Contacts of the helix formed by residues 66 - 83 (chain A) in PDB entry 1WH6
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 THR 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A LYS 3.4 7.8 + - - +
65A LEU* 1.3 74.6 - - - +
67A GLN* 1.3 65.4 + - - +
68A LYS* 3.8 7.2 + - - +
69A GLY* 2.9 12.9 + - - +
70A ARG* 2.8 29.5 + - - +
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Residues in contact with GLN 67 (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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13A MET* 5.5 16.6 - - + +
66A THR* 1.3 77.3 - - - +
68A LYS* 1.3 60.8 + - - +
70A ARG* 3.3 16.7 + - - +
71A GLU* 3.2 26.1 + - - +
74A ILE* 5.1 2.0 - - - +
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Residues in contact with LYS 68 (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 THR* 3.3 6.6 + - - +
67A GLN* 1.3 77.1 - - - +
69A GLY* 1.3 58.8 + - - +
71A GLU* 3.8 30.5 - - - +
72A PRO* 4.0 4.3 - - - +
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Residues in contact with GLY 69 (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 MET* 5.7 0.2 - - - +
65A LEU* 3.7 17.9 - - - +
66A THR* 2.9 19.0 + - - -
68A LYS* 1.3 78.6 - - - +
70A ARG* 1.3 59.6 + - - +
71A GLU 3.4 0.2 - - - -
72A PRO* 3.4 9.2 - - - +
73A PHE* 3.4 20.4 - - - -
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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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12A TYR 4.7 1.4 + - - -
13A MET* 4.4 16.4 + - - -
14A TYR 5.2 3.4 + - - -
16A GLU* 5.4 1.2 + - - +
62A TRP* 2.9 73.2 + - + +
63A SER* 4.3 6.3 + - - +
65A LEU* 2.8 29.8 + - + -
66A THR* 2.8 21.4 + - - +
67A GLN* 3.3 16.9 + - - +
69A GLY* 1.3 71.0 - - - +
71A GLU* 1.3 56.8 + - - +
73A PHE* 3.0 10.1 + - - +
74A ILE* 2.8 48.0 + - + +
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Residues in contact with GLU 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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67A GLN 3.2 16.3 + - - +
68A LYS* 3.8 24.2 - - - +
70A ARG* 1.3 74.5 - - - +
72A PRO* 1.3 67.6 - - + +
74A ILE* 3.5 11.7 + - + +
75A ARG* 2.8 62.2 + - - +
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Residues in contact with PRO 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 3.3 23.7 - - + +
47A LEU* 3.6 33.9 - - + -
55A MET* 3.8 25.1 - - + -
68A LYS 4.0 4.9 - - - +
69A GLY* 3.4 18.8 - - - +
71A GLU* 1.3 95.7 - - + +
73A PHE* 1.3 56.2 + - + +
75A ARG* 3.2 8.5 + - + +
76A MET* 2.9 26.4 + - - +
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Residues in contact with PHE 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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19A THR* 3.9 18.6 - - + -
22A LEU* 3.6 13.4 - - + +
23A THR* 4.0 12.3 - - + -
55A MET* 3.4 37.7 - - + -
59A PRO* 3.8 30.5 - - + -
60A LYS 4.5 3.8 - - - -
62A TRP* 3.8 17.7 - - + -
65A LEU* 3.4 36.8 - - + -
69A GLY 3.4 12.6 - - - -
70A ARG 3.0 6.5 + - - +
72A PRO* 1.3 78.3 - - + +
74A ILE* 1.3 50.5 + - - +
76A MET* 3.0 16.2 - - + +
77A GLN* 2.8 40.2 + - - +
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Residues in contact with ILE 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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9A TYR* 3.4 29.2 - - + -
12A TYR* 4.4 11.0 - - + -
13A MET* 3.4 31.0 - - + -
62A TRP* 3.8 19.1 - - + -
67A GLN* 5.1 2.2 - - - +
70A ARG* 2.8 39.8 + - + +
71A GLU* 3.5 11.9 - - + +
73A PHE* 1.3 72.0 - - - +
75A ARG* 1.3 63.1 + - + +
77A GLN* 3.1 10.3 + - - +
78A LEU* 2.9 41.9 + - + +
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Residues in contact with ARG 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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44A VAL* 4.1 13.4 + - + +
45A LEU* 3.8 34.8 + - + -
71A GLU* 2.8 53.1 + - - +
72A PRO 3.2 7.2 + - - +
74A ILE* 1.3 80.0 - - + +
76A MET* 1.3 56.4 + - - +
78A LEU* 3.8 11.2 - - + +
79A TRP* 2.9 32.2 + - - +
84A LEU* 4.1 12.1 - - + +
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Residues in contact with MET 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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22A LEU* 4.1 10.3 - - + -
23A THR* 3.7 15.7 - - + -
26A VAL* 3.6 40.3 - - + +
40A PHE* 3.9 11.0 - - + -
45A LEU* 3.6 20.3 - - + +
55A MET* 4.4 14.4 - - + -
56A LEU* 3.5 33.4 - - + -
72A PRO 2.9 14.1 + - - +
73A PHE* 3.0 38.1 - - + +
75A ARG* 1.3 74.2 - - - +
77A GLN* 1.3 59.5 + - - +
79A TRP* 3.4 6.5 + - - +
80A LEU* 3.3 18.7 + - - +
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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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12A TYR* 3.3 50.7 + - + +
17A VAL* 3.8 29.8 - - + +
22A LEU* 3.5 26.5 - - + +
62A TRP* 3.1 29.0 - - - -
73A PHE 2.8 23.9 + - - +
74A ILE* 3.1 9.5 + - - +
76A MET* 1.3 69.6 - - - +
78A LEU* 1.3 67.4 + - - +
80A LEU* 3.5 16.1 - - - +
81A SER* 4.1 5.0 + - - -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A SER 4.4 6.1 - - - +
7A GLY 3.1 28.5 - - - +
8A GLN* 3.9 13.5 - - + -
9A TYR* 3.9 15.0 - - + +
12A TYR* 3.9 11.0 - - + +
74A ILE* 2.9 38.6 + - + +
75A ARG* 3.8 10.5 - - + +
77A GLN* 1.3 75.1 - - - +
79A TRP* 1.3 57.6 + - - +
80A LEU 2.9 1.7 + - - -
81A SER* 2.9 5.4 + - - -
82A ASP* 2.7 48.6 + - + +
84A LEU* 4.7 9.9 - - + -
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Residues in contact with TRP 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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26A VAL* 4.1 17.0 - - + -
29A LYS* 3.8 43.3 - - + -
30A LEU* 3.4 35.2 - - + -
35A ILE* 4.4 12.1 - - + -
40A PHE* 3.6 25.9 - + + -
44A VAL* 3.6 27.4 - - + +
75A ARG 2.9 19.4 + - - +
76A MET 3.7 7.6 - - - +
78A LEU* 1.3 74.3 - - - +
80A LEU* 1.3 70.4 + - + +
83A GLN* 3.1 37.4 + - + +
84A LEU* 3.4 19.3 - - + +
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Residues in contact with LEU 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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22A LEU* 3.6 30.1 - - + -
25A GLN* 3.7 45.8 - - + +
26A VAL* 3.7 16.2 - - + -
29A LYS* 3.3 42.8 - - + +
76A MET 3.3 6.7 + - - +
77A GLN* 3.5 11.9 - - - +
78A LEU 2.9 0.4 + - - -
79A TRP* 1.3 83.9 - - + +
81A SER* 1.3 62.2 + - - +
83A GLN* 4.5 1.4 - - - +
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Residues in contact with SER 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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5A SER 6.1 0.4 - - - -
6A SER* 4.9 11.2 - - - -
77A GLN 4.7 4.3 - - - -
78A LEU* 2.9 5.6 + - - -
80A LEU* 1.3 77.7 - - - +
82A ASP* 1.3 65.1 + - - +
83A GLN* 3.3 14.4 + - - +
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Residues in contact with ASP 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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6A SER* 3.7 29.8 + - - +
78A LEU* 2.7 41.6 + - + +
81A SER* 1.3 74.0 - - - +
83A GLN* 1.3 58.8 + - - +
84A LEU* 3.0 36.9 + - + +
85A GLY 4.2 4.6 + - - -
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Residues in contact with GLN 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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29A LYS* 4.6 16.9 + - - -
79A TRP* 3.1 35.1 + - + +
80A LEU 4.5 5.2 - - - +
81A SER 3.7 14.3 + - - +
82A ASP* 1.3 75.4 + - - +
84A LEU* 1.3 70.9 + - - +
85A GLY* 4.3 3.6 - - - +
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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