Contacts of the helix formed by residues 50 - 68 (chain A) in PDB entry 4WNF
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 ASP 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLU* 4.2 1.7 + - + +
48A THR* 2.9 18.3 + - - +
49A GLU* 1.3 75.8 - - - +
51A LEU* 1.3 64.0 + - - +
52A LYS* 3.0 22.7 + - - +
53A THR* 2.7 35.0 + - - +
54A LEU 3.1 9.4 + - - -
1010B TYR* 3.5 29.0 - - + +
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Residues in contact with LEU 51 (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 THR 4.4 8.5 - - - +
49A GLU* 3.6 8.9 + - - +
50A ASP* 1.3 73.6 + - - +
52A LYS* 1.3 67.6 + - - +
54A LEU* 3.8 25.1 - - + +
55A SER* 2.8 26.4 + - - -
84A LEU* 4.0 27.7 - - + +
87A THR* 5.0 6.5 - - + -
88A ILE* 4.0 26.5 - - + -
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Residues in contact with LYS 52 (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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50A ASP* 3.0 13.9 + - - +
51A LEU* 1.3 80.2 - - - +
53A THR* 1.3 63.4 + - - +
55A SER* 3.2 6.9 + - - -
56A ALA* 3.0 21.5 + - + +
88A ILE* 4.2 20.6 - - + +
90A ASP* 2.8 35.2 + - - -
93A GLY* 5.0 0.6 - - - -
1005B LYS* 4.4 20.0 - - - +
1009B ASP* 5.0 17.8 + - + +
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Residues in contact with THR 53 (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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17A CYS* 4.8 4.3 - - - -
18A LEU* 4.0 19.2 - - + +
48A THR* 4.5 9.0 - - + +
50A ASP* 2.7 37.0 + - - +
52A LYS* 1.3 78.8 - - - +
54A LEU* 1.3 62.2 + - - +
56A ALA* 3.2 8.3 + - - +
57A ILE* 3.0 40.2 + - + +
1007B VAL* 4.0 21.3 + - + +
1010B TYR* 4.5 9.4 - - - +
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Residues in contact with LEU 54 (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 ALA 5.3 0.7 - - - +
44A VAL* 4.6 19.5 - - + +
47A GLY* 5.1 5.4 - - - -
48A THR* 4.3 23.7 - - + +
50A ASP 3.1 9.7 + - - +
51A LEU* 3.8 27.1 - - + +
53A THR* 1.3 79.3 - - - +
55A SER* 1.3 64.7 + - - +
57A ILE* 2.8 26.1 + - + +
58A TYR* 2.9 57.0 + - + +
84A LEU* 4.3 3.8 - - + -
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Residues in contact with SER 55 (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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51A LEU 2.8 22.8 + - - -
52A LYS* 3.2 11.7 + - - -
54A LEU* 1.3 72.4 - - - +
56A ALA* 1.3 66.1 + - - +
58A TYR* 3.3 5.5 + - - +
59A SER* 3.2 15.2 + - - -
81A ASP* 2.6 36.5 + - - +
84A LEU* 3.8 20.5 - - - +
85A ALA* 4.7 5.6 + - - +
88A ILE* 5.8 3.6 - - - -
90A ASP* 5.2 0.9 + - - -
1005B LYS* 3.2 14.2 + - - +
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Residues in contact with ALA 56 (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 LYS* 3.0 16.7 + - + +
53A THR* 3.3 12.8 - - - +
55A SER* 1.3 75.4 + - - +
57A ILE* 1.3 63.2 + - - +
59A SER* 3.0 14.0 + - - -
60A GLN* 3.0 18.6 + - + +
1005B LYS* 4.0 21.0 - - + +
1006B SER 3.8 31.0 - - - +
1007B VAL* 4.0 6.7 - - + +
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Residues in contact with ILE 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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17A CYS* 4.1 20.0 - - - -
21A ALA* 4.1 21.5 - - + -
40A PHE* 3.9 28.9 - - + +
43A ALA* 4.6 4.9 - - + +
44A VAL* 4.0 8.3 - - + -
53A THR* 3.0 33.6 + - + +
54A LEU* 2.8 24.8 + - + +
56A ALA* 1.3 71.9 - - - +
58A TYR* 1.3 61.7 + - - +
60A GLN* 3.1 10.2 + - - +
61A LEU* 3.0 42.2 + - + +
1007B VAL* 4.2 5.6 - - + -
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Residues in contact with TYR 58 (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* 4.2 22.2 - - + +
54A LEU* 2.9 50.8 + - + +
55A SER* 3.8 5.8 - - - +
57A ILE* 1.3 76.9 - - - +
59A SER* 1.3 56.7 + - - +
61A LEU* 3.3 5.9 + - - +
62A GLY* 2.8 24.6 + - - -
77A TYR* 3.5 47.7 - + + +
80A HIS* 3.9 28.0 - + + -
81A ASP* 4.3 6.7 - - + -
84A LEU* 3.6 29.5 - - + +
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Residues in contact with SER 59 (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 SER 3.2 8.0 + - - -
56A ALA 3.0 11.1 + - - -
58A TYR* 1.3 76.6 - - - +
60A GLN* 1.3 64.7 + - - +
62A GLY* 2.9 12.8 + - - -
63A ASN* 3.0 18.2 + - - -
78A HIS* 3.6 9.6 + - - -
81A ASP* 3.3 24.3 + - - -
100A ASN* 3.8 18.5 + - - -
1003B GLU 4.8 0.2 + - - -
1005B LYS* 3.7 26.9 + - - +
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Residues in contact with GLN 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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25A GLU* 3.0 39.6 + - - +
28A CYS* 5.3 6.2 - - - +
40A PHE* 3.5 37.9 - - + -
56A ALA 3.2 16.8 - - - +
57A ILE* 3.4 7.4 - - + +
59A SER* 1.3 76.3 - - - +
61A LEU* 1.3 58.1 + - - +
63A ASN* 3.4 6.2 + - - +
64A ALA* 2.9 31.2 + - - +
1004B THR* 6.0 2.1 - - - -
1005B LYS 2.7 25.0 + - - +
1006B SER* 3.7 1.2 - - - +
1007B VAL* 4.4 1.7 - - + +
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Residues in contact with LEU 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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37A VAL* 3.8 17.5 - - + +
40A PHE* 3.5 32.1 - - + -
41A GLU* 3.8 23.6 - - + +
44A VAL* 4.2 10.5 - - + -
57A ILE* 3.0 34.5 + - + +
58A TYR* 3.5 10.5 - - - +
60A GLN* 1.3 74.3 - - - +
62A GLY* 1.3 66.9 + - - +
64A ALA* 4.1 3.8 - - - -
65A TYR* 2.8 39.0 + - + -
77A TYR* 3.8 28.3 - - + +
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Residues in contact with GLY 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 TYR 2.8 18.0 + - - -
59A SER 2.9 4.7 + - - -
61A LEU* 1.3 73.5 - - - +
63A ASN* 1.3 56.3 + - - +
66A PHE* 2.9 22.3 + - - +
74A ALA* 3.0 19.1 - - - +
77A TYR* 3.7 15.0 - - - +
78A HIS* 3.2 21.3 - - - -
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Residues in contact with ASN 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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59A SER* 3.0 19.5 + - - +
60A GLN* 4.0 4.9 - - - +
62A GLY* 1.3 73.3 - - - +
64A ALA* 1.3 69.3 + - - +
66A PHE* 2.7 8.5 + - - +
67A TYR* 2.7 25.3 + - - +
78A HIS* 3.1 17.1 + - - -
100A ASN* 3.7 3.4 + - - +
1002B MET* 3.2 31.6 - - + +
1003B GLU 3.2 22.6 + - - -
1004B THR* 4.0 17.2 - - - +
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Residues in contact with ALA 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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28A CYS* 4.4 16.4 - - - -
33A CYS* 4.6 12.9 - - + +
37A VAL* 3.7 26.2 - - + -
40A PHE* 5.3 1.8 - - + -
60A GLN 2.9 19.3 + - - +
61A LEU* 3.5 7.2 - - - +
63A ASN* 1.3 80.1 - - - +
65A TYR* 1.3 61.7 + - - +
67A TYR* 3.0 12.1 + - - +
68A LEU* 3.1 19.0 + - - +
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Residues in contact with TYR 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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37A VAL* 3.4 26.7 - - + +
41A GLU* 3.0 24.5 + - - -
61A LEU* 2.8 33.5 + - + +
62A GLY 4.0 2.7 - - - +
64A ALA* 1.3 72.8 - - - +
66A PHE* 1.3 62.1 + - - +
68A LEU* 3.1 22.6 + - + +
70A ASP* 3.1 59.9 + - + +
73A LYS* 4.1 18.4 + - + -
74A ALA* 4.2 7.4 - - - +
77A TYR* 3.6 31.4 - + - -
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Residues in contact with PHE 66 (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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62A GLY 2.9 17.1 + - - +
63A ASN* 2.7 22.1 + - + +
65A TYR* 1.3 71.3 - - - +
67A TYR* 1.3 64.9 + - + +
69A HIS* 3.0 11.3 + - - -
71A TYR* 3.5 30.5 + + - -
74A ALA* 3.8 6.7 - - + +
103A ASN 4.5 0.7 - - - -
104A THR* 3.8 30.1 - - + -
107A VAL* 3.8 28.0 - - + -
1000B GLU* 3.4 31.0 - - + -
1002B MET* 3.8 36.1 - - + -
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Residues in contact with TYR 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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33A CYS* 5.8 9.0 - - + -
63A ASN 2.7 13.8 + - - +
64A ALA* 3.5 10.3 - - - +
66A PHE* 1.3 79.2 - - + +
68A LEU* 1.3 60.4 + - + +
69A HIS* 3.2 21.3 + - - -
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Residues in contact with LEU 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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33A CYS* 4.9 6.5 - - + +
34A ARG* 4.2 37.2 - - + +
37A VAL* 3.9 26.0 - - + -
64A ALA* 3.1 16.7 + - - +
65A TYR* 3.1 22.1 + - + +
67A TYR* 1.3 79.3 - - + +
69A HIS* 1.3 73.2 + - - +
70A ASP* 3.2 5.3 + - + +
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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