Contacts of the helix formed by residues 66 - 78 (chain A) in PDB entry 2OR4
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 LYS 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ASP 3.0 23.4 + - - +
64A GLU* 3.2 24.9 + - - +
65A LEU* 1.3 78.6 - - - +
67A ALA* 1.3 64.1 - - - +
68A GLU* 4.2 6.7 - - + +
69A ASN* 3.1 37.5 + - - +
70A ILE* 3.2 14.8 + - - +
397A GLU* 2.8 10.3 + - - +
400A ARG* 4.4 0.9 - - - +
574A LEU* 4.1 4.9 - - - +
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Residues in contact with ALA 67 (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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66A LYS* 1.3 71.2 - - - +
68A GLU* 1.3 58.4 + - - +
70A ILE* 3.2 11.4 + - - +
71A LYS* 3.0 28.4 + - - +
569A MET 3.6 16.8 - - - +
570A PHE* 3.5 31.3 - - - +
571A LYS* 5.0 1.1 - - - -
574A LEU* 4.0 18.8 - - + +
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Residues in contact with GLU 68 (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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66A LYS* 3.2 6.6 - - + +
67A ALA* 1.3 78.9 - - - +
69A ASN* 1.3 58.6 + - - +
71A LYS* 3.4 28.6 + - - +
72A LYS* 3.1 67.6 + - - +
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Residues in contact with ASN 69 (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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66A LYS* 3.1 18.6 + - - +
68A GLU* 1.3 74.9 - - - +
70A ILE* 1.3 61.8 + - - +
72A LYS* 3.3 18.0 + - - +
73A PHE* 2.9 44.8 + - + -
397A GLU* 3.0 37.1 + - - +
400A ARG* 3.3 25.4 - - - +
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Residues in contact with ILE 70 (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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66A LYS 3.2 13.6 + - - +
67A ALA* 3.6 9.0 - - - +
69A ASN* 1.3 77.3 - - - +
71A LYS* 1.3 56.3 + - - +
73A PHE* 3.3 6.9 + - - -
74A LEU* 2.9 29.6 + - + +
393A ALA* 3.7 16.7 - - + +
394A VAL* 4.1 8.3 - - + -
397A GLU* 3.9 20.0 - - + -
570A PHE* 4.2 3.1 - - + -
573A HIS* 3.6 43.1 - - + +
574A LEU* 3.9 33.2 - - + +
577A ALA* 4.1 14.1 - - + -
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Residues in contact with LYS 71 (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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67A ALA 3.0 13.6 + - - +
68A GLU* 3.5 32.1 + - - +
70A ILE* 1.3 76.9 - - - +
72A LYS* 1.3 57.6 + - + +
74A LEU* 3.3 2.8 + - - +
75A TYR* 3.0 28.6 + - - +
559A TYR* 3.2 25.3 - - - +
563A GLU* 4.2 12.9 + - - -
568A PRO 4.6 7.6 + - - +
570A PHE* 3.4 42.4 - - + -
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Residues in contact with LYS 72 (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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68A GLU* 3.1 48.2 + - + +
69A ASN* 3.3 17.5 + - - +
71A LYS* 1.3 76.4 - - + +
73A PHE* 1.3 70.2 + - + +
75A TYR* 3.4 7.6 + - - +
76A ASN* 3.0 23.3 + - - +
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Residues in contact with PHE 73 (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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69A ASN* 2.9 30.1 + - + +
70A ILE 3.8 3.1 - - - +
72A LYS* 1.3 79.1 - - + +
74A LEU* 1.3 60.3 + - - +
76A ASN* 3.0 9.4 + - + +
77A PHE* 2.8 45.3 + + + -
99A GLN* 5.0 8.5 - - - -
103A PHE* 4.0 17.5 - + - -
393A ALA* 3.8 28.0 - - + -
396A HIS* 3.7 30.7 - + + -
397A GLU* 3.5 32.8 - - + -
400A ARG* 4.5 8.1 - - - -
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Residues in contact with LEU 74 (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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70A ILE* 2.9 18.7 + - + +
71A LYS 3.6 4.5 - - - +
73A PHE* 1.3 76.0 - - - +
75A TYR* 1.3 56.1 + - - +
77A PHE* 3.1 10.1 + - - -
78A THR* 2.7 33.0 + - + +
385A GLY 3.4 19.3 - - - +
389A GLN* 3.4 41.7 - - + +
390A SER* 3.5 3.8 - - - +
393A ALA* 3.7 8.2 - - + +
559A TYR* 4.0 16.8 - - + -
562A VAL* 3.9 21.3 - - + -
570A PHE* 3.7 25.6 - - + -
573A HIS* 4.4 4.7 - - - +
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Residues in contact with TYR 75 (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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71A LYS 3.0 14.4 + - - +
72A LYS* 3.6 10.5 - - - +
74A LEU* 1.3 78.8 - - - +
76A ASN* 1.3 65.9 - - + +
78A THR* 3.2 4.4 + - - -
79A GLN* 2.9 64.1 + - + +
559A TYR* 3.6 41.5 - + + +
560A GLU* 5.1 4.7 - - - -
1B NAG 4.9 8.7 - - + -
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Residues in contact with ASN 76 (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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72A LYS 3.0 14.4 + - - +
73A PHE* 3.0 15.5 + - + +
75A TYR* 1.3 83.6 - - + +
77A PHE* 1.3 67.9 + - + +
78A THR 3.6 0.5 + - - -
79A GLN 4.5 1.9 + - - -
82A HIS* 5.1 2.6 - - - -
92A LEU* 5.2 1.7 - - - +
95A GLN* 2.7 23.1 + - - +
99A GLN* 6.0 0.2 - - - -
1B NAG 1.4 79.1 + - - +
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Residues in contact with PHE 77 (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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73A PHE* 2.8 23.6 + + + +
74A LEU 3.1 2.2 + - - +
76A ASN* 1.3 96.0 - - + +
78A THR* 1.4 58.3 + - - +
79A GLN 3.7 1.1 - - - -
82A HIS* 3.0 29.5 + - - -
92A LEU* 3.9 13.2 - - + -
95A GLN* 3.8 7.0 - - - -
96A ILE* 3.4 33.2 - - + -
99A GLN* 4.6 0.2 - - - -
383A PHE 4.1 0.7 - - - +
389A GLN* 3.6 43.9 - - + +
392A ALA* 3.8 27.1 - - + -
393A ALA* 3.8 15.9 - - - -
396A HIS* 3.7 23.6 - + + -
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Residues in contact with THR 78 (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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74A LEU* 2.7 28.3 + - + +
75A TYR 3.2 6.7 + - - -
77A PHE* 1.4 80.2 - - - +
79A GLN* 1.3 66.9 + - - +
80A ILE 3.4 4.0 - - - -
151A TYR* 4.6 6.9 + - - -
383A PHE* 3.5 37.6 - - - +
385A GLY* 3.8 15.5 - - - -
389A GLN* 3.6 21.5 - - + -
559A TYR* 3.4 29.2 + - - +
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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