Contacts of the helix formed by residues 81 - 94 (chain A) in PDB entry 1NOY
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A LYS* 3.2 55.9 + - + +
45A SER 3.5 25.1 - - - +
46A LYS* 5.3 6.7 - - + -
76A ILE* 5.4 1.2 - - - +
79A GLU 3.9 4.9 + - - +
80A ALA* 1.3 69.7 - - - +
82A GLY* 1.3 65.2 + - - +
83A MET 3.0 2.9 + - - -
84A ASN* 3.2 21.0 + - + +
85A ASP* 3.9 3.1 + - - -
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Residues in contact with GLY 82 (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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42A LYS* 4.0 17.9 + - - +
43A GLU* 5.5 0.6 - - - +
69A TRP* 3.5 30.2 - - - -
73A MET* 4.0 11.3 - - - +
80A ALA 3.4 1.2 - - - -
81A LEU* 1.3 77.7 - - - +
83A MET* 1.3 50.2 + - - +
85A ASP* 2.9 10.3 + - - +
86A PHE 2.8 30.8 + - - -
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Residues in contact with MET 83 (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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10A THR* 4.2 20.4 - - + +
12A GLY 4.9 7.9 - - - +
13A ASN* 5.3 3.4 - - - +
69A TRP* 5.7 0.4 - - + -
70A MET* 4.8 10.8 - - - -
73A MET* 4.3 24.1 - - + +
77A GLY 5.4 1.8 - - - +
78A LEU 4.2 17.5 - - - +
79A GLU* 6.0 0.2 - - - -
80A ALA* 3.0 22.7 + - - +
81A LEU 3.0 0.4 - - - -
82A GLY* 1.3 76.9 - - - +
84A ASN* 1.3 60.5 + - - +
86A PHE* 3.1 57.5 - - + +
87A LYS* 3.2 19.4 + - - +
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Residues in contact with ASN 84 (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 ALA 4.3 0.4 + - - -
81A LEU* 3.2 13.2 + - + +
82A GLY 3.2 0.6 - - - -
83A MET* 1.3 74.9 - - - +
85A ASP* 1.3 64.0 + - - +
87A LYS* 3.3 20.3 + - - +
88A LEU* 2.9 39.9 + - - +
351A PRO* 4.8 9.4 - - - +
360A LYS* 4.1 26.9 - - - +
363A ASP* 5.0 9.3 + - - -
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Residues in contact with ASP 85 (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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35A PRO* 5.9 0.2 - - - -
37A MET 5.6 0.2 - - - +
38A PHE* 5.5 1.3 - - - -
39A ARG* 2.9 49.7 + - - +
42A LYS* 3.5 20.7 - - - +
69A TRP* 5.0 7.0 - - + -
81A LEU 3.9 2.7 + - - +
82A GLY* 2.9 12.6 + - - +
84A ASN* 1.3 77.2 - - - +
86A PHE* 1.3 57.8 + - - +
88A LEU* 3.1 14.1 + - - +
89A ALA* 2.8 36.1 + - - +
363A ASP* 4.4 1.7 - - - +
367A PHE* 3.4 25.7 - - + -
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Residues in contact with PHE 86 (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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10A THR* 3.4 28.0 - - + -
13A ASN 3.4 23.6 - - - -
14A ASN 4.4 0.4 - - - -
15A ILE* 3.9 9.0 - - + +
33A TYR* 3.2 54.1 - + + -
35A PRO* 3.6 12.3 - - + -
69A TRP* 4.4 8.4 - + + -
70A MET* 3.4 26.2 - - + -
82A GLY 2.8 11.9 + - - +
83A MET* 3.1 40.4 - - + +
85A ASP* 1.3 76.8 - - - +
87A LYS* 1.3 58.4 + - - +
89A ALA* 3.4 6.4 + - - +
90A TYR* 3.1 19.1 + - - +
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Residues in contact with LYS 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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8A ILE* 3.5 36.2 + - + +
9A GLU* 3.6 27.3 + - - +
10A THR* 3.8 25.7 + - + +
15A ILE* 4.3 8.5 - - - -
83A MET* 3.2 18.2 + - - +
84A ASN* 3.6 21.1 - - - +
85A ASP 3.2 0.2 - - - -
86A PHE* 1.3 74.4 - - - +
88A LEU* 1.3 65.6 + - - +
90A TYR* 3.3 2.8 + - - +
91A ILE* 3.0 29.4 + - + +
244A ARG* 5.6 0.2 - - - +
351A PRO* 4.8 15.3 - - + -
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Residues in contact with LEU 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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39A ARG* 4.4 2.0 - - - +
84A ASN* 2.9 25.0 + - - +
85A ASP* 3.4 28.0 - - - +
87A LYS* 1.3 77.0 - - - +
89A ALA* 1.3 51.2 + - - +
91A ILE* 3.5 4.2 + - - +
92A SER* 2.8 37.9 + - - -
349A LYS 4.0 18.7 - - - +
350A MET* 4.1 17.5 - - + -
351A PRO* 4.1 13.0 - - + -
363A ASP* 4.5 4.5 - - - +
364A ALA* 4.0 28.3 - - + +
367A PHE* 3.9 22.7 - - + -
368A ASN* 3.8 6.7 - - - +
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Residues in contact with ALA 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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33A TYR* 3.1 19.8 + - - +
35A PRO* 3.8 21.5 - - + -
36A THR* 4.7 3.8 - - - +
37A MET* 4.9 2.2 - - + +
85A ASP 2.8 20.0 + - - +
86A PHE 3.5 6.1 - - - +
88A LEU* 1.3 71.1 - - - +
90A TYR* 1.3 54.3 + - - +
92A SER* 2.8 7.9 + - - -
93A ASP* 2.8 35.6 + - - +
367A PHE* 3.8 15.0 - - + -
372A GLY 5.1 1.3 - - - +
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Residues in contact with TYR 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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8A ILE* 3.9 19.1 - - + -
15A ILE* 3.1 51.6 - - + -
17A GLU* 3.1 37.1 + - - +
29A ARG* 3.5 12.3 + - - -
31A VAL* 3.8 28.0 - - + +
33A TYR* 3.3 28.1 + + + -
86A PHE 3.1 4.0 + - - +
87A LYS 3.6 5.4 - - - +
89A ALA* 1.3 78.6 - - - +
91A ILE* 1.3 57.8 + - - +
94A THR* 2.7 68.7 + - + +
95A TYR* 4.5 1.3 - + - -
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Residues in contact with ILE 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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5A TYR* 3.6 40.2 - - + -
8A ILE* 4.0 32.1 - - + -
87A LYS 3.0 20.2 + - - +
88A LEU* 3.9 4.9 - - - +
90A TYR* 1.3 82.0 - - - +
92A SER* 1.3 55.3 + - - +
95A TYR* 2.7 40.9 + - + +
349A LYS* 3.7 27.4 - - + +
350A MET* 4.1 21.8 - - - -
351A PRO* 4.2 11.7 - - + -
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Residues in contact with SER 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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88A LEU 2.8 17.4 + - - -
89A ALA* 2.8 25.1 + - - -
91A ILE* 1.3 78.8 - - - +
93A ASP* 1.3 58.3 + - - -
95A TYR 4.6 4.0 - - - -
96A GLY* 3.5 11.3 - - - -
349A LYS* 4.6 9.4 - - - +
367A PHE* 4.9 0.3 - - - -
368A ASN* 3.6 20.9 + - - -
372A GLY* 3.4 24.0 + - - -
373A GLU* 3.1 22.7 - - - +
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Residues in contact with ASP 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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33A TYR* 2.5 37.7 + - + +
36A THR* 3.4 26.7 + - - +
89A ALA 2.8 15.6 + - - +
90A TYR 3.9 1.8 - - - +
92A SER* 1.3 75.8 + - - +
94A THR* 1.3 61.4 + - - +
96A GLY 4.0 2.4 + - - -
372A GLY 2.7 27.4 - - - +
373A GLU* 3.2 23.6 - - - +
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Residues in contact with THR 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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29A ARG* 4.2 9.6 - - - +
33A TYR* 5.4 1.0 - - - -
90A TYR* 2.7 61.6 + - + +
93A ASP* 1.3 76.1 - - - +
95A TYR* 1.3 88.5 + - + +
96A GLY 3.5 2.0 + - - -
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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