3.6 18.8 - - + +
138J ALA* 4.4 11.8 - - + +
139J PHE* 5.3 5.0 - - + -
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Residues in contact with ARG 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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74J GLN* 6.0 0.2 + - - -
77J LEU* 3.3 36.3 + - - +
78J GLY* 3.2 17.5 + - - +
80J LEU* 1.3 80.7 - - - +
82J GLU* 1.3 62.2 + - + +
83J LEU 3.3 5.9 + - - +
85J ARG* 4.9 10.6 + - - +
138J ALA* 6.1 2.0 - - - -
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Residues in contact with GLU 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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78J GLY 3.3 20.7 + - - +
79J ALA* 3.3 11.7 + - - +
81J ARG* 1.3 79.1 - - + +
83J LEU* 1.3 65.8 + - - +
84J PRO* 3.5 6.1 - - - +
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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