Contacts of the helix formed by residues 65 - 81 (chain B) in PDB entry 1WZ9
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 ASP 65 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 5.5 2.3 - - + +
63B VAL* 3.7 2.9 + - - +
64B LYS* 1.3 77.1 - - + +
66B VAL* 1.3 65.5 + - - +
67B PRO* 3.6 10.6 - - - +
68B PHE* 3.4 33.5 + - + +
69B GLY* 3.2 17.3 + - - -
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.2 2.5 - - + +
40B SER* 3.8 15.5 - - - +
43B GLN* 4.8 7.0 - - - +
60B PHE* 3.9 28.5 - - + +
63B VAL* 3.8 39.5 - - + +
65B ASP* 1.3 74.1 - - - +
67B PRO* 1.4 71.7 - - + +
69B GLY* 3.0 4.6 + - - -
70B PHE* 3.0 49.0 + - + -
112B TYR* 4.5 0.2 - - - +
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Residues in contact with PRO 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 4.2 17.5 - - + -
65B ASP* 3.5 14.1 - - - +
66B VAL* 1.4 95.0 - - + +
68B PHE* 1.3 55.6 + - - +
70B PHE* 3.4 2.5 + - - +
71B GLN* 2.8 27.2 + - - +
107B SER 5.6 1.6 - - - +
111B PRO* 3.4 20.7 - - + +
112B TYR* 3.3 35.4 + - + +
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Residues in contact with PHE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASP* 3.4 30.6 + - + +
66B VAL 3.3 0.6 - - - -
67B PRO* 1.3 77.1 - - - +
69B GLY* 1.3 62.2 + - - +
71B GLN* 3.4 35.0 - - - +
72B THR* 3.0 44.7 + - - -
111B PRO* 4.6 1.0 - - + +
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Residues in contact with GLY 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 5.3 13.5 - - - -
4B LEU* 3.6 17.3 - - - -
63B VAL* 6.5 0.2 - - - -
65B ASP 3.2 10.5 + - - -
66B VAL 3.0 7.8 + - - -
68B PHE* 1.3 80.4 - - - +
70B PHE* 1.3 56.4 + - - +
72B THR* 3.3 8.6 + - - -
73B VAL* 3.1 28.8 + - - +
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Residues in contact with PHE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.7 8.5 - - + -
8B ASN* 3.4 40.4 - - - -
33B ILE* 4.0 9.0 - - + -
36B SER* 3.7 11.4 - - - -
37B THR* 3.3 41.5 - - + -
40B SER* 3.3 20.6 - - - -
60B PHE* 3.5 28.5 - + - -
66B VAL* 3.0 31.8 + - + -
67B PRO 3.9 5.6 - - - +
69B GLY* 1.3 72.8 - - - +
71B GLN* 1.3 54.8 + - - +
73B VAL* 3.2 7.4 + - + +
74B THR* 2.7 42.3 + - - -
111B PRO 4.7 0.9 - - - -
112B TYR* 4.3 8.3 - - + -
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Residues in contact with GLN 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 PRO 2.8 15.7 + - - +
68B PHE* 3.4 35.5 - - + +
70B PHE* 1.3 75.7 - - - +
72B THR* 1.3 57.0 + - - +
74B THR* 3.4 3.1 + - - -
75B SER* 3.0 32.2 + - - -
110B ARG* 4.0 17.5 - - - +
111B PRO* 3.4 48.4 + - + +
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Residues in contact with THR 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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1B MET 6.0 4.7 - - - +
68B PHE* 3.0 34.8 + - - -
69B GLY* 3.5 10.9 - - - -
70B PHE 3.2 0.2 - - - -
71B GLN* 1.3 74.0 - - - +
73B VAL* 1.3 65.8 + - + +
75B SER* 3.7 4.6 - - - -
76B ASP* 3.2 42.6 + - - +
362B LYS* 6.3 0.4 - - - -
363B THR* 5.2 6.3 - - + -
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.6 8.3 - - + -
33B ILE* 4.1 29.6 - - + -
69B GLY 3.1 18.2 + - - +
70B PHE* 3.2 12.8 + - + +
72B THR* 1.3 76.2 - - + +
74B THR* 1.3 64.5 + - - +
76B ASP* 3.4 7.3 + - - +
77B VAL* 3.0 33.4 + - + +
360B HIS* 5.2 2.5 - - - +
363B THR* 4.6 13.2 - - + +
365B ASN* 3.6 29.6 - - + +
367B ILE* 5.3 1.3 - - + -
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Residues in contact with THR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B THR* 4.4 10.9 + - - +
70B PHE* 2.7 28.9 + - - -
71B GLN* 3.8 5.4 - - - -
73B VAL* 1.3 70.9 - - - +
75B SER* 1.3 58.7 + - - +
77B VAL* 3.3 4.1 + - - -
78B ASN* 2.9 53.7 + - - +
90B LYS* 3.5 30.4 + - - +
111B PRO 4.9 6.1 + - - +
113B ALA 6.0 0.7 - - - +
115B GLU* 3.6 13.2 + - - +
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Residues in contact with SER 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLN* 3.0 20.7 + - - -
72B THR* 3.7 7.2 - - - -
74B THR* 1.3 76.5 - - - +
76B ASP* 1.3 67.5 + - - +
78B ASN* 3.9 4.8 - - - +
79B LYS* 3.1 41.1 + - - +
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Residues in contact with ASP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 3.2 26.8 + - - +
73B VAL 3.7 4.0 - - - +
74B THR 3.4 0.2 - - - -
75B SER* 1.3 81.8 + - - +
77B VAL* 1.3 62.1 + - - +
79B LYS* 3.7 15.7 + - - +
80B LEU* 3.3 21.8 + - - +
360B HIS* 3.6 25.6 + - + +
362B LYS* 3.4 31.7 + - + -
363B THR* 3.6 22.0 - - - +
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 6.2 0.4 - - + -
73B VAL* 3.0 27.1 + - + +
74B THR* 3.9 4.9 - - - +
75B SER 3.3 0.2 - - - -
76B ASP* 1.3 74.9 - - - +
78B ASN* 1.3 72.4 + - - +
80B LEU* 3.1 20.6 + - + +
81B SER* 3.1 13.6 + - - +
86B LEU* 4.3 11.3 - - + +
88B LEU* 3.3 42.2 - - + +
90B LYS* 6.1 2.2 - - - +
226B LEU* 5.9 0.4 - - + -
360B HIS* 4.9 14.1 - - + +
367B ILE* 4.2 18.4 - - + -
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Residues in contact with ASN 78 (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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74B THR* 2.9 40.0 + - - +
75B SER* 3.9 5.6 - - - +
77B VAL* 1.3 81.0 - - - +
79B LYS* 1.3 62.5 + - + +
81B SER* 2.5 24.7 + - - -
82B SER* 3.7 6.9 + - - -
88B LEU 4.9 12.1 + - - +
89B ILE* 6.4 0.2 - - - +
90B LYS* 5.3 1.6 - - - +
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Residues in contact with LYS 79 (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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238A ASP* 4.7 15.9 + - + +
240A SER* 3.7 19.5 + - - +
75B SER* 3.1 33.7 + - - +
76B ASP* 3.8 20.3 + - - +
78B ASN* 1.3 76.0 - - + +
80B LEU* 1.3 57.6 + - - +
82B SER* 3.1 29.4 + - - -
83B PHE* 3.4 13.7 - - + -
362B LYS* 4.9 7.8 - - - +
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Residues in contact with LEU 80 (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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76B ASP 3.3 11.5 + - - +
77B VAL* 3.1 16.4 + - + +
79B LYS* 1.3 77.0 - - - +
81B SER* 1.3 54.4 + - - +
82B SER 3.1 5.4 - - - -
83B PHE* 3.2 28.1 + - + -
84B TYR* 2.9 48.5 + - + +
86B LEU* 4.1 12.1 - - + -
225B HIS* 3.4 32.1 - - + +
226B LEU* 3.9 33.2 - - + -
360B HIS* 4.3 13.9 - - + +
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Residues in contact with SER 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 3.1 7.1 + - - +
78B ASN* 2.5 35.2 + - - +
80B LEU* 1.3 71.0 - - - +
82B SER* 1.3 61.6 + - - +
83B PHE 3.2 0.4 - - - -
84B TYR* 3.1 21.3 - - - +
86B LEU* 3.0 29.1 - - - +
87B LYS* 4.9 15.7 + - - +
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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
------------------------------------------------------------
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