Contacts of the helix formed by residues 75 - 91 (chain A) in PDB entry 2Y43
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 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA* 2.9 23.4 + - + +
37A ILE* 3.9 12.6 - - + +
44A ASN* 2.7 32.4 + - - +
73A LYS 3.5 0.6 + - - -
74A ASN* 1.3 71.5 - - - +
76A ARG* 1.3 64.3 + - - +
77A ILE* 3.5 10.2 - - - +
78A LEU* 3.2 33.9 + - + +
79A ASP* 4.1 1.4 + - - +
37B ILE* 3.7 8.2 - - - +
42B SER* 3.6 1.3 - - - -
44B ASN* 4.7 0.3 + - - -
75B ASN* 3.0 43.0 + - - -
77B ILE* 4.3 0.6 - - - +
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Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ILE* 6.1 0.6 - - - +
74A ASN* 3.6 41.1 + - + +
75A ASN* 1.3 68.8 - - - +
77A ILE* 1.3 65.3 + - - +
79A ASP* 3.2 28.2 + - - +
80A GLU* 3.4 15.7 + - + +
41B CYS 4.7 5.9 + - - -
42B SER* 2.9 33.4 + - - +
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Residues in contact with ILE 77 (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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75A ASN* 3.5 19.5 - - - +
76A ARG* 1.3 76.9 - - - +
78A LEU* 1.3 63.6 + - + +
80A GLU* 3.3 7.7 + - - +
81A LEU* 2.9 36.1 + - + +
22B LEU* 3.3 38.1 - - + +
32B PHE* 3.9 13.2 - - + -
42B SER* 4.7 2.6 + - - +
44B ASN* 3.7 25.9 - - + +
75B ASN* 4.2 2.0 - - - +
78B LEU* 3.8 31.6 - - + -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.9 16.8 - - + +
32A PHE* 3.9 16.2 - - + -
35A ALA* 3.6 22.4 - - + -
44A ASN* 3.6 37.5 - - + +
75A ASN* 3.2 24.4 + - - +
77A ILE* 1.3 80.2 - - + +
79A ASP* 1.3 59.2 + - - +
81A LEU* 3.3 14.8 + - + +
82A VAL* 2.9 35.4 + - - +
77B ILE* 3.7 28.5 - - + -
81B LEU* 4.2 1.8 - - + -
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Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE 4.6 4.8 - - - +
33A ASN 4.4 0.3 - - - -
34A ILE* 3.4 23.7 + - - +
35A ALA* 2.8 31.6 + - - +
74A ASN* 5.6 1.2 - - - +
75A ASN 4.5 2.6 - - - +
76A ARG* 3.2 23.3 + - - +
78A LEU* 1.3 76.4 - - - +
80A GLU* 1.3 61.3 + - + +
82A VAL* 3.5 7.5 + - - +
83A LYS* 3.0 28.2 + - - +
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Residues in contact with GLU 80 (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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76A ARG* 3.4 12.3 + - + +
77A ILE* 3.3 10.9 + - - +
79A ASP* 1.3 76.9 - - - +
81A LEU* 1.3 61.1 + - - +
83A LYS* 3.4 18.6 + - - +
84A SER* 2.9 35.2 + - - -
22B LEU* 4.0 24.7 - - + +
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Residues in contact with LEU 81 (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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19A ILE* 6.6 0.2 - - + -
23A LEU* 3.9 16.4 - - + -
77A ILE* 2.9 36.1 + - + +
78A LEU* 3.6 10.3 - - + +
80A GLU* 1.3 74.0 - - - +
82A VAL* 1.3 59.7 + - - +
84A SER* 3.3 1.5 + - - -
85A LEU* 2.8 33.8 + - - +
19B ILE* 4.2 23.4 - - + +
22B LEU* 3.8 31.0 - - + -
23B LEU* 4.2 12.1 - - + -
78B LEU* 4.1 10.1 - - + -
81B LEU* 3.8 29.6 - - + -
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Residues in contact with VAL 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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23A LEU* 4.1 27.8 - - + -
31A TYR* 3.9 19.3 - - + -
32A PHE* 3.8 38.1 - - + +
78A LEU 2.9 21.8 + - - +
79A ASP* 3.7 5.8 - - - +
81A LEU* 1.3 75.8 - - - +
83A LYS* 1.3 58.1 + - - +
85A LEU* 3.9 1.2 - - - +
86A ASN* 2.9 52.4 + - - +
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Residues in contact with LYS 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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79A ASP 3.0 16.8 + - - +
80A GLU* 3.6 20.6 - - - +
81A LEU 3.3 0.2 - - - -
82A VAL* 1.3 78.3 - - - +
84A SER* 1.3 63.8 + - - +
86A ASN* 3.5 8.8 + - - +
87A PHE* 3.1 21.5 + - - +
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Residues in contact with SER 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 GLU* 2.9 20.9 + - - -
81A LEU 3.8 3.4 - - - -
83A LYS* 1.3 75.8 - - - +
85A LEU* 1.3 60.4 + - - +
87A PHE* 3.3 8.8 + - - +
88A ALA* 3.0 27.2 + - - +
15B VAL* 5.5 0.9 - - - +
18B THR* 3.2 33.8 - - - +
19B ILE* 3.9 15.2 - - - +
22B LEU* 3.7 9.5 - - - +
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Residues in contact with LEU 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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9A TRP* 3.8 20.9 - - + -
16A MET* 3.9 16.4 - - + -
19A ILE* 3.7 28.0 - - + -
20A ASP* 3.6 14.8 - - - +
23A LEU* 3.7 16.4 - - + -
31A TYR* 5.7 0.2 - - + -
81A LEU 2.8 18.1 + - - +
82A VAL* 4.0 2.2 - - - +
84A SER* 1.3 72.1 - - - +
86A ASN* 1.3 56.9 + - - +
88A ALA* 3.3 1.1 + - + +
89A ARG* 2.8 60.8 + - - +
19B ILE* 3.5 26.2 - - + +
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Residues in contact with ASN 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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31A TYR* 4.0 14.2 - - - -
82A VAL* 2.9 38.4 + - - +
83A LYS* 3.6 8.0 - - - +
85A LEU* 1.3 77.0 - - - +
87A PHE* 1.3 56.9 + - - +
89A ARG* 3.0 27.1 + - - +
90A ASN* 2.9 45.7 + - - +
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Residues in contact with PHE 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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83A LYS* 3.1 10.6 + - + +
84A SER* 3.5 10.8 - - - +
86A ASN* 1.3 79.6 - - - +
88A ALA* 1.3 61.9 + - - +
90A ASN* 3.4 3.3 + - - +
91A HIS* 2.8 67.4 + + + +
15B VAL* 3.6 27.4 - - + -
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Residues in contact with ALA 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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9A TRP* 4.4 4.9 - - + -
84A SER 3.0 13.8 + - - +
85A LEU* 3.6 7.2 - - - +
87A PHE* 1.3 76.4 - - - +
89A ARG* 1.3 64.1 + - - +
91A HIS* 3.1 3.1 + - - +
92A LEU* 3.0 30.3 + - + +
15B VAL* 3.7 32.3 - - + +
16B MET* 4.3 7.2 - - - -
19B ILE* 4.0 19.7 - - + -
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Residues in contact with ARG 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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8A ARG* 4.6 15.5 - - - +
9A TRP* 3.5 40.1 - - + +
20A ASP* 2.9 31.5 + - - -
31A TYR* 3.3 29.7 + - - -
85A LEU* 2.8 41.5 + - - +
86A ASN* 3.0 32.4 + - - +
88A ALA* 1.3 72.5 - - - +
90A ASN* 1.3 66.6 + - - +
92A LEU 3.1 11.6 + - - -
93A LEU* 3.4 29.1 + - + +
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Residues in contact with ASN 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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86A ASN* 2.9 32.0 + - - +
87A PHE* 3.9 5.7 - - - +
88A ALA 3.3 0.2 - - - -
89A ARG* 1.3 80.6 + - - +
91A HIS* 1.3 69.7 + - + +
92A LEU 3.5 0.2 - - - -
93A LEU* 4.1 24.5 + - - +
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Residues in contact with HIS 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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87A PHE* 2.8 67.7 + + + +
88A ALA* 3.1 7.0 + - - +
90A ASN* 1.3 86.9 - - + +
92A LEU* 1.3 68.4 + - + +
93A LEU 3.7 1.6 - - - -
94A GLN 5.5 0.2 + - - -
15B VAL* 5.3 4.9 - - + -
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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