Contacts of the helix formed by residues 61 - 73 (chain C) in PDB entry 1ORR
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 ASN 61 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C ASP* 2.8 17.9 + - + +
59C ILE 3.1 0.2 - - - -
60C ARG* 1.3 76.7 - - - +
62C LYS* 1.3 67.9 + - - +
63C ASN* 3.2 12.5 + - - +
64C ASP* 2.9 39.2 + - - +
65C VAL* 3.1 23.9 + - - +
106C ASN* 3.6 1.3 - - - -
58D ASP* 5.2 0.2 + - - -
60D ARG* 3.5 30.0 + - - +
98D GLU* 2.9 28.0 + - - -
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Residues in contact with LYS 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A CYS* 4.8 17.9 - - - +
62B LYS* 6.5 0.7 - - + -
63B ASN* 6.1 2.5 - - - -
60C ARG 3.5 2.2 + - - -
61C ASN* 1.3 72.8 - - - +
63C ASN* 1.3 55.8 + - - +
65C VAL* 3.3 1.0 + - - +
66C THR* 2.7 47.5 + - - +
106C ASN* 3.4 36.8 + - + +
109C GLU* 3.7 32.5 + - - +
110C ALA 5.4 0.4 - - - +
113C GLN* 5.2 5.1 - - - +
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Residues in contact with ASN 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LYS* 6.5 0.4 - - - -
61C ASN* 3.2 10.5 + - - +
62C LYS* 1.3 76.2 - - - +
64C ASP* 1.3 67.7 + - - +
66C THR* 4.6 3.7 - - - -
67C ARG* 2.9 46.5 + - - +
92D ASN* 2.9 34.2 + - - +
94D CYS* 3.6 27.2 - - - +
95D MET* 3.6 18.2 - - - +
98D GLU* 4.5 5.0 + - - +
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Residues in contact with ASP 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C PHE* 4.3 10.8 - - + -
56C HIS 5.6 0.2 - - - -
57C GLY* 3.7 6.9 - - - -
58C ASP 2.9 29.0 + - - +
61C ASN* 2.9 22.9 + - - +
63C ASN* 1.3 78.0 + - - +
65C VAL* 1.3 63.1 + - - +
67C ARG* 4.0 5.1 - - - +
68C LEU* 3.1 23.6 + - - +
60D ARG* 2.9 40.5 + - - -
92D ASN* 5.4 1.4 + - - -
95D MET* 4.4 10.7 - - - +
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Residues in contact with VAL 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C PHE* 4.3 6.1 - - + -
58C ASP 4.1 1.8 - - - +
59C ILE* 3.4 44.4 - - + +
61C ASN 3.1 16.0 + - - +
62C LYS 3.9 2.7 - - - +
64C ASP* 1.3 75.7 - - - +
66C THR* 1.3 65.7 + - - +
68C LEU* 3.2 11.4 + - + +
69C ILE* 3.1 24.8 + - + +
106C ASN* 3.7 33.4 - - + +
107C LEU* 3.8 21.3 - - + +
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Residues in contact with THR 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LYS* 2.7 40.0 + - - +
63C ASN* 4.0 4.5 - - - -
65C VAL* 1.3 71.8 - - - +
67C ARG* 1.3 60.6 + - + +
69C ILE* 3.3 2.4 + - - +
70C THR* 3.0 33.1 + - + +
106C ASN 4.9 2.4 + - - -
110C ALA* 4.0 15.3 + - + +
114C TYR* 3.6 33.7 - - + +
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Residues in contact with ARG 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ARG* 6.1 1.2 - - - +
63C ASN* 2.9 42.4 + - - +
64C ASP* 4.0 4.5 - - - +
66C THR* 1.3 73.8 - - + +
68C LEU* 1.3 60.9 + - - +
70C THR* 3.4 7.1 + - - +
71C LYS* 2.8 40.2 + - + +
91D ASP* 3.1 43.4 + - - -
92D ASN* 3.2 36.5 + - - +
93D PRO* 5.5 0.2 - - - +
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Residues in contact with LEU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 3.9 39.0 - - + -
7C THR* 4.9 3.6 - - + -
29C ILE* 4.3 2.9 - - + -
31C PHE* 3.6 43.5 - - + -
55C VAL* 4.3 15.3 - - + -
59C ILE* 6.0 0.4 - - + -
64C ASP 3.1 14.8 + - - +
65C VAL* 3.3 17.3 - - + +
66C THR 3.2 0.2 - - - -
67C ARG* 1.3 76.1 - - - +
69C ILE* 1.3 61.0 + - + +
71C LYS* 5.8 0.2 - - - -
72C TYR* 3.0 61.7 + - + +
74C PRO* 4.9 0.3 - - - +
107C LEU* 5.7 0.9 - - + -
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Residues in contact with ILE 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 3.9 22.2 - - + -
65C VAL* 3.1 14.3 + - + +
66C THR 3.8 5.8 - - - +
68C LEU* 1.3 78.8 - - + +
70C THR* 1.3 59.3 - - + +
73C MET* 2.7 30.3 + - - +
74C PRO* 4.2 13.2 - - + -
77C CYS* 5.9 0.2 - - - -
107C LEU* 3.7 28.7 - - + -
110C ALA* 3.8 31.6 - - + +
111C VAL* 4.3 9.0 - - + +
114C TYR* 4.6 3.6 - - + -
115C ASN* 3.7 30.3 - - + +
118C CYS* 5.7 0.7 - - - -
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Residues in contact with THR 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C THR* 3.0 23.5 + - + +
67C ARG* 3.4 10.6 + - - +
69C ILE* 1.3 76.2 - - - +
71C LYS* 1.3 66.1 + - - +
73C MET* 3.5 20.4 - - - +
114C TYR* 3.5 46.0 - - + -
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Residues in contact with LYS 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ARG* 2.8 25.5 + - + +
70C THR* 1.3 82.2 + - - +
72C TYR* 1.3 98.8 + - + +
73C MET* 5.0 1.0 - - - +
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Residues in contact with TYR 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LYS* 3.2 22.9 + - + +
5C LEU* 6.5 0.4 - - + -
29C ILE* 4.0 30.7 - - + -
53C GLU* 3.5 34.1 + - + -
55C VAL* 3.5 33.4 - - + +
68C LEU* 3.0 36.2 + - + +
71C LYS* 1.3 117.5 - - + +
73C MET* 1.3 71.3 + - - +
74C PRO* 3.1 6.3 - - + -
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Residues in contact with MET 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LYS* 3.0 23.6 + - - +
69C ILE 2.7 27.1 + - - +
70C THR* 3.5 23.8 - - - +
71C LYS 4.9 0.9 - - - +
72C TYR* 1.3 71.3 - - - +
74C PRO* 1.3 73.1 - - - +
75C ASP* 4.7 2.3 - - - +
114C TYR* 3.2 29.8 - - - +
115C ASN* 3.3 29.0 - - - +
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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