Contacts of the helix formed by residues 61 - 73 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASP* 5.1 0.6 + - - +
60A ARG* 3.2 29.8 + - - +
98A GLU* 3.0 29.0 + - - +
58B ASP* 2.9 16.4 + - + +
60B ARG* 1.3 76.6 - - - +
62B LYS* 1.3 67.7 + - - +
63B ASN* 3.2 12.1 + - - +
64B ASP* 2.9 36.9 + - - +
65B VAL* 3.2 24.8 + - - +
106B ASN* 3.6 1.3 - - - -
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ARG 3.5 2.4 + - - +
61B ASN* 1.3 71.3 + - - +
63B ASN* 1.3 59.0 + - - +
65B VAL* 3.4 1.0 + - - +
66B THR* 2.7 44.7 + - - +
105B LEU 5.8 0.2 - - - -
106B ASN* 3.4 36.4 + - + +
109B GLU* 3.9 29.7 + - - +
113B GLN* 5.1 7.5 - - - +
62C LYS* 6.5 0.4 - - + -
63C ASN* 6.5 0.2 - - - -
94D CYS* 4.6 19.6 - - - +
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Residues in contact with ASN 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASN* 2.9 30.0 + - - +
94A CYS* 3.7 26.4 - - - +
95A MET* 3.8 17.0 - - - +
98A GLU* 4.7 4.0 + - - +
61B ASN* 3.2 9.0 + - - +
62B LYS* 1.3 76.1 - - - +
64B ASP* 1.4 67.7 + - - +
66B THR* 4.0 4.5 - - - -
67B ARG* 3.0 51.6 + - - +
62C LYS* 6.1 2.5 - - - -
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Residues in contact with ASP 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ARG* 2.7 46.3 + - - -
92A ASN* 5.4 0.9 + - - -
95A MET* 4.4 12.0 - - - +
31B PHE* 4.2 15.0 - - + -
56B HIS 5.5 0.7 - - - -
57B GLY* 3.7 5.6 - - - -
58B ASP 3.0 25.2 + - - +
61B ASN* 2.9 21.2 + - - +
63B ASN* 1.4 75.4 + - - +
65B VAL* 1.3 62.5 + - - +
67B ARG* 4.0 5.7 - - - +
68B LEU* 3.1 24.5 + - - +
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 4.2 5.6 - - + -
58B ASP 4.1 1.3 - - - +
59B ILE* 3.5 43.7 - - + +
61B ASN 3.2 16.8 + - - +
62B LYS 3.9 2.9 - - - +
64B ASP* 1.3 75.6 - - - +
66B THR* 1.3 65.5 + - - +
68B LEU* 3.2 12.4 + - + +
69B ILE* 3.1 22.1 + - + +
106B ASN* 3.7 10.8 - - + +
107B LEU* 3.6 45.1 - - + +
110B ALA* 4.6 2.0 - - + -
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Residues in contact with THR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS* 2.7 33.5 + - - +
63B ASN* 4.0 4.5 - - - -
65B VAL* 1.3 77.2 - - - +
67B ARG* 1.3 58.7 + - + +
69B ILE* 3.2 2.6 + - - +
70B THR* 2.9 33.7 + - + +
106B ASN 4.9 2.1 + - - -
110B ALA* 4.0 15.1 - - + +
114B TYR* 3.6 35.7 - - + +
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Residues in contact with ARG 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ASP* 3.0 45.5 + - - -
92A ASN* 3.3 32.1 + - - +
93A PRO* 5.5 0.4 - - - +
63B ASN* 3.0 47.1 + - - +
64B ASP* 4.0 4.9 - - - +
66B THR* 1.3 73.7 - - + +
68B LEU* 1.3 66.3 + - - +
70B THR* 3.2 7.4 + - - +
71B LYS* 2.8 31.6 + - + +
112C ARG* 5.9 1.8 - - - +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 3.7 29.4 - - + -
7B THR* 5.0 3.1 - - + -
29B ILE* 4.2 9.4 - - + -
31B PHE* 3.7 44.9 - - + -
55B VAL* 4.0 20.2 - - + -
59B ILE* 6.3 0.4 - - + -
64B ASP 3.1 19.7 + - - +
65B VAL* 3.4 13.0 - - + +
66B THR 3.2 0.4 - - - -
67B ARG* 1.3 77.1 - - - +
69B ILE* 1.3 64.3 + - + +
71B LYS* 4.7 0.2 - - - -
72B TYR* 3.0 52.1 + - + +
74B PRO* 4.9 0.3 - - - +
107B LEU* 5.8 1.1 - - + -
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Residues in contact with ILE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 4.1 19.7 - - + -
65B VAL* 3.1 14.1 + - + +
66B THR 3.7 5.4 - - - +
67B ARG 3.2 0.2 - - - -
68B LEU* 1.3 79.6 - - + +
70B THR* 1.3 59.0 + - + +
73B MET* 2.7 31.7 + - - +
74B PRO* 4.1 14.8 - - + -
77B CYS* 6.1 0.4 - - + -
107B LEU* 3.9 26.5 - - + -
110B ALA* 3.7 30.7 - - + +
111B VAL* 4.1 10.1 - - + +
114B TYR* 4.6 4.3 - - + -
115B ASN* 3.7 30.5 - - + +
118B CYS* 5.6 0.7 - - - -
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Residues in contact with THR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B THR* 2.9 23.2 + - + +
67B ARG* 3.2 10.7 + - - +
69B ILE* 1.3 73.7 - - + +
71B LYS* 1.3 68.8 + - - +
73B MET* 3.6 18.7 - - - +
114B TYR* 3.5 45.3 - - + -
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ARG* 2.8 21.0 + - + +
70B THR* 1.3 83.6 + - - +
72B TYR* 1.3 103.5 + - + +
73B MET* 4.7 1.4 - - - +
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Residues in contact with TYR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LYS* 3.2 22.5 + - + +
29B ILE* 3.9 31.6 - - + -
53B GLU* 3.3 38.2 + - + -
55B VAL* 3.6 30.4 - - + +
68B LEU* 3.0 35.5 + - + +
71B LYS* 1.3 117.0 + - + +
73B MET* 1.3 71.8 + - - +
74B PRO* 3.2 4.3 - - + -
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Residues in contact with MET 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LYS* 2.9 23.0 + - - +
69B ILE 2.7 26.0 + - - +
70B THR* 3.6 24.0 - - - +
71B LYS 4.7 1.6 - - - +
72B TYR* 1.3 71.6 - - - +
74B PRO* 1.3 72.5 - - - +
75B ASP* 4.5 2.6 - - - +
114B TYR* 3.3 28.9 - - - +
115B ASN* 3.5 23.9 + - - +
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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