Contacts of the helix formed by residues 82 - 101 (chain A) in PDB entry 1ORN
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 LEU 82 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA* 4.1 8.7 - - + +
42A GLN* 4.0 26.7 - - + -
81A GLY* 1.3 70.2 - - - +
83A TYR* 1.3 57.1 + - - +
84A ARG 3.4 0.5 + - - -
85A ASN* 3.6 4.3 + - + +
86A LYS* 3.1 41.5 + - + +
5B C 3.4 37.2 - - + +
6B G 2.7 68.5 + - + +
19C G 3.8 23.6 - - + +
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Residues in contact with TYR 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLU* 3.7 31.1 - - + +
75A GLN* 4.8 9.0 + - - -
77A ILE* 3.7 36.5 - - + +
78A ARG* 3.8 32.8 + - + +
81A GLY 2.7 10.0 + - - +
82A LEU* 1.3 71.1 - - - +
84A ARG* 1.3 104.4 + - + +
86A LYS* 3.9 1.1 - - - -
87A ALA* 3.0 31.5 + - - +
6B G 3.6 14.3 + - - -
7B T 3.8 32.4 + - - -
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Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 5.1 0.5 - - - +
74A GLU* 4.0 25.4 + - - +
83A TYR* 1.3 114.0 + - + +
85A ASN* 1.3 62.9 + - - +
87A ALA* 4.0 1.6 - - - +
88A ARG* 3.2 23.7 + - - +
6B G 2.7 50.0 + - - +
7B T 5.2 2.8 + - - -
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Residues in contact with ASN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 4.2 5.6 - - + +
84A ARG* 1.3 79.4 - - - +
86A LYS* 1.3 59.6 + - + +
88A ARG* 3.4 5.2 + - - +
89A ASN* 2.8 42.0 + - - +
4B A 5.7 2.6 + - - -
5B C 3.4 42.0 + - - -
6B G 2.9 8.4 + - - +
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Residues in contact with LYS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 3.6 26.2 - - + +
39A LEU* 2.7 36.2 + - + -
41A ALA* 2.7 28.3 + - - -
42A GLN 5.2 0.2 + - - -
43A CYS* 4.5 1.4 - - - +
77A ILE* 4.1 12.8 - - + -
80A ILE* 3.6 17.6 + - + +
81A GLY 3.8 10.0 + - - +
82A LEU* 3.1 38.2 + - + +
83A TYR* 5.1 0.2 - - - -
84A ARG 3.3 0.2 - - - -
85A ASN* 1.3 75.6 - - + +
87A ALA* 1.3 60.2 + - - +
89A ASN* 3.2 8.4 + - - +
90A ILE* 2.8 38.4 + - + +
6B G 5.6 0.2 - - - +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 3.7 9.4 - - + -
73A LEU* 3.7 12.8 - - + +
74A GLU* 3.6 31.4 - - + +
77A ILE* 3.6 15.8 - - + +
83A TYR 3.0 21.9 + - - +
84A ARG 4.0 0.7 - - - +
86A LYS* 1.3 76.9 - - - +
88A ARG* 1.3 62.6 + - - +
90A ILE* 3.3 0.8 + - - -
91A GLN* 3.1 27.9 + - - +
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Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 3.7 23.9 - - + +
84A ARG 3.2 15.2 + - - +
85A ASN* 3.7 6.1 - - - +
87A ALA* 1.3 79.3 - - - +
89A ASN* 1.3 65.9 + - - +
91A GLN* 3.4 4.7 + - - +
92A LYS* 3.1 22.7 + - - +
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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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38A VAL* 5.3 4.0 - - + -
85A ASN* 2.8 26.9 + - - +
86A LYS* 3.2 8.4 + - - +
88A ARG* 1.3 80.2 - - - +
90A ILE* 1.3 52.2 + - + +
92A LYS* 3.3 2.8 + - - +
93A LEU* 2.7 38.5 + - - +
116A PRO* 3.6 30.1 - - - +
117A GLY* 3.5 22.5 - - - +
21C C 4.4 14.5 + - - +
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Residues in contact with ILE 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 4.0 34.1 - - + -
38A VAL* 4.5 16.6 - - + -
39A LEU* 3.8 29.6 - - + -
55A LEU* 5.8 0.2 - - + -
65A TYR* 3.7 34.1 - - + -
73A LEU* 4.2 7.4 - - + -
77A ILE* 4.4 11.0 - - + -
86A LYS* 2.8 28.4 + - + +
87A ALA* 3.7 4.9 - - - +
89A ASN* 1.3 72.0 - - - +
91A GLN* 1.3 57.8 + - - +
93A LEU* 3.2 8.7 + - + +
94A CYS* 2.9 30.3 + - - -
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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
----------------------------------------------------------
65A TYR* 2.9 28.6 + - - +
66A ILE* 3.5 22.6 + - + +
68A VAL* 3.0 28.7 + - - +
70A LEU* 3.5 35.1 + - - +
73A LEU* 3.8 10.3 - - + +
87A ALA 3.1 17.1 + - - +
88A ARG* 3.9 4.5 - - - +
89A ASN 3.3 0.2 - - - -
90A ILE* 1.3 76.5 - - - +
92A LYS* 1.3 62.8 + - - +
94A CYS* 3.4 1.1 + - - -
95A ALA* 3.1 21.1 + - - +
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Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ARG 3.1 16.5 + - - +
89A ASN* 3.7 4.3 - - - +
91A GLN* 1.3 74.3 - - - +
93A LEU* 1.3 65.6 + - - +
95A ALA* 3.4 7.5 + - + +
96A MET* 3.1 29.2 + - + +
116A PRO* 3.3 27.1 - - + -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 4.9 0.4 - - + -
34A LEU* 3.8 25.8 - - + -
35A ILE* 4.6 11.0 - - + -
38A VAL* 4.1 17.3 - - + -
89A ASN 2.7 21.6 + - - +
90A ILE* 3.5 8.7 - - + +
92A LYS* 1.3 74.6 - - - +
94A CYS* 1.3 72.4 + - - +
96A MET* 3.2 4.2 + - - +
97A LEU* 3.0 35.3 + - + +
115A LEU* 3.9 14.2 - - + +
116A PRO* 3.9 28.2 - - + +
118A VAL* 4.0 21.1 - - + -
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Residues in contact with CYS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 3.8 12.6 - - - -
35A ILE* 4.6 0.7 - - - -
62A PRO* 3.5 42.6 - - + +
65A TYR* 3.7 25.1 - - - -
66A ILE* 3.7 11.7 - - + -
90A ILE* 2.9 24.0 + - - +
93A LEU* 1.3 79.7 - - - +
95A ALA* 1.3 66.1 + - - +
97A LEU* 3.3 4.7 + - - +
98A ILE* 3.3 27.7 + - - +
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Residues in contact with ALA 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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66A ILE* 4.0 12.3 - - + +
91A GLN 3.1 16.3 + - - +
92A LYS* 3.7 9.0 - - + +
93A LEU 3.3 0.2 - - - -
94A CYS* 1.3 77.1 - - - +
96A MET* 1.3 57.3 + - - +
98A ILE* 3.4 8.5 + - - +
99A ASP* 2.7 43.7 + - - +
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Residues in contact with MET 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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92A LYS* 3.1 16.4 + - + +
93A LEU 3.5 8.3 - - - +
94A CYS 3.2 0.4 - - - -
95A ALA* 1.3 75.6 - - - +
97A LEU* 1.3 58.7 + - - +
99A ASP* 4.4 4.0 - - - +
100A LYS* 2.7 53.2 + - + +
101A TYR* 3.5 8.5 + - + -
114A LYS* 3.5 26.9 - - - +
115A LEU* 3.6 19.7 - - + -
116A PRO* 3.7 26.9 - - + -
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 3.8 33.9 - - + -
34A LEU* 4.5 4.5 - - + -
62A PRO* 4.5 7.6 - - + -
93A LEU* 3.0 30.6 + - + +
94A CYS* 3.3 9.4 + - - +
96A MET* 1.3 75.8 - - - +
98A ILE* 1.3 54.1 + - - +
101A TYR* 3.0 26.1 + - + -
103A GLY* 2.8 33.0 + - - +
104A GLU 3.6 22.7 - - - +
105A VAL* 4.2 6.3 - - + -
106A PRO* 3.7 19.3 - - + -
115A LEU* 4.1 16.8 - - + -
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Residues in contact with ILE 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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62A PRO* 4.2 13.5 - - + -
63A HIS* 3.8 41.3 - - + +
66A ILE* 3.8 28.0 - - + -
94A CYS 3.3 16.1 + - - +
95A ALA* 3.6 7.0 - - - +
96A MET 3.2 0.2 - - - -
97A LEU* 1.3 80.1 - - - +
99A ASP* 1.3 71.1 + - - +
102A ASN* 4.2 5.7 + - - -
103A GLY* 3.9 13.8 + - - +
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Residues in contact with ASP 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ALA* 2.7 29.1 + - - +
96A MET* 4.3 2.4 - - - +
98A ILE* 1.3 87.9 - - - +
100A LYS* 1.3 66.6 + - + +
102A ASN 5.2 0.2 - - - -
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A MET* 2.7 34.0 + - + +
99A ASP* 1.3 84.2 - - + +
101A TYR* 1.3 83.0 + - + +
102A ASN 3.7 2.4 + - - -
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Residues in contact with TYR 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A MET* 3.9 16.4 - - + -
97A LEU* 3.0 16.8 + - + +
100A LYS* 1.3 98.2 - - + +
102A ASN* 1.3 70.1 + - - +
103A GLY 3.1 1.8 - - - -
104A GLU* 3.0 30.8 + - - +
106A PRO* 3.9 26.7 - - + -
111A GLU* 2.7 59.0 + - + -
114A LYS* 3.6 12.5 - - - +
115A LEU* 4.1 19.1 - - + -
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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
------------------------------------------------------------
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