Contacts of the helix formed by residues 63 - 79 (chain J) in PDB entry 5C3I
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 63 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99D ASP* 3.1 41.3 + - + +
60J LEU* 3.5 31.5 - - - +
62J ILE* 1.3 80.0 - - - +
64J LYS* 1.3 65.0 + - - +
66J PRO* 3.7 23.5 - - + +
67J PHE* 3.4 21.0 + - - +
36K ARG* 3.7 15.6 - - - +
79L ARG 5.8 0.4 + - - -
80L ASP 4.1 5.1 + - - -
82L ARG* 2.8 31.3 + - - +
83L ALA* 4.4 0.2 - - - +
84L ILE* 3.4 23.4 - - - +
87L LEU* 4.4 10.5 - - + +
88L ASP* 2.9 34.3 + - - -
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Residues in contact with LYS 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62J ILE 4.8 1.1 - - - +
63J ARG* 1.3 72.2 - - - +
65J LEU* 1.3 62.2 + - - +
67J PHE* 3.0 5.5 + - - +
68J GLN 2.9 24.4 + - - -
90J MET* 5.8 6.7 - - - +
93J GLN* 3.8 27.6 - - - +
87L LEU 3.4 9.3 + - - +
88L ASP* 3.4 26.0 + - - +
89L ALA* 4.2 9.4 - - - -
90L TYR* 3.7 33.0 - - + -
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Residues in contact with LEU 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D ALA* 4.5 12.8 - - + +
64J LYS* 1.3 71.9 - - - +
66J PRO* 1.4 68.0 - - + +
68J GLN* 3.2 7.3 + - + +
69J ARG* 3.1 52.2 + - + +
86L GLU 3.4 22.0 - - - +
87L LEU* 2.9 30.0 + - + +
89L ALA 3.7 11.4 + - - +
91L GLU* 3.3 48.2 - - + +
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Residues in contact with PRO 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LEU 3.8 19.5 - - - +
98D ASP* 3.8 19.3 - - + -
99D ASP* 5.0 0.2 - - - +
62J ILE* 5.7 1.1 - - + -
63J ARG* 3.7 29.2 - - + +
64J LYS 3.6 2.7 - - - -
65J LEU* 1.4 94.1 - - + +
67J PHE* 1.3 56.6 + - - +
69J ARG* 3.2 10.9 + - + +
70J LEU* 3.0 27.1 + - - +
28K GLY* 3.5 29.9 - - - +
87L LEU* 4.0 8.5 - - + +
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Residues in contact with PHE 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62J ILE* 4.4 20.1 - - + +
63J ARG 3.4 14.6 + - - +
64J LYS 3.0 9.4 + - - +
66J PRO* 1.3 78.6 - - - +
68J GLN* 1.3 59.1 + - - +
70J LEU* 3.2 16.1 + - + +
71J VAL* 3.0 43.7 + - + +
89J VAL* 3.7 8.7 - - + -
92J LEU* 3.8 8.1 - - + -
93J GLN* 3.5 60.3 - - + +
96J CYS* 4.0 11.4 - - + -
28K GLY 5.7 0.7 - - - -
58K LEU* 5.4 0.9 - - + -
62K LEU* 3.9 35.4 - - + -
90L TYR* 4.0 4.9 - - - -
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Residues in contact with GLN 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64J LYS 2.9 6.2 + - - +
65J LEU* 3.6 9.5 - - + +
67J PHE* 1.3 75.8 - - - +
69J ARG* 1.3 57.7 + - - +
71J VAL* 3.4 3.2 + - + +
72J ARG* 3.1 45.4 + - + +
89J VAL* 4.4 14.6 - - + -
90L TYR* 3.1 31.2 - - + -
91L GLU* 2.6 49.0 + - - +
93L GLU 3.0 20.4 + - - -
94L GLY* 4.8 0.4 - - - -
95L LEU* 3.7 17.5 - - + +
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Residues in contact with ARG 69 (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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92D ALA* 4.5 18.8 + - - +
93D GLU* 5.7 1.4 - - - +
96D ALA 4.8 1.8 + - - -
97D LEU* 3.4 47.7 + - - +
65J LEU* 3.1 46.7 + - + +
66J PRO* 3.6 9.6 - - - +
68J GLN* 1.3 71.9 - - - +
70J LEU* 1.3 66.1 + - - +
72J ARG* 3.5 25.6 + - - +
73J GLU* 3.1 29.7 + - + +
91L GLU* 3.6 19.6 + - - +
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Residues in contact with LEU 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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66J PRO 3.0 12.3 + - - +
67J PHE* 3.2 19.7 + - + +
69J ARG* 1.3 74.7 - - - +
71J VAL* 1.3 64.7 + - - +
73J GLU* 3.4 12.4 - - + +
74J ILE* 3.3 43.1 + - + +
26K ILE* 3.8 37.7 - - + -
28K GLY* 4.3 20.2 - - - +
29K ILE* 4.4 5.4 - - + +
58K LEU* 5.0 6.1 - - + -
59K LYS* 5.2 3.4 - - - +
62K LEU* 3.8 27.6 - - + -
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Residues in contact with VAL 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J PHE* 3.0 49.3 + - + +
68J GLN* 3.6 7.4 - - + +
69J ARG 3.3 0.2 - - - -
70J LEU* 1.3 76.0 - - + +
72J ARG* 1.3 57.1 + - + +
74J ILE* 3.3 3.1 + - - +
75J ALA* 2.9 32.1 + - - +
84J PHE* 3.7 36.6 - - + -
89J VAL* 4.2 12.1 - - + -
92J LEU* 4.1 16.4 - - + -
62K LEU* 4.5 7.2 - - + -
66K ILE* 4.4 12.5 - - + +
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Residues in contact with ARG 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68J GLN* 3.1 36.7 + - + +
69J ARG* 3.6 25.2 - - - +
71J VAL* 1.3 77.6 - - + +
73J GLU* 1.3 62.8 + - + +
75J ALA* 3.8 4.7 - - - +
76J GLN* 3.0 27.8 + - - +
84J PHE* 5.2 11.2 - - + -
91L GLU* 3.1 33.1 + - - +
93L GLU* 2.6 55.6 + - - -
94L GLY* 3.8 14.3 - - - +
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Residues in contact with GLU 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J ARG* 3.1 23.4 + - + +
70J LEU* 3.4 15.5 - - + +
72J ARG* 1.3 77.9 - - - +
74J ILE* 1.3 65.9 + - + +
76J GLN* 3.4 15.4 + - - +
77J ASP* 3.7 13.2 + - - +
59K LYS* 6.2 0.7 - - - +
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Residues in contact with ILE 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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70J LEU* 3.3 37.2 + - + +
71J VAL 3.9 0.7 - - - +
73J GLU* 1.3 73.5 - - + +
75J ALA* 1.3 67.2 + - - +
77J ASP* 3.1 24.6 + - + +
78J PHE* 3.6 29.7 + - + -
26K ILE* 5.6 0.2 - - + -
59K LYS* 4.3 23.1 - - + +
62K LEU* 3.9 19.7 - - + -
63K GLU* 3.9 22.7 - - + +
66K ILE* 3.9 27.8 - - + -
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Residues in contact with ALA 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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71J VAL 2.9 18.6 + - - +
72J ARG* 4.0 2.9 - - - +
74J ILE* 1.3 77.4 - - - +
76J GLN* 1.3 56.5 + - - +
77J ASP 3.3 0.2 - - - -
78J PHE* 3.3 5.2 + - - +
79J LYS 3.0 32.2 + - - +
82J LEU* 4.5 9.9 - - + +
84J PHE* 3.5 34.1 - - + -
66K ILE* 4.0 16.8 - - + +
70K VAL* 4.7 0.7 - - + -
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Residues in contact with GLN 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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72J ARG 3.0 18.8 + - - +
73J GLU* 3.4 9.0 - - - +
75J ALA* 1.3 77.9 - - - +
77J ASP* 1.3 66.6 + - - +
78J PHE 3.5 0.2 + - - -
79J LYS 3.7 6.9 + - - +
80J THR* 3.4 52.0 - - + +
81J ASP* 4.1 8.0 + - - +
82J LEU 5.5 0.5 + - - -
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Residues in contact with ASP 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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73J GLU 3.8 14.8 - - - +
74J ILE* 3.1 12.6 + - + +
76J GLN* 1.3 82.1 - - - +
78J PHE* 1.3 68.6 + - + +
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Residues in contact with PHE 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 ILE* 3.6 31.8 + - + -
75J ALA 3.3 4.6 + - - +
76J GLN 3.3 0.6 - - - -
77J ASP* 1.3 88.6 - - + +
79J LYS* 1.3 62.3 + - - +
63K GLU* 3.4 32.5 - - + -
66K ILE* 4.0 11.2 - - + -
67K ARG* 3.6 55.4 - - + +
70K VAL* 4.4 15.5 - - + -
74K GLU* 4.4 5.0 - - - +
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Residues in contact with LYS 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 ALA 3.0 19.2 + - - +
76J GLN* 3.7 3.8 - - - +
77J ASP 3.7 0.6 - - - -
78J PHE* 1.3 79.8 - - - +
80J THR* 1.3 70.0 + - - +
82J LEU* 3.5 32.2 - - + +
70K VAL* 3.9 11.7 - - + -
74K GLU* 3.4 37.5 - - + +
78K ARG 4.7 3.8 - - - -
79K LYS* 3.4 43.7 - - - +
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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
------------------------------------------------------------
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