Contacts of the helix formed by residues 68 - 87 (chain A) in PDB entry 1WYN
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 GLN 68 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A SER* 3.2 9.1 - - - -
67A MET* 1.3 82.7 - - - +
69A ASN* 1.3 62.4 + - - +
70A TRP* 3.1 50.2 - - + +
71A HIS* 3.1 30.8 - - - +
72A GLN* 2.9 34.2 + - - +
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Residues in contact with ASN 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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67A MET 5.1 1.6 - - - +
68A GLN* 1.3 69.9 - - - +
70A TRP* 1.3 79.7 + - + +
71A HIS 3.0 0.9 - - - -
72A GLN* 2.7 17.3 + - - +
73A LEU* 2.8 19.6 + - + +
100A PHE* 3.9 31.7 - - + -
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Residues in contact with TRP 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 GLN* 3.1 49.1 - - + +
69A ASN* 1.3 82.1 - - + +
71A HIS* 1.3 89.5 + + - -
73A LEU* 3.4 7.6 + - - +
74A GLU* 2.9 31.3 + - - +
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Residues in contact with HIS 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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64A ASN* 3.2 47.3 + - + +
66A SER* 3.2 35.3 - - - +
68A GLN* 3.1 38.8 + - + +
69A ASN 2.8 1.2 + - - -
70A TRP* 1.3 93.3 + + + +
72A GLN* 1.3 65.5 + - - +
73A LEU 3.3 0.7 + - - -
74A GLU 3.3 5.0 + - - -
75A ASN* 3.4 9.0 + - - -
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Residues in contact with GLN 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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43A LYS* 3.7 17.7 + - - +
44A ASP* 2.9 60.0 + - + +
66A SER 4.0 11.4 - - - +
67A MET* 3.8 27.7 + - - +
68A GLN 2.9 25.2 + - - +
69A ASN* 2.7 11.8 + - - +
71A HIS* 1.3 72.0 - - - +
73A LEU* 1.3 62.1 + - - +
75A ASN* 3.2 13.3 - - - +
76A LEU* 3.7 3.6 + - - +
100A PHE* 3.6 24.4 - - + -
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Residues in contact with LEU 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 ASN* 2.8 20.1 + - + +
70A TRP* 3.6 11.0 - - - +
72A GLN* 1.3 68.4 - - - +
74A GLU* 1.3 67.9 + - - +
75A ASN 2.8 3.4 + - - -
76A LEU* 2.8 18.9 + - + +
77A SER* 3.1 14.1 + - - +
96A ALA* 3.6 27.8 - - + +
97A ASN* 4.3 11.9 - - - +
100A PHE* 3.1 61.5 - - + -
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Residues in contact with GLU 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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64A ASN* 3.5 21.3 - - - +
70A TRP 2.9 18.0 + - - +
71A HIS* 3.6 0.7 - - + +
73A LEU* 1.3 75.0 - - - +
75A ASN* 1.3 51.8 + - - +
77A SER* 3.2 14.1 + - - -
78A ASN* 2.7 65.0 + - - +
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Residues in contact with ASN 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 ASP* 2.9 21.0 + - - +
45A GLY 3.0 28.0 + - - +
46A THR* 4.7 2.0 - - - +
49A CYS* 3.6 16.0 - - - -
62A LYS 4.8 1.4 - - - +
63A ILE* 3.9 6.5 - - - +
64A ASN* 3.1 46.6 + - - +
71A HIS 3.4 12.0 + - - +
72A GLN* 3.2 9.4 - - - +
73A LEU 2.8 4.2 + - - -
74A GLU* 1.3 72.1 - - - +
76A LEU* 1.3 63.6 + - - +
78A ASN* 3.0 8.9 + - - +
79A PHE* 2.9 20.3 + - - +
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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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43A LYS 4.0 13.9 - - - +
45A GLY* 4.2 10.1 - - - -
48A LEU* 3.3 36.3 - - + -
72A GLN 4.4 3.8 - - - +
73A LEU* 2.8 13.3 + - + +
75A ASN* 1.3 75.7 - - - +
77A SER* 1.3 56.6 + - - +
79A PHE* 3.2 4.1 + - + +
80A ILE* 2.8 40.0 + - + +
94A PHE* 4.0 9.0 - - + -
96A ALA* 2.9 44.4 - - + +
99A LEU* 3.7 21.3 - - + -
100A PHE* 4.0 7.9 - - + +
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Residues in contact with SER 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 LEU* 3.1 13.7 + - - +
74A GLU* 3.5 21.2 - - - -
76A LEU* 1.3 77.2 - - - +
78A ASN* 1.3 61.9 + - - +
80A ILE* 4.0 9.0 - - - +
81A LYS* 3.2 27.4 + - - +
96A ALA* 4.1 12.3 - - - +
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Residues in contact with ASN 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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49A CYS* 5.8 0.2 - - - -
59A SER 4.7 2.1 - - - +
60A VAL* 4.2 18.8 - - + +
61A PRO* 4.8 16.2 - - + +
62A LYS 4.0 17.6 + - - -
64A ASN* 5.3 1.0 + - - +
74A GLU* 2.7 55.1 + - - +
75A ASN* 3.3 8.9 + - - +
77A SER* 1.3 73.9 - - - +
79A PHE* 1.3 61.9 + - - +
81A LYS* 3.0 32.4 + - + +
82A ALA* 3.3 10.4 + - - +
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Residues in contact with PHE 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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48A LEU* 3.3 51.1 - - + +
49A CYS* 4.5 5.4 - - - -
51A LEU* 4.6 3.4 - - + -
52A MET* 3.6 31.9 - - + -
60A VAL* 4.2 5.3 - - - +
75A ASN 2.9 14.7 + - - +
76A LEU* 3.2 4.9 + - + +
78A ASN* 1.3 74.0 - - - +
80A ILE* 1.3 67.5 + - - +
82A ALA* 2.8 21.5 + - - +
83A MET* 3.0 35.9 + - + -
94A PHE* 3.7 37.9 - + - -
112A LEU* 4.3 8.1 - - + -
115A LEU* 4.0 13.0 - - + -
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Residues in contact with ILE 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* 2.8 39.1 + - + +
77A SER* 4.0 9.6 - - - +
79A PHE* 1.3 70.8 - - - +
81A LYS* 1.3 57.9 + - - +
82A ALA 2.7 0.7 + - - -
83A MET* 2.5 43.3 + - + +
84A VAL* 3.4 4.9 + - + +
93A LEU* 4.5 24.9 - - + -
94A PHE* 3.2 46.2 - - + +
95A GLU* 4.0 2.2 - - - +
96A ALA* 3.8 21.1 - - + +
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Residues in contact with LYS 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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59A SER 4.9 8.7 + - - -
61A PRO* 5.6 6.1 - - - +
77A SER 3.2 15.7 + - - +
78A ASN* 3.0 37.5 + - - +
80A ILE* 1.3 79.4 - - - +
82A ALA* 1.3 60.7 + - - +
84A VAL* 3.5 23.3 + - - +
85A SER* 3.7 6.2 + - - -
139A GLU 5.7 2.7 - - - -
140A ARG* 4.3 27.2 - - - +
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Residues in contact with ALA 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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52A MET* 4.0 9.2 - - + +
56A GLN* 4.1 6.3 + - - +
59A SER* 3.8 38.6 - - - +
60A VAL* 4.6 0.7 - - + -
78A ASN 3.4 10.5 - - - +
79A PHE* 2.8 16.8 + - - +
80A ILE 2.7 4.6 + - - -
81A LYS* 1.3 77.6 - - + +
83A MET* 1.3 61.6 - - - -
85A SER* 3.2 17.1 + - - -
86A TYR* 3.3 9.2 + - - +
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Residues in contact with MET 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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52A MET* 4.4 6.7 - - - -
79A PHE* 3.0 44.0 + - + +
80A ILE* 2.5 23.0 + - + +
82A ALA* 1.3 70.7 - - - +
84A VAL* 1.3 62.3 + - - +
86A TYR* 2.9 24.9 + - - +
87A GLY 3.3 4.7 + - - -
88A MET* 3.4 36.7 - - - +
93A LEU* 3.8 16.8 - - + -
94A PHE* 3.4 27.8 - - + +
111A SER* 3.2 25.6 - - - +
112A LEU* 5.4 0.4 - - - -
115A LEU* 4.3 9.6 - - + -
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Residues in contact with VAL 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 ILE* 4.1 9.4 - - + +
81A LYS* 3.6 15.0 - - - +
82A ALA 3.3 0.4 - - - -
83A MET* 1.3 77.5 - - - +
85A SER* 1.3 62.0 + - - +
87A GLY* 3.3 10.7 + - - -
88A MET* 3.9 14.7 + - - +
93A LEU* 3.4 31.4 - - + -
136A GLU* 3.5 33.7 - - + +
138A GLN* 4.9 3.8 - - - +
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Residues in contact with SER 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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56A GLN* 3.8 18.4 + - - -
81A LYS 3.7 5.4 + - - -
82A ALA* 3.2 13.5 + - - -
83A MET 3.1 0.6 - - - -
84A VAL* 1.3 77.3 - - - +
86A TYR* 1.3 68.2 + - - +
87A GLY* 3.2 1.7 + - - -
136A GLU* 4.2 13.7 + - - +
138A GLN* 4.7 13.4 + - - +
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Residues in contact with TYR 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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2A SER* 4.6 13.9 - - - -
52A MET* 3.2 31.6 - - + -
55A LEU* 3.7 18.6 - - + +
56A GLN* 4.4 12.7 - - + +
82A ALA 3.3 2.2 + - - -
83A MET* 2.9 13.7 + - - +
85A SER* 1.3 80.6 - - - +
87A GLY* 1.3 53.4 + - - +
88A MET* 4.7 0.9 - - + -
115A LEU* 3.7 20.6 - - + -
118A LYS* 2.6 58.2 + - + +
119A ALA* 3.4 27.5 - - + +
121A THR* 5.8 0.4 - - + -
122A LYS* 2.8 39.2 + - - +
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Residues in contact with GLY 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 MET 3.3 0.8 + - - -
84A VAL 3.3 6.2 + - - -
85A SER 3.1 4.5 - - - -
86A TYR* 1.3 80.4 - - - +
88A MET* 1.3 66.9 + - - +
89A ASN* 4.8 3.1 - - - +
118A LYS* 3.4 18.7 - - - +
134A TYR* 3.9 31.7 + - - -
136A GLU* 5.5 1.3 - - - -
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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
------------------------------------------------------------
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