Contacts of the helix formed by residues 67 - 87 (chain A) in PDB entry 5WIU
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 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ALA 3.9 19.1 - - - +
65A LEU* 3.0 6.1 + - - -
66A GLN* 1.3 79.9 - - - +
68A PRO* 1.3 76.6 - - - +
69A THR* 3.7 6.8 + - - -
70A ASN* 3.0 35.5 + - - +
71A SER* 3.2 9.5 + - - -
1205A OLA 3.3 7.9 + - - +
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Residues in contact with PRO 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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67A THR* 1.3 86.9 - - - +
69A THR* 1.3 59.2 + - - +
71A SER* 2.6 29.0 + - - +
72A PHE* 3.3 8.4 - - - -
132A ASP* 4.7 0.2 - - - -
133A ARG* 3.5 21.5 - - - +
152A GLN* 3.8 25.7 - - + +
1202A PO4 4.6 4.0 - - - +
1223A GOL 3.8 33.0 - - - +
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Residues in contact with THR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR* 3.3 7.3 + - - -
68A PRO* 1.3 79.4 - - - +
70A ASN* 1.3 71.6 + - - +
72A PHE* 3.1 23.6 + - - +
73A ILE* 3.4 15.5 + - + +
129A ILE* 4.8 7.6 - - + -
133A ARG* 3.4 31.0 + - - +
393A MET* 5.6 2.0 - - + +
395A VAL* 6.2 0.7 - - + -
396A LEU* 4.2 31.9 - - + +
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Residues in contact with ASN 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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59A VAL* 4.5 6.3 - - + -
65A LEU* 2.8 48.2 + - - +
67A THR* 3.0 17.9 + - - +
69A THR* 1.3 80.1 - - - +
71A SER* 1.3 64.3 + - - +
73A ILE* 3.2 26.1 - - - +
74A VAL* 3.0 27.2 + - - +
455A PHE* 3.8 21.5 - - - -
1205A OLA 3.5 4.3 - - - +
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Residues in contact with SER 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 THR 3.2 6.6 + - - -
68A PRO* 2.6 23.7 + - - -
70A ASN* 1.3 77.8 - - - +
72A PHE* 1.3 63.0 + - - +
74A VAL* 3.4 5.0 + - - +
75A SER* 3.1 16.6 + - - -
152A GLN* 3.4 22.1 - - - +
153A LEU* 5.3 3.8 - - - -
156A ILE* 3.4 20.2 - - - +
1205A OLA 3.3 32.8 + - - +
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Residues in contact with PHE 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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68A PRO 3.3 10.8 - - - -
69A THR* 3.1 9.7 + - - +
71A SER* 1.3 79.5 + - - +
73A ILE* 1.3 60.3 + - - +
75A SER* 3.2 4.9 + - - -
76A LEU* 2.9 33.3 + - - +
125A ASN* 4.1 8.3 - - - +
128A ALA* 3.7 30.1 - - + -
129A ILE* 3.3 32.8 - - + -
132A ASP* 3.6 31.9 - - + -
152A GLN* 3.5 35.0 - - + -
155A LEU* 3.8 13.5 - - + -
156A ILE* 3.5 27.8 - - + -
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Residues in contact with ILE 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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55A VAL* 4.1 11.2 - - + -
59A VAL* 5.5 0.7 - - + -
69A THR* 3.4 21.0 + - + +
70A ASN* 3.2 31.1 + - - +
72A PHE* 1.3 76.2 - - - +
74A VAL* 1.3 62.7 - - - +
76A LEU* 3.4 10.0 + - + +
77A ALA* 3.0 21.3 + - - +
129A ILE* 4.9 8.7 - - + -
395A VAL* 5.3 5.8 - - + -
396A LEU* 5.2 7.9 - - + -
448A TYR* 3.4 49.8 + - + +
455A PHE* 4.2 15.5 - - + -
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Residues in contact with VAL 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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55A VAL* 5.2 1.6 - - + +
56A CYS* 4.3 22.5 - - + +
59A VAL* 3.7 36.8 - - + -
70A ASN 3.0 18.9 + - - +
71A SER 3.6 7.0 - - - +
72A PHE 3.2 0.2 - - - -
73A ILE* 1.3 77.7 - - - +
75A SER* 1.3 56.6 + - - +
77A ALA* 3.1 9.1 + - - +
78A ALA* 2.9 28.2 + - + +
1205A OLA 3.7 32.8 - - + -
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Residues in contact with SER 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 SER 3.1 14.2 + - - -
72A PHE* 3.3 10.5 - - - -
74A VAL* 1.3 76.8 - - - +
76A LEU* 1.3 61.3 + - - +
78A ALA* 3.2 6.2 + - - +
79A ALA* 3.1 18.4 + - - +
125A ASN* 2.8 26.1 + - - -
156A ILE* 3.6 8.7 - - - +
160A TRP* 2.9 29.6 + - - -
1205A OLA 3.6 19.5 - - - -
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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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72A PHE 2.9 17.6 + - - +
73A ILE* 3.6 13.5 - - + +
75A SER* 1.3 72.8 - - - +
77A ALA* 1.3 66.8 + - - +
79A ALA* 3.3 6.1 + - - +
80A ASP* 3.1 28.0 + - - +
122A SER* 3.3 45.2 + - - +
125A ASN* 3.8 11.9 - - + +
126A LEU* 3.8 27.6 - - + -
129A ILE* 4.1 14.4 - - + -
399A VAL* 5.0 1.3 - - + -
403A PHE* 6.4 0.2 - - + -
444A ASN* 4.6 13.7 - - - +
448A TYR* 4.4 13.7 - - - +
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Residues in contact with ALA 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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52A ASN* 3.5 28.7 - - - +
55A VAL* 4.1 12.1 - - + -
56A CYS* 3.7 20.6 - - - -
73A ILE 3.0 14.3 + - - +
74A VAL 3.1 9.4 + - - +
76A LEU* 1.3 75.2 - - - +
78A ALA* 1.3 57.4 + - - +
80A ASP* 3.2 3.8 + - - +
81A LEU* 2.9 34.9 + - - +
448A TYR* 6.1 1.1 - - + -
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Residues in contact with ALA 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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56A CYS* 4.7 3.5 - - - -
74A VAL* 2.9 13.2 + - + +
75A SER* 3.3 11.0 - - - +
77A ALA* 1.3 74.9 - - - +
79A ALA* 1.3 59.4 + - - +
81A LEU* 3.2 11.2 + - - +
82A LEU* 2.8 40.7 + - + +
160A TRP* 4.6 1.6 - - + -
1205A OLA 3.9 28.0 - - + -
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Residues in contact with ALA 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 SER 3.1 10.3 + - - +
76A LEU* 3.5 11.4 - - - +
77A ALA 3.3 0.2 - - - -
78A ALA* 1.3 76.1 - - - +
80A ASP* 1.3 60.0 + - - +
82A LEU* 3.6 2.6 + - - +
83A LEU* 3.0 26.0 + - - +
118A LEU* 3.9 17.7 - - + +
121A ALA 5.2 0.2 - - - -
122A SER* 3.6 26.7 - - - +
125A ASN* 5.9 0.7 - - - +
160A TRP* 3.8 26.6 - - + -
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Residues in contact with ASP 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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48A VAL* 3.3 13.5 - - - +
52A ASN* 3.7 23.5 - - - +
76A LEU* 3.1 15.9 + - - +
77A ALA 3.6 6.7 - - - +
79A ALA* 1.3 77.7 - - - +
81A LEU* 1.3 64.7 + - - +
83A LEU* 3.2 5.0 + - - +
84A ALA 3.0 18.5 + - - -
122A SER* 4.2 11.5 + - - -
440A ASN* 4.8 3.3 - - - +
441A SER* 2.5 46.5 + - - +
444A ASN* 4.6 14.0 + - - +
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Residues in contact with LEU 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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48A VAL 4.0 0.7 - - - +
49A LEU* 3.6 31.4 - - + +
52A ASN* 3.7 16.4 - - + +
53A SER* 3.6 26.9 - - - +
56A CYS* 4.2 23.1 - - + -
77A ALA 2.9 20.5 + - - +
78A ALA* 3.6 7.6 - - - +
80A ASP* 1.3 77.0 - - - +
82A LEU* 1.3 62.2 + - + +
84A ALA* 3.2 5.1 + - - +
85A LEU* 3.0 35.5 + - + +
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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 ALA* 2.8 21.9 + - + +
79A ALA 3.8 4.3 - - - +
81A LEU* 1.3 78.9 - - + +
83A LEU* 1.3 57.3 + - - +
85A LEU* 4.6 11.7 - - + -
86A LEU* 2.9 56.4 + - + +
114A MET* 5.6 1.6 - - - -
117A MET* 6.1 0.7 - - + -
118A LEU* 3.7 17.0 - - + +
160A TRP* 4.2 13.5 - - + -
1205A OLA 4.0 36.6 - - + -
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Residues in contact with LEU 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 ALA 3.0 15.2 + - - +
80A ASP* 3.4 9.6 - - - +
81A LEU 3.2 0.2 - - - -
82A LEU* 1.3 76.7 - - - +
84A ALA* 1.3 57.4 + - - +
87A VAL* 3.0 56.3 + - + -
88A LEU* 3.0 25.2 + - + -
115A ASP* 4.2 5.4 - - - +
118A LEU* 3.5 19.5 - - + +
119A CYS 5.9 0.9 - - - +
407A TRP* 5.9 2.7 - - + -
438A TYR* 3.8 33.4 - - + -
441A SER* 3.3 29.6 - - - +
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Residues in contact with ALA 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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45A ILE* 4.0 15.3 - - + +
48A VAL* 3.7 20.0 - - + -
49A LEU* 3.6 29.8 - - + -
80A ASP 3.0 15.9 + - - +
81A LEU 3.2 0.4 + - - +
83A LEU* 1.3 76.9 - - - +
85A LEU* 1.3 60.1 + - - +
88A LEU* 3.8 15.6 - - + +
89A PRO* 3.1 22.7 - - - +
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Residues in contact with LEU 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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49A LEU* 3.7 29.4 - - + -
81A LEU* 3.0 28.1 + - + +
82A LEU* 4.0 12.1 - - + +
84A ALA* 1.3 79.1 - - - +
86A LEU* 1.3 68.4 + - + +
87A VAL 3.7 0.2 - - - -
89A PRO* 3.8 6.5 - - - +
1204A PO4 3.2 37.3 + - - +
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Residues in contact with LEU 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* 2.9 37.9 + - + +
85A LEU* 1.3 89.3 - - + +
87A VAL* 1.3 60.3 + - + +
89A PRO* 4.4 2.2 - - - -
90A LEU* 5.3 3.6 - - - +
111A LEU* 3.2 19.6 - - - +
114A MET* 3.8 41.7 - - + +
1204A PO4 4.5 14.1 + - - +
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Residues in contact with VAL 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 LEU* 3.0 28.0 + - + +
86A LEU* 1.3 83.5 - - - +
88A LEU* 1.3 69.4 + - - +
89A PRO* 3.3 3.2 - - - -
90A LEU* 3.4 4.0 + - - +
91A PHE* 3.0 18.2 + - + +
111A LEU* 4.0 7.0 - - + +
114A MET* 3.8 27.4 - - + -
115A ASP* 3.6 33.2 - - + +
118A LEU* 4.2 4.0 - - + -
438A TYR* 3.8 8.3 - - + +
1201A AQD 3.8 24.1 - - + -
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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