Contacts of the helix formed by residues 65 - 79 (chain A) in PDB entry 4WMJ
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 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A TYR* 3.2 10.8 + - - -
27A ILE* 5.5 3.6 - - + +
32A LEU* 3.9 21.9 - - + +
39A ARG* 4.4 3.1 - - - +
43A TYR* 3.3 10.1 - - - -
64A ILE* 1.3 74.4 - - - +
66A ASP* 1.3 67.5 + - - +
67A THR* 3.0 19.2 + - - -
68A THR* 2.9 25.9 + - - -
69A PHE* 2.9 24.4 + - - +
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Residues in contact with ASP 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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36A ASP* 5.4 1.7 - - - +
42A LYS* 4.1 21.3 + - - +
43A TYR* 3.2 14.3 + - - -
65A ASP* 1.3 78.8 - - - +
67A THR* 1.3 63.5 + - - +
69A PHE* 3.5 2.9 + - - +
70A SER* 3.2 27.5 + - - -
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Residues in contact with THR 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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19A TYR* 3.5 31.9 - - + -
65A ASP* 3.0 12.9 + - - -
66A ASP* 1.3 75.8 - - - +
68A THR* 1.3 68.7 + - - +
69A PHE 3.3 0.2 + - - -
70A SER* 3.3 5.2 + - - -
71A LEU* 3.0 35.0 + - + +
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Residues in contact with THR 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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16A LEU* 5.0 0.9 - - + -
19A TYR* 2.7 31.8 + - + -
27A ILE* 4.4 1.2 - - - +
63A ARG 4.2 1.1 + - - +
64A ILE* 3.5 15.0 - - + -
65A ASP* 2.9 25.9 + - - -
67A THR* 1.3 78.1 - - - +
69A PHE* 1.3 58.2 + - - +
71A LEU* 3.2 4.8 + - - +
72A LEU* 2.9 35.0 + - + +
329A TRP* 3.6 43.3 - - + +
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Residues in contact with PHE 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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42A LYS 6.0 0.4 - - - -
43A TYR* 4.0 20.0 - + + +
59A TYR* 3.6 33.9 - + - -
64A ILE* 4.2 18.2 - - + -
65A ASP 2.9 18.4 + - - +
66A ASP* 4.0 3.1 - - - +
68A THR* 1.3 76.0 - - - +
70A SER* 1.4 60.2 + - - +
72A LEU* 3.2 15.0 + - + +
73A LEU* 3.0 59.3 + - + +
316A GLU* 3.9 26.9 - - + -
322A ILE* 4.4 15.0 - - + -
325A LEU* 6.0 2.2 - - + -
326A LEU* 6.4 0.7 - - + -
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Residues in contact with SER 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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66A ASP 3.2 18.5 + - - -
67A THR* 3.3 5.3 + - - -
69A PHE* 1.4 77.4 - - - +
71A LEU* 1.3 59.9 + - - +
73A LEU* 3.4 11.8 + - - +
74A ASN* 3.0 40.2 + - - +
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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 ALA* 4.9 2.8 - - - +
15A LYS* 3.5 52.3 - - + +
16A LEU* 3.6 27.1 - - + +
19A TYR* 3.5 42.6 - - + -
67A THR* 3.0 32.9 + - + +
68A THR 3.7 1.8 - - - +
70A SER* 1.3 76.8 - - - +
72A LEU* 1.3 65.3 + - - +
74A ASN* 3.3 7.7 + - - +
75A LEU* 3.2 16.3 + - - +
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Residues in contact with LEU 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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16A LEU* 3.9 27.8 - - + -
64A ILE* 4.3 13.5 - - + -
68A THR* 2.9 34.4 + - + +
69A PHE* 3.2 11.2 + - + +
71A LEU* 1.3 74.3 - - - +
73A LEU* 1.3 65.9 + - - +
75A LEU* 3.0 14.9 + - + +
76A ALA 3.2 8.3 + - - -
325A LEU* 3.4 53.1 - - + +
326A LEU* 5.0 4.5 - - + +
328A VAL* 5.3 2.0 - - + -
329A TRP* 4.1 26.0 - - + +
333A PHE* 5.7 0.2 - - + -
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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 PHE* 3.0 50.9 + - + +
70A SER* 3.6 11.0 - - - +
72A LEU* 1.3 75.8 - - - +
74A ASN* 1.3 63.6 + - - +
76A ALA* 3.1 5.9 + - - +
77A LYS* 3.0 40.1 + - - +
315A LEU* 3.9 33.2 - - + +
316A GLU* 3.8 23.6 - - + +
322A ILE* 5.4 0.9 - - + -
325A LEU* 3.9 17.3 - - + -
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Residues in contact with ASN 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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12A ALA* 3.7 11.5 - - + +
15A LYS* 3.9 23.6 - - - +
70A SER* 3.0 25.7 + - - +
71A LEU* 3.6 8.8 - - - +
72A LEU 3.1 0.4 - - - -
73A LEU* 1.3 74.3 - - - +
75A LEU* 1.3 58.1 + - - +
77A LYS* 3.2 29.1 + - - +
78A SER* 2.8 30.8 + - - -
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Residues in contact with LEU 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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7A LEU* 4.2 5.8 - - + -
10A ASP* 3.8 20.2 - - - +
12A ALA* 3.7 6.0 - - + +
13A TYR* 3.8 29.6 - - + +
16A LEU* 3.8 26.7 - - + -
71A LEU 3.2 4.8 + - - +
72A LEU* 3.0 11.2 + - + +
74A ASN* 1.3 75.7 - - - +
76A ALA* 1.3 62.3 + - - +
78A SER* 3.3 0.3 + - - -
79A ARG* 3.0 45.6 + - + +
325A LEU* 4.6 8.5 - - + -
328A VAL* 4.1 18.6 - - + -
507A ILE* 4.0 20.4 - - + -
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Residues in contact with ALA 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 LEU 3.2 2.8 + - - -
73A LEU 3.1 10.2 + - - +
75A LEU* 1.3 79.9 - - - +
77A LYS* 1.3 61.1 + - - +
80A ASN 3.3 3.5 + - - -
81A VAL* 3.2 45.8 + - + +
315A LEU* 3.9 17.7 - - + -
321A VAL* 4.3 9.4 - - + -
325A LEU* 4.2 25.9 - - + +
503A THR* 5.8 0.2 - - + -
507A ILE* 4.9 2.7 - - + -
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Residues in contact with LYS 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* 3.0 33.5 + - - +
74A ASN* 3.2 32.9 + - - +
76A ALA* 1.3 76.3 - - - +
78A SER* 1.3 62.7 + - - +
80A ASN* 3.1 21.7 + - - +
82A GLU* 5.2 5.4 - - - +
315A LEU* 3.7 20.7 - - + +
316A GLU* 6.1 0.4 - - - -
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Residues in contact with SER 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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4A LYS* 5.4 1.0 - - - -
10A ASP* 2.8 37.8 + - - +
11A PRO* 5.6 2.2 - - - -
12A ALA* 3.2 16.3 - - - +
74A ASN 2.8 15.9 + - - -
75A LEU* 3.3 8.0 + - - +
77A LYS* 1.3 73.5 - - - +
79A ARG* 1.3 57.5 + - - +
80A ASN* 3.2 12.0 + - - -
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Residues in contact with ARG 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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4A LYS* 2.9 48.5 + - - +
5A VAL* 2.9 31.7 + - - +
7A LEU* 3.6 22.2 - - - +
10A ASP* 3.5 34.8 + - - +
75A LEU* 3.0 31.5 + - + +
76A ALA 4.2 2.5 - - - +
77A LYS 3.2 0.2 - - - -
78A SER* 1.3 73.7 - - - +
80A ASN* 1.3 68.8 + - - +
81A VAL* 3.3 2.8 + - + -
376A TYR* 4.8 0.6 + - - -
506A VAL* 3.4 4.0 - - - +
507A ILE* 3.0 51.0 + - + +
508A TRP 4.4 0.8 + - - -
509A ASP* 3.8 22.0 - - - +
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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