Contacts of the helix formed by residues 86 - 103 (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 THR 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A PRO 5.0 0.2 + - - -
83A LEU* 2.7 51.7 + - + +
84A ALA 4.2 2.9 - - - +
85A GLY* 1.3 85.3 - - - +
87A GLU* 1.3 66.1 + - - +
88A GLN* 3.5 18.3 + - - +
89A ASN* 3.1 18.9 + - - +
90A PHE* 3.2 11.5 + - - +
119A TYR* 4.6 6.1 - - + +
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Residues in contact with GLU 87 (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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86A THR* 1.3 73.2 - - - +
88A GLN* 1.3 62.2 + - + +
90A PHE* 3.2 24.0 + - - +
91A GLN* 2.6 67.3 + - + +
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Residues in contact with GLN 88 (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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80A ILE* 3.8 25.5 - - + +
81A PRO* 3.4 22.9 - - + +
82A HIS* 3.4 11.7 + - - -
86A THR* 3.5 21.1 + - - +
87A GLU* 1.3 81.6 + - + +
89A ASN* 1.3 57.6 + - - +
91A GLN* 3.5 7.4 + - - +
92A LEU* 3.1 21.0 + - - +
156A ASP* 2.8 33.9 + - + +
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Residues in contact with ASN 89 (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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82A HIS* 3.5 29.4 + - - +
83A LEU 3.5 18.4 - - - +
84A ALA* 4.0 4.0 - - - +
85A GLY 4.9 0.7 - - - +
86A THR* 3.1 9.7 + - - +
88A GLN* 1.3 77.4 - - - +
90A PHE* 1.3 59.3 + - - +
92A LEU* 3.4 1.0 + - - +
93A ALA* 2.9 23.9 + - - +
378A ARG* 3.0 40.0 + - - +
379A ASP* 3.7 12.9 - - - +
422A ASP* 2.8 31.6 + - - +
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Residues in contact with PHE 90 (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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86A THR 3.2 10.9 + - - +
87A GLU* 3.2 33.8 + - - +
89A ASN* 1.3 71.7 - - - +
91A GLN* 1.4 65.8 + - - +
93A ALA* 3.1 6.0 + - + +
94A LYS* 3.0 59.1 + - + +
110A LEU* 4.1 8.5 - - + -
356A TYR* 3.6 60.7 - + + -
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Residues in contact with GLN 91 (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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87A GLU* 2.6 48.5 + - + +
88A GLN* 3.8 7.2 - - - +
90A PHE* 1.4 78.3 - - - +
92A LEU* 1.3 62.6 + - - +
94A LYS* 2.8 42.0 + - - +
95A GLN* 3.0 21.8 + - - +
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Residues in contact with LEU 92 (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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76A ASN* 4.7 2.0 - - - +
77A PHE* 3.9 29.8 - - + +
82A HIS* 3.8 39.3 - - + +
88A GLN 3.1 17.7 + - - +
89A ASN* 3.7 5.2 - - - +
90A PHE 3.3 0.2 - - - -
91A GLN* 1.3 75.7 - - - +
93A ALA* 1.3 65.0 + - - +
95A GLN* 3.1 28.1 + - - +
96A ILE* 2.9 32.8 + - + +
378A ARG* 3.6 28.3 - - + -
389A GLN* 4.2 11.7 - - - +
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Residues in contact with ALA 93 (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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89A ASN 2.9 15.6 + - - +
90A PHE* 3.1 13.7 + - + +
92A LEU* 1.3 76.2 - - - +
94A LYS* 1.3 56.8 + - - +
96A ILE* 3.4 0.6 + - - -
97A GLN* 2.9 30.0 + - - +
110A LEU* 4.2 11.0 - - + -
356A TYR* 4.3 8.5 - - + -
358A VAL* 3.6 17.8 - - + +
378A ARG* 3.7 28.8 - - - +
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Residues in contact with LYS 94 (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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90A PHE* 3.0 49.9 + - + +
91A GLN* 2.8 48.0 + - - +
92A LEU 3.2 0.2 - - - -
93A ALA* 1.3 77.5 - - - +
95A GLN* 1.3 57.6 + - - +
97A GLN* 3.4 14.1 + - - +
98A SER* 3.0 29.3 + - - -
110A LEU* 4.2 10.1 - - + -
2B NAG 5.8 0.2 - - - -
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Residues in contact with GLN 95 (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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76A ASN* 2.7 29.6 + - - +
77A PHE* 3.8 10.3 - - - -
91A GLN 3.0 13.6 + - - +
92A LEU* 3.4 22.8 - - - +
94A LYS* 1.3 75.3 - - - +
96A ILE* 1.3 59.3 + - - +
98A SER* 3.2 3.1 + - - -
99A GLN* 2.9 60.3 + - - +
1B NAG 3.7 23.0 + - - +
2B NAG 4.0 29.7 - - + +
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Residues in contact with ILE 96 (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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77A PHE* 3.4 40.8 - - + -
92A LEU* 2.9 32.7 + - + +
93A ALA 3.7 3.6 - - - +
95A GLN* 1.3 70.8 - - - +
97A GLN* 1.3 62.0 + - - +
99A GLN* 3.2 2.2 + - - +
100A TRP* 2.8 70.5 + - + +
358A VAL* 4.4 8.7 - - + -
378A ARG* 4.6 9.4 - - + -
392A ALA* 6.3 0.4 - - + -
396A HIS* 3.5 15.0 - - + +
420A SER* 4.4 9.0 - - - +
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Residues in contact with GLN 97 (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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93A ALA 2.9 17.6 + - - +
94A LYS* 3.7 11.7 - - - +
95A GLN 3.3 0.2 - - - -
96A ILE* 1.3 76.4 - - - +
98A SER* 1.3 62.9 + - - +
100A TRP 3.5 0.2 + - - -
101A LYS* 3.2 39.8 + - + +
108A VAL* 3.0 44.4 + - + +
109A GLU* 3.8 13.1 + - - +
110A LEU* 3.7 28.5 - - + +
358A VAL* 3.9 10.5 - - + +
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Residues in contact with SER 98 (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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94A LYS 3.0 18.0 + - - -
95A GLN* 3.5 5.6 - - - -
97A GLN* 1.3 78.9 - - - +
99A GLN* 1.3 56.7 + - - +
101A LYS* 3.4 11.2 + - - +
102A GLU* 2.8 55.1 + - - +
2B NAG 3.9 12.7 + - - -
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Residues in contact with GLN 99 (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* 5.0 8.7 - - - -
76A ASN* 6.0 0.2 - - - -
77A PHE* 4.6 0.3 - - - -
95A GLN* 2.9 48.2 + - - +
96A ILE* 3.9 0.6 - - - +
98A SER* 1.3 76.3 - - - +
100A TRP* 1.3 59.7 + - - +
102A GLU* 3.1 19.5 + - - +
103A PHE* 2.7 47.0 + - + -
396A HIS* 2.9 38.6 + - + +
1B NAG 3.6 21.8 + - - -
2B NAG 4.3 9.9 - - - +
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Residues in contact with TRP 100 (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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96A ILE* 2.8 28.3 + - + +
97A GLN 3.9 1.1 - - - +
99A GLN* 1.3 76.9 - - - +
101A LYS* 1.3 60.8 + - - +
103A PHE* 3.4 9.0 + + - +
104A GLY 3.4 4.9 + - - -
105A LEU* 3.2 36.9 + - + +
108A VAL* 3.8 19.7 - - + -
358A VAL* 3.9 29.4 - - + -
360A GLY 4.0 5.8 - - - -
395A VAL* 3.9 21.3 - - + -
396A HIS* 2.9 37.0 + + - +
399A VAL* 3.9 23.9 - - + +
418A PHE* 3.5 30.1 - - + -
419A ALA 3.9 6.7 - - - -
420A SER* 3.8 25.8 - - - -
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Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A GLN* 3.2 37.0 + - + +
98A SER* 3.4 12.1 - - - +
100A TRP* 1.3 73.6 - - - +
102A GLU* 1.3 66.3 + - + +
104A GLY* 3.0 15.6 + - - -
105A LEU 4.0 9.4 + - - +
107A SER* 5.9 0.9 - - - +
108A VAL* 3.4 39.6 + - + +
109A GLU* 5.2 4.1 + - - -
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Residues in contact with GLU 102 (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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98A SER* 2.8 44.7 + - - +
99A GLN* 3.1 20.8 + - - +
101A LYS* 1.3 76.4 - - + +
103A PHE* 1.3 64.9 + - + +
104A GLY 3.2 0.9 + - - -
407A LYS* 2.8 24.3 + - - -
2B NAG 4.0 8.7 + - - +
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Residues in contact with PHE 103 (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* 4.0 17.0 - + - -
99A GLN* 2.7 34.5 + - + +
100A TRP* 3.7 9.6 - + - +
101A LYS 3.2 0.4 - - - -
102A GLU* 1.3 79.6 - - + +
104A GLY* 1.3 56.3 + - - +
105A LEU 3.8 0.4 - - - -
396A HIS* 3.6 54.5 - + - -
399A VAL* 3.9 18.4 - - + +
400A ARG* 3.8 45.3 - - + +
403A GLY* 3.1 25.9 - - - -
407A LYS* 3.7 8.5 + - - +
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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