Contacts of the helix formed by residues 61 - 73 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C ASP* 5.0 0.4 + - - +
60C ARG* 3.3 31.5 + - - +
98C GLU* 2.8 27.5 + - - +
58D ASP* 2.9 16.9 + - + +
60D ARG* 1.3 76.9 - - - +
62D LYS* 1.3 67.0 + - - +
63D ASN* 3.2 11.4 + - - +
64D ASP* 2.9 38.8 + - - +
65D VAL* 3.2 24.3 + - - +
106D ASN* 3.6 1.1 - - - -
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Residues in contact with LYS 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LYS* 6.3 2.7 - - + -
63A ASN* 4.9 6.1 + - - +
94B CYS* 3.1 36.4 - - - +
98B GLU* 5.0 2.0 + - - -
60D ARG 3.4 1.6 + - - -
61D ASN* 1.3 73.3 - - - +
63D ASN* 1.3 57.3 + - - +
65D VAL* 3.4 1.0 + - - +
66D THR* 2.8 44.9 + - - +
106D ASN* 3.4 35.8 - - + +
109D GLU* 5.2 15.8 + - - +
113D GLN* 6.0 3.4 - - - +
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Residues in contact with ASN 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ASN* 3.0 31.7 + - - +
94C CYS* 3.7 26.9 - - - +
95C MET* 3.6 19.8 - - - +
98C GLU* 4.3 6.0 + - - +
61D ASN* 3.2 10.4 + - - +
62D LYS* 1.3 77.1 - - - +
64D ASP* 1.3 68.4 + - - +
66D THR* 4.7 3.8 - - - -
67D ARG* 3.1 37.8 + - - +
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Residues in contact with ASP 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ARG* 2.7 42.1 + - - -
92C ASN* 5.5 0.9 + - - -
95C MET* 4.6 9.9 - - - +
31D PHE* 4.3 12.9 - - + -
55D VAL* 6.1 0.3 - - - +
56D HIS 5.6 0.4 - - - -
57D GLY* 3.7 5.9 - - - -
58D ASP 2.9 28.8 + - - +
61D ASN* 2.9 24.1 + - - +
63D ASN* 1.3 78.1 + - - +
65D VAL* 1.3 57.6 - - - +
67D ARG* 4.0 4.6 - - - +
68D LEU* 3.1 28.1 + - - +
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Residues in contact with VAL 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D PHE* 4.3 4.9 - - + -
58D ASP 4.1 2.0 - - - +
59D ILE* 3.6 44.4 - - + +
61D ASN 3.2 15.5 + - - +
62D LYS 3.9 2.9 - - - +
64D ASP* 1.3 74.8 - - - +
66D THR* 1.3 65.4 + - - +
68D LEU* 3.3 11.7 - - + +
69D ILE* 3.1 22.3 + - + +
106D ASN* 3.8 12.6 - - + +
107D LEU* 3.7 44.6 - - + +
110D ALA* 4.6 2.0 - - + -
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Residues in contact with THR 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D LYS* 2.8 33.4 + - - +
63D ASN* 4.1 5.6 - - - -
65D VAL* 1.3 76.8 - - - +
67D ARG* 1.3 65.3 + - + +
69D ILE* 3.3 2.6 + - - +
70D THR* 3.0 28.3 + - + +
106D ASN 5.1 1.9 + - - -
110D ALA* 4.0 15.2 - - + +
114D TYR* 3.8 32.5 - - + +
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Residues in contact with ARG 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ARG* 6.0 1.2 - - - +
91C ASP* 2.9 46.1 + - - -
92C ASN* 3.3 36.8 + - - +
93C PRO* 5.5 0.2 - - - +
63D ASN* 3.1 38.5 + - - +
64D ASP* 4.1 4.0 - - - +
66D THR* 1.3 76.2 - - + +
68D LEU* 1.3 67.8 + - - +
70D THR* 3.4 8.2 + - - +
71D LYS* 2.9 31.3 + - + +
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Residues in contact with LEU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LEU* 3.8 39.0 - - + -
7D THR* 4.8 3.6 - - + -
29D ILE* 4.3 1.3 - - + -
31D PHE* 3.5 44.4 - - + -
55D VAL* 4.1 20.2 - - + -
59D ILE* 5.8 0.2 - - + -
64D ASP 3.1 19.1 + - - +
65D VAL* 3.3 14.6 - - + +
66D THR 3.2 0.2 - - - -
67D ARG* 1.3 76.5 - - - +
69D ILE* 1.3 65.5 + - + +
72D TYR* 3.0 48.3 + - + +
74D PRO* 4.8 0.9 - - - +
107D LEU* 5.6 0.9 - - + -
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Residues in contact with ILE 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LEU* 3.9 28.3 - - + -
65D VAL* 3.1 16.4 + - + +
66D THR 3.3 3.6 + - - +
68D LEU* 1.3 82.5 - - + +
70D THR* 1.3 59.6 + - - +
73D MET* 2.8 30.5 + - - +
74D PRO* 4.0 14.1 - - + -
77D CYS* 6.0 0.4 - - + -
107D LEU* 3.9 20.0 - - + -
110D ALA* 3.8 31.9 - - + +
111D VAL* 4.3 9.6 - - + +
114D TYR* 4.6 3.8 - - + -
115D ASN* 3.7 28.9 - - + +
118D CYS* 5.7 0.7 - - - -
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Residues in contact with THR 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D THR* 3.0 21.8 + - + +
67D ARG* 3.4 10.6 + - - +
69D ILE* 1.3 76.6 - - + +
71D LYS* 1.3 64.3 + - - +
73D MET* 3.5 20.2 - - - +
114D TYR* 3.7 44.6 - - + -
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Residues in contact with LYS 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ARG* 2.9 21.9 + - + +
70D THR* 1.3 81.7 + - - +
72D TYR* 1.3 102.7 + - + +
73D MET* 4.8 1.4 - - - +
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Residues in contact with TYR 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LYS* 3.0 23.8 + - + +
5D LEU* 6.4 0.2 - - + -
29D ILE* 3.9 34.3 - - + -
53D GLU* 3.9 33.8 + - + -
55D VAL* 3.7 30.6 - - + +
68D LEU* 3.0 34.5 + - + +
71D LYS* 1.3 122.7 + - + +
73D MET* 1.3 68.3 + - - +
74D PRO* 3.2 4.3 - - + -
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Residues in contact with MET 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LYS* 2.8 23.4 + - - +
69D ILE 2.8 27.3 + - - +
70D THR* 3.5 22.7 - - - +
71D LYS 4.8 1.1 - - - +
72D TYR* 1.3 69.4 - - - +
74D PRO* 1.3 74.1 - - - +
75D ASP* 4.6 2.9 - - - +
114D TYR* 3.2 28.5 - - - +
115D ASN* 3.6 23.5 - - - +
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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