Contacts of the helix formed by residues 56 - 76 (chain A) in PDB entry 5WC9
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 SER 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A LEU* 1.3 79.6 - - - +
57A PHE* 1.3 61.2 + - - +
58A LYS* 3.6 20.4 - - - +
59A ASN* 3.1 18.4 + - - +
60A ALA* 2.8 28.6 + - - +
147A LYS* 4.0 16.8 - - - -
148A ARG* 4.4 0.9 - - - +
149A VAL* 4.3 0.2 - - - -
182D A 2.5 30.0 + - - -
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Residues in contact with PHE 57 (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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3A SER* 5.0 0.4 - - - -
5A GLU* 3.5 44.6 - - + -
6A ILE* 3.9 26.5 - - + -
9A LEU* 4.0 12.8 - - + -
55A LEU 3.9 0.6 + - - -
56A SER* 1.3 74.4 - - - +
58A LYS* 1.3 75.9 + - + +
60A ALA* 3.4 2.6 + - - +
61A CYS* 3.2 48.7 + - - -
147A LYS 4.6 2.6 + - - -
149A VAL* 3.8 17.7 - - + +
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 3.6 26.3 - - - +
57A PHE* 1.3 88.9 - - + +
59A ASN* 1.3 61.4 + - - +
61A CYS* 3.3 8.1 + - - +
62A LYS* 3.0 21.7 + - - +
147A LYS* 5.4 11.7 + - - +
181D A 4.3 22.1 + - - +
182D A 4.0 16.1 + - - +
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Residues in contact with ASN 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 3.6 27.7 - - + +
56A SER* 3.1 27.5 + - - +
58A LYS* 1.3 77.5 - - - +
60A ALA* 1.3 62.2 + - - +
62A LYS* 3.3 6.3 + - - +
63A LEU* 3.0 31.3 + - - +
182D A 3.8 33.3 + - - +
183D T 2.7 31.3 + - - +
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Residues in contact with ALA 60 (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 LEU* 3.6 30.1 - - + -
50A PHE* 3.5 11.2 - - + -
53A LEU* 5.5 9.0 - - + -
55A LEU* 4.3 18.3 - - + +
56A SER 2.8 20.6 + - - +
57A PHE* 3.8 1.1 - - - +
58A LYS 3.3 0.2 - - - -
59A ASN* 1.3 73.4 - - - +
61A CYS* 1.3 57.3 + - - +
63A LEU 3.4 0.2 + - - -
64A LYS* 2.8 33.1 + - - +
149A VAL* 5.3 2.5 - - + -
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Residues in contact with CYS 61 (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 GLU* 6.1 0.9 - - - -
9A LEU* 4.2 13.7 - - - -
57A PHE* 3.2 48.8 + - - -
58A LYS* 3.7 8.7 - - - +
60A ALA* 1.3 75.8 - - - +
62A LYS* 1.3 62.6 + - - +
64A LYS* 3.8 7.4 - - - +
65A ALA* 3.2 21.5 + - - +
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Residues in contact with LYS 62 (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 LYS 3.0 13.2 + - - +
59A ASN* 3.5 13.0 - - - +
61A CYS* 1.3 76.9 - - - +
63A LEU* 1.3 70.3 + - + +
65A ALA* 3.1 15.4 + - - +
66A ILE* 3.3 21.4 + - + +
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Residues in contact with LEU 63 (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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42A PHE* 4.6 18.2 - - + -
46A THR* 3.6 28.7 - - + -
47A ILE* 5.8 1.1 - - + -
50A PHE* 3.9 21.3 - - + -
55A LEU* 3.6 25.8 - - + -
59A ASN* 3.0 33.9 + - - +
62A LYS* 1.3 78.5 - - + +
64A LYS* 1.3 61.9 + - - +
66A ILE* 3.1 7.8 + - + -
67A LEU* 2.7 50.0 + - + +
183D T 3.5 13.0 - - - +
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Residues in contact with LYS 64 (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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8A GLU* 4.1 25.1 + - - +
9A LEU* 3.7 23.8 - - + -
12A PHE* 3.6 46.2 - - + -
50A PHE* 3.6 16.5 - - + -
60A ALA 2.8 22.5 + - - +
61A CYS* 3.8 7.4 - - - +
63A LEU* 1.3 72.0 - - - +
65A ALA* 1.3 53.9 + - - +
68A SER* 2.1 45.3 + - - +
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Residues in contact with ALA 65 (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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61A CYS 3.2 11.7 + - - +
62A LYS* 3.1 11.5 + - - +
63A LEU 3.1 0.6 - - - -
64A LYS* 1.3 74.3 - - - +
66A ILE* 1.3 66.2 + - + +
68A SER* 3.5 3.9 + - - -
69A LYS* 3.2 41.7 + - - +
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Residues in contact with ILE 66 (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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34A LEU* 4.6 15.7 - - + -
37A VAL* 4.6 6.6 - - + +
38A HIS* 3.6 50.5 - - + +
42A PHE* 4.3 16.6 - - + -
62A LYS* 3.3 17.9 - - + +
63A LEU* 3.1 12.9 + - + +
65A ALA* 1.3 75.8 - - + +
67A LEU* 1.3 66.5 + - + +
69A LYS* 3.4 11.4 + - + +
70A TRP* 3.1 20.3 + - - +
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Residues in contact with LEU 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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12A PHE* 4.2 9.6 - - + -
16A PHE* 3.5 32.8 - - + -
34A LEU* 4.1 25.6 - - + -
42A PHE* 5.6 2.0 - - + -
47A ILE* 4.5 16.8 - - + -
50A PHE* 3.5 36.6 - - + -
63A LEU* 2.7 44.8 + - + +
64A LYS 4.3 1.3 - - - +
66A ILE* 1.3 75.5 - - + +
68A SER* 1.3 60.4 + - - +
70A TRP* 3.1 9.7 + - - +
71A LEU* 2.8 30.0 + - - +
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Residues in contact with SER 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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12A PHE* 3.1 30.4 - - - -
64A LYS* 2.1 36.4 + - - +
65A ALA* 4.0 4.6 - - - -
67A LEU* 1.3 76.9 - - - +
69A LYS* 1.3 63.9 + - - +
71A LEU* 3.3 5.3 + - - +
72A GLU* 3.1 34.5 + - - +
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Residues in contact with LYS 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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37A VAL* 4.8 13.4 - - + +
65A ALA* 3.2 26.9 + - - +
66A ILE* 3.6 10.5 - - + +
67A LEU 3.3 0.4 - - - -
68A SER* 1.3 78.0 - - - +
70A TRP* 1.3 60.6 + - - +
72A GLU* 3.7 13.2 + - - +
73A GLU* 3.2 24.3 + - - +
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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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16A PHE* 3.9 24.7 - + - -
20A ARG* 5.3 5.4 - - + -
23A LEU* 5.2 2.0 - - + -
25A TYR* 4.0 36.1 - + + -
30A VAL* 3.9 22.2 - - + -
33A ALA* 2.7 35.6 + - + +
34A LEU* 3.3 25.4 - - + -
37A VAL* 3.9 23.7 - - + +
66A ILE 3.1 12.4 + - - +
67A LEU* 3.1 7.9 + - - +
69A LYS* 1.3 75.8 - - - +
71A LEU* 1.3 89.5 + - + +
73A GLU* 3.0 3.9 + - + +
74A ALA* 2.5 61.2 + - + +
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Residues in contact with LEU 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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12A PHE* 4.4 16.2 - - + -
15A GLU* 5.1 2.2 - - + -
16A PHE* 3.8 38.6 - - + -
19A ARG* 3.9 39.9 - - + -
20A ARG 5.0 0.2 - - - +
23A LEU* 4.6 7.4 - - + -
67A LEU 2.8 14.9 + - - +
68A SER* 3.3 6.0 + - - +
70A TRP* 1.3 92.9 - - + +
72A GLU* 1.3 54.3 + - + +
74A ALA* 4.3 0.4 - - - +
75A GLU* 2.6 55.0 + - - +
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Residues in contact with GLU 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 SER* 3.1 19.8 + - - +
69A LYS* 3.8 12.1 - - - +
71A LEU* 1.3 80.9 - - + +
73A GLU* 1.3 61.6 + - - +
74A ALA 3.4 0.2 + - - -
75A GLU* 3.5 9.3 + - - +
76A GLN* 3.5 18.2 + - - +
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Residues in contact with GLU 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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37A VAL* 4.0 24.5 - - + +
69A LYS 3.2 13.5 + - - +
70A TRP* 3.0 4.1 + - + +
72A GLU* 1.3 81.0 - - - +
74A ALA* 1.3 59.4 + - - +
75A GLU 3.5 0.2 - - - -
76A GLN* 4.2 6.7 + - - +
77A VAL* 4.3 12.6 + - - +
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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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23A LEU* 3.5 15.7 - - + +
25A TYR* 4.4 12.3 + - + +
70A TRP* 2.5 61.3 + - + +
71A LEU* 3.4 1.8 - - - +
73A GLU* 1.3 71.5 - - - +
75A GLU* 1.3 58.4 + - - +
76A GLN 3.5 1.1 - - - -
77A VAL 4.5 6.1 - - - -
78A GLY* 4.0 15.2 - - - +
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Residues in contact with GLU 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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19A ARG* 2.5 58.5 + - - +
23A LEU* 4.0 22.3 - - + +
71A LEU* 2.6 32.3 + - - +
72A GLU* 4.1 3.7 - - - +
74A ALA* 1.3 72.9 - - - +
76A GLN* 1.3 58.6 + - - +
77A VAL 3.5 1.6 - - - -
78A GLY 4.9 6.7 - - - +
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Residues in contact with GLN 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 GLU 3.5 14.9 + - - +
73A GLU* 4.2 4.7 + - - +
75A GLU* 1.3 78.4 - - - +
77A VAL* 1.3 62.2 + - - +
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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