Contacts of the helix formed by residues 69 - 82 (chain A) in PDB entry 1WDR
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 TRP 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A VAL* 3.8 10.1 - - + -
59A ILE* 3.6 42.8 - - + -
67A TYR* 3.5 19.5 + + + +
68A ASP* 1.3 70.7 + - - +
70A ARG* 1.3 59.4 + - - +
71A ALA 3.5 2.0 - - - -
72A TYR* 3.4 7.3 + - + +
73A ARG* 2.9 34.3 + - + +
157A TYR* 3.8 23.8 - + - -
160A SER* 2.8 23.7 + - - -
161A PHE* 3.5 48.0 - + + -
164A ASN* 3.4 34.8 - - + +
165A MET* 4.1 22.0 - - + -
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Residues in contact with ARG 70 (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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68A ASP* 2.8 38.4 + - - +
69A TRP* 1.3 77.9 - - - +
71A ALA* 1.3 63.0 + - - +
73A ARG* 3.2 12.6 + - - +
74A SER* 3.1 23.3 + - - -
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Residues in contact with ALA 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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23A VAL* 4.0 9.1 - - + +
27A ASN* 3.4 39.1 + - - +
28A VAL* 4.3 0.4 - - - -
29A PHE* 3.9 26.4 - - + +
68A ASP* 4.7 0.8 + - - -
69A TRP 3.5 0.2 - - - -
70A ARG* 1.3 78.7 - - - +
72A TYR* 1.3 58.4 + - - +
74A SER* 3.2 9.7 + - - +
75A LEU* 3.0 25.6 + - - +
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Residues in contact with TYR 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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22A VAL* 5.7 1.0 - - - +
23A VAL* 3.8 31.4 + - + +
27A ASN* 4.4 2.0 + - - -
52A VAL* 4.5 3.5 - - + +
53A ASP 2.7 29.5 + - - -
54A VAL* 3.8 26.9 - - + -
55A TRP* 3.4 23.1 + - - -
58A ILE* 4.1 8.6 - - + +
59A ILE* 3.5 34.1 - - + -
69A TRP* 3.4 9.0 + - + +
70A ARG 3.3 0.4 - - - -
71A ALA* 1.3 77.4 - - - +
73A ARG* 1.3 64.7 + - - +
75A LEU* 3.2 26.9 + - + +
76A LEU* 2.9 34.2 + - + +
161A PHE* 6.0 0.2 - - + -
165A MET* 3.9 16.8 - - + -
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Residues in contact with ARG 73 (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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69A TRP* 2.9 25.7 + - + +
70A ARG* 3.2 12.1 + - - +
72A TYR* 1.3 77.2 - - - +
74A SER* 1.3 56.4 + - - +
76A LEU 3.4 0.2 + - - -
77A GLN* 2.9 30.8 + - - +
164A ASN* 2.9 25.0 + - - -
165A MET* 3.5 16.8 - - - +
167A ASP* 2.8 42.6 + - - -
168A PHE* 3.6 30.2 - - - -
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Residues in contact with SER 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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29A PHE* 3.9 18.0 - - - -
70A ARG 3.1 14.5 + - - -
71A ALA* 3.2 10.6 + - - -
73A ARG* 1.3 74.4 - - - +
75A LEU* 1.3 62.7 + - - +
77A GLN* 3.4 8.6 + - - +
78A LEU* 3.1 21.8 + - - +
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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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18A LEU* 4.1 9.9 - - + -
22A VAL* 4.0 11.9 - - + -
23A VAL* 4.4 5.6 - - + -
29A PHE* 3.7 20.5 - - + -
35A LEU* 3.5 31.9 - - + -
52A VAL* 4.0 33.2 - - + -
71A ALA 3.0 12.9 + - - +
72A TYR* 3.2 26.0 + - + +
74A SER* 1.3 74.5 - - - +
76A LEU* 1.3 69.5 + - + +
78A LEU* 3.1 3.8 + - + +
79A VAL* 3.0 33.2 + - + +
86A LEU* 6.3 0.4 - - + -
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Residues in contact with LEU 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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52A VAL* 5.3 1.1 - - + -
54A VAL* 5.9 1.3 - - + -
72A TYR* 2.9 34.0 + - + +
75A LEU* 1.3 86.3 - - + +
77A GLN* 1.3 63.8 - - - +
79A VAL* 3.2 5.9 + - + +
80A GLN* 2.9 23.9 + - - +
86A LEU* 3.6 27.1 - - + -
161A PHE* 4.7 5.8 - - + -
165A MET* 4.1 20.4 - - + -
168A PHE* 3.7 33.7 - - + -
173A LEU* 3.6 14.3 - - + +
174A ILE* 4.1 23.3 - - + -
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Residues in contact with GLN 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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73A ARG* 2.9 19.7 + - - +
74A SER* 3.5 8.3 - - - +
75A LEU 3.2 0.2 - - - -
76A LEU* 1.3 77.6 - - - +
78A LEU* 1.3 57.1 + - - +
80A GLN* 3.3 18.8 + - - +
81A GLU* 2.9 66.6 + - - +
168A PHE* 3.6 24.0 - - + -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A PHE* 3.8 24.2 - - + -
32A PRO* 3.7 24.9 - - + +
35A LEU* 4.2 3.6 - - + -
36A LYS* 3.9 31.9 - - + +
39A LEU* 4.1 15.0 - - + -
74A SER 3.1 11.7 + - - +
75A LEU 3.1 9.0 + - - +
77A GLN* 1.3 75.5 - - - +
79A VAL* 1.3 65.5 + - - +
81A GLU* 3.1 20.4 + - + +
82A CYS* 3.0 36.8 + - - -
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Residues in contact with VAL 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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18A LEU* 4.7 2.9 - - + -
39A LEU* 4.2 20.0 - - + -
50A VAL* 3.9 26.0 - - + -
75A LEU* 3.0 32.2 + - + +
76A LEU* 3.2 10.5 + - - +
78A LEU* 1.3 75.0 - - - +
80A GLN* 1.3 61.6 + - - +
82A CYS* 3.2 11.1 + - - +
83A GLY 3.3 8.3 + - - -
84A LEU* 3.3 36.8 + - + +
85A THR 3.9 5.8 - - - +
86A LEU* 4.6 11.0 - - + -
173A LEU* 4.3 7.0 - - + -
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Residues in contact with GLN 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 LEU 2.9 16.6 + - - +
77A GLN* 3.5 29.1 + - - +
79A VAL* 1.3 78.6 - - - +
81A GLU* 1.3 63.7 + - - +
83A GLY* 3.0 13.7 + - - -
84A LEU 4.4 1.8 - - - -
168A PHE* 3.7 16.1 - - + -
171A SER* 3.5 24.4 + - - -
173A LEU* 3.8 21.6 - - + +
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Residues in contact with GLU 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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36A LYS* 5.9 1.2 + - - -
40A LEU* 5.4 1.2 - - - +
77A GLN* 2.9 49.9 + - - +
78A LEU* 3.1 27.3 + - + +
80A GLN* 1.3 77.6 - - + +
82A CYS* 1.3 60.5 + - - +
83A GLY* 3.2 1.6 + - - -
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Residues in contact with CYS 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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36A LYS* 4.3 8.1 - - - -
39A LEU* 3.9 32.5 - - + -
40A LEU* 4.0 29.6 - - + +
43A ARG* 3.3 26.5 - - - +
78A LEU* 3.0 38.6 + - - +
79A VAL 3.2 4.2 + - - +
80A GLN 3.1 0.4 - - - -
81A GLU* 1.3 76.7 - - - +
83A GLY* 1.3 60.8 + - - +
84A LEU* 3.4 7.3 + - + +
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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