Contacts of the helix formed by residues 70 - 88 (chain A) in PDB entry 4WNF
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 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A TYR* 3.1 34.1 + - + +
68A LEU* 3.2 5.4 - - + +
69A HIS* 1.3 75.9 - - - +
71A TYR* 1.3 62.7 + - - +
72A ALA* 3.9 8.1 + - - +
73A LYS* 3.0 44.9 + - - +
74A ALA* 3.4 7.8 + - - +
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Residues in contact with TYR 71 (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 PHE* 3.5 51.1 + + - -
69A HIS* 3.2 48.1 + - + -
70A ASP* 1.3 70.4 + - - +
72A ALA* 1.3 66.1 + - - +
74A ALA* 2.9 7.3 + - - +
75A LEU* 2.9 22.3 + - - +
104A THR* 3.5 9.2 - - + +
107A VAL* 3.5 35.6 - - + +
108A LEU* 4.0 25.4 - - + -
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Residues in contact with ALA 72 (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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70A ASP* 3.9 8.7 + - - +
71A TYR* 1.3 77.0 - - - +
73A LYS* 1.3 58.8 + - + +
75A LEU* 3.4 8.2 - - - +
76A GLU* 3.0 30.3 + - - +
108A LEU* 4.8 10.6 - - + +
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Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU* 6.0 0.4 + - - -
65A TYR* 4.1 28.2 + - + +
70A ASP* 3.0 32.7 + - - +
71A TYR 3.2 0.8 - - - -
72A ALA* 1.3 78.9 - - + +
74A ALA* 1.3 59.1 + - - +
76A GLU* 3.8 5.9 - - + +
77A TYR* 2.9 51.9 + - + +
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Residues in contact with ALA 74 (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 GLY* 3.0 31.0 - - - +
65A TYR* 4.2 2.2 - - - +
66A PHE* 3.8 20.9 - - + +
70A ASP 3.4 5.0 + - - +
71A TYR* 2.9 10.9 + - - +
73A LYS* 1.3 75.0 - - - +
75A LEU* 1.3 66.8 + - - +
77A TYR* 3.0 2.4 + - - +
78A HIS* 2.8 35.0 + - - +
104A THR* 4.1 9.6 - - + +
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Residues in contact with LEU 75 (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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71A TYR 2.9 11.0 + - - +
72A ALA* 3.4 11.4 - - - +
74A ALA* 1.3 75.6 - - - +
76A GLU* 1.3 83.6 + - - +
79A HIS* 2.9 32.4 + - + +
101A LEU* 3.4 21.7 - - + +
104A THR* 3.6 12.1 - - + +
105A LEU* 3.5 27.6 - - + -
108A LEU* 3.4 26.5 - - + -
110A ASN* 5.2 1.6 - - - +
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Residues in contact with GLU 76 (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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72A ALA 3.0 14.7 + - - +
73A LYS* 3.4 7.4 + - + +
74A ALA 3.2 0.4 - - - -
75A LEU* 1.3 92.9 - - - +
77A TYR* 1.3 58.9 + - + +
79A HIS* 3.3 19.4 + - - +
80A HIS* 2.7 50.8 + - + -
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Residues in contact with TYR 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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41A GLU* 3.7 23.9 + - - +
44A VAL* 5.4 6.1 - - + +
58A TYR* 3.5 48.6 - + - +
61A LEU* 3.8 33.9 - - + +
62A GLY* 3.7 9.2 - - - +
65A TYR* 3.6 28.4 + + - -
73A LYS* 2.9 40.4 + - + +
74A ALA 3.0 0.4 + - - -
76A GLU* 1.3 77.4 - - + +
78A HIS* 1.3 58.7 + - - +
80A HIS* 3.5 9.9 + + - +
81A ASP* 3.1 23.4 + - - +
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Residues in contact with HIS 78 (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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59A SER* 3.6 18.8 + - - -
62A GLY* 3.2 37.3 - - - -
63A ASN* 3.1 22.8 + - - -
74A ALA* 2.8 27.0 + - + +
77A TYR* 1.3 70.7 - - - +
79A HIS* 1.3 57.0 + - - +
80A HIS 3.2 0.4 - - - -
81A ASP* 3.4 8.2 - - - +
82A LEU* 2.6 36.7 + - - +
97A ALA* 4.0 4.9 - - - +
100A ASN* 3.4 31.0 + - + +
101A LEU* 3.7 23.1 - - + +
104A THR* 3.9 9.9 + - - -
1002B MET* 3.9 7.9 - - + -
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Residues in contact with HIS 79 (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 LEU* 2.9 24.8 + - + +
76A GLU* 3.5 21.4 + - - +
78A HIS* 1.3 78.2 - - - +
80A HIS* 1.3 59.2 + + - +
82A LEU* 3.6 8.4 - - + +
83A THR* 2.6 51.7 + - + -
101A LEU* 3.5 20.1 - - + +
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Residues in contact with HIS 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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58A TYR* 3.9 25.5 - + + -
76A GLU* 2.7 49.1 + - + -
77A TYR* 3.7 15.5 - + - +
78A HIS 3.2 0.2 - - - -
79A HIS* 1.3 79.7 + - - +
81A ASP* 1.3 65.6 + - - +
83A THR* 3.5 6.6 + - - -
84A LEU* 3.0 26.7 + - - +
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Residues in contact with ASP 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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55A SER* 2.6 42.6 + - - +
58A TYR* 4.3 10.9 - - + -
59A SER* 3.3 15.5 + - - +
77A TYR 3.1 15.0 + - - +
78A HIS* 3.1 13.3 + - - +
80A HIS* 1.3 77.0 - - - +
82A LEU* 1.3 58.2 + - - +
84A LEU* 3.1 4.0 + - - +
85A ALA* 2.9 28.1 + - - +
97A ALA* 3.2 18.3 - - - +
1005B LYS* 3.0 24.1 + - - -
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Residues in contact with LEU 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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78A HIS 2.6 20.8 + - - +
79A HIS* 3.6 8.3 - - + +
81A ASP* 1.3 74.0 - - - +
83A THR* 1.3 65.4 + - - +
85A ALA* 3.4 1.9 + - - +
86A ARG* 3.1 49.3 + - - +
94A GLU* 3.7 37.0 - - + +
97A ALA* 3.4 12.3 - - + +
98A SER* 4.0 15.7 - - - +
101A LEU* 3.5 26.9 - - + -
117A CYS* 5.4 4.0 - - - -
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Residues in contact with THR 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 HIS* 2.6 40.4 + - - -
80A HIS* 3.7 7.0 - - - -
82A LEU* 1.3 79.8 - - - +
84A LEU* 1.3 58.8 + - + +
86A ARG* 3.3 10.8 + - + +
87A THR* 2.8 33.6 + - - +
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Residues in contact with LEU 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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51A LEU* 4.0 39.0 - - + +
54A LEU* 4.3 9.2 - - + -
55A SER* 3.8 26.7 - - - +
58A TYR* 3.6 29.4 - - + -
80A HIS 3.0 15.9 + - - +
81A ASP* 3.1 4.2 + - - +
83A THR* 1.3 75.8 - - + +
85A ALA* 1.3 59.9 + - - +
87A THR* 2.9 28.6 + - + +
88A ILE* 3.0 20.9 + - + +
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Residues in contact with ALA 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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55A SER* 4.7 4.4 + - - +
81A ASP 2.9 16.1 + - - +
82A LEU* 3.8 2.5 - - - +
84A LEU* 1.3 72.5 - - - +
86A ARG* 1.3 66.4 + - - +
88A ILE* 3.5 7.9 + - - -
89A GLY* 3.2 3.1 + - - -
90A ASP* 2.9 34.8 + - + +
93A GLY* 3.6 11.2 - - - +
94A GLU* 3.4 34.3 - - - +
1005B LYS* 4.2 5.4 - - - +
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Residues in contact with ARG 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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82A LEU* 3.1 45.4 + - - +
83A THR* 3.3 12.5 - - + +
85A ALA* 1.3 75.2 - - - +
87A THR* 1.3 65.4 + - - +
88A ILE 3.2 0.9 + - - -
89A GLY* 3.2 11.2 + - - +
94A GLU* 3.1 32.0 + - - +
98A SER* 4.8 0.6 + - - -
120A ARG* 3.4 36.9 - - - +
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Residues in contact with THR 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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51A LEU* 5.0 5.6 - - + -
83A THR* 2.8 29.6 + - - +
84A LEU* 2.9 26.6 + - + +
86A ARG* 1.3 78.8 - - - +
88A ILE* 1.3 64.7 + - + +
89A GLY 3.6 0.5 + - - -
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Residues in contact with ILE 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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51A LEU* 4.0 34.5 - - + +
52A LYS* 4.2 34.8 - - + +
55A SER* 5.8 3.4 - - - -
84A LEU* 3.0 18.8 + - + +
85A ALA* 3.9 2.2 - - - +
86A ARG 3.2 0.2 - - - -
87A THR* 1.3 81.7 - - + +
89A GLY* 1.3 62.6 + - - +
90A ASP* 3.8 27.4 - - + +
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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