Contacts of the helix formed by residues 65 - 79 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B TYR* 2.6 23.0 + - - -
23B ASN* 5.9 0.2 - - - -
27B ILE* 4.6 8.1 - - + +
32B LEU* 4.0 21.9 - - + +
39B ARG* 4.4 4.0 - - - +
43B TYR* 3.2 11.6 + - - -
64B ILE* 1.3 73.5 - - - +
66B ASP* 1.3 66.9 + - - +
67B THR* 3.0 10.2 + - - -
68B THR* 2.8 35.8 + - - -
69B PHE* 3.0 20.4 + - - +
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Residues in contact with ASP 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LYS* 4.3 20.2 + - - +
43B TYR* 3.1 17.3 + - - +
65B ASP* 1.3 76.6 - - - +
67B THR* 1.3 62.7 + - - +
69B PHE* 3.5 7.2 + - - +
70B SER* 3.1 27.6 + - - -
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 3.7 29.4 - - + -
65B ASP* 3.0 11.4 + - - -
66B ASP* 1.3 75.2 - - - +
68B THR* 1.3 66.0 + - - +
70B SER* 3.3 7.4 + - - -
71B LEU* 3.0 39.8 + - + +
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Residues in contact with THR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 4.8 0.9 - - + -
19B TYR* 2.7 33.0 + - + -
27B ILE* 4.2 2.4 - - - +
64B ILE* 3.9 13.5 - - + -
65B ASP* 2.8 30.9 + - - -
67B THR* 1.3 73.2 - - - +
69B PHE* 1.3 57.5 + - - +
71B LEU* 3.3 6.4 + - - +
72B LEU* 2.9 41.1 + - + +
329B TRP* 3.6 44.2 - - + +
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Residues in contact with PHE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LYS 6.1 0.2 - - - -
43B TYR* 4.0 25.4 - + + +
59B TYR* 3.6 31.6 - + - -
64B ILE* 4.4 13.6 - - + +
65B ASP 3.0 16.1 + - - +
66B ASP* 3.9 8.3 - - - +
68B THR* 1.3 75.1 - - - +
70B SER* 1.3 67.0 + - - +
72B LEU* 3.2 14.0 + - + +
73B LEU* 2.9 58.3 + - + +
316B GLU* 3.8 24.9 - - + -
322B ILE* 4.4 13.7 - - + -
325B LEU* 6.0 2.2 - - + -
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Residues in contact with SER 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ASP* 3.1 21.8 + - - -
67B THR* 3.6 7.4 - - - -
69B PHE* 1.3 79.8 - - - +
71B LEU* 1.3 59.4 + - - +
73B LEU* 3.3 12.0 + - - +
74B ASN* 2.9 37.9 + - - +
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA 4.8 2.6 - - - +
15B LYS* 3.5 43.9 - - + +
16B LEU* 3.6 26.9 - - + +
19B TYR* 3.6 41.1 - - + -
67B THR* 3.0 30.4 + - + +
68B THR* 3.7 1.3 - - - +
70B SER* 1.3 75.9 - - - +
72B LEU* 1.3 65.3 + - - +
74B ASN* 3.4 10.6 + - - +
75B LEU* 3.1 16.3 + - - +
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 3.8 26.7 - - + -
64B ILE* 4.3 12.6 - - + -
68B THR* 2.9 37.5 + - + +
69B PHE* 3.7 10.3 - - + +
71B LEU* 1.3 74.8 - - - +
73B LEU* 1.3 66.7 + - - +
75B LEU* 3.0 12.3 + - + +
76B ALA 3.2 8.8 + - - -
325B LEU* 3.3 48.4 - - + +
326B LEU* 5.1 4.0 - - + -
328B VAL* 4.5 10.1 - - + -
329B TRP* 4.0 24.5 - - + -
333B PHE* 5.5 1.1 - - + -
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PHE* 2.9 54.8 + - + +
70B SER* 3.6 11.4 - - - +
72B LEU* 1.3 76.2 - - - +
74B ASN* 1.3 63.4 + - - +
76B ALA* 3.1 5.9 + - - +
77B LYS* 3.1 29.4 + - + +
315B LEU* 3.9 39.3 - - + +
316B GLU* 3.7 18.6 - - + +
322B ILE* 5.5 0.9 - - + -
325B LEU* 4.1 17.5 - - + -
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Residues in contact with ASN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA* 3.7 3.2 - - + +
15B LYS* 3.7 34.3 - - - +
70B SER* 2.9 25.7 + - - +
71B LEU* 3.7 11.0 - - - +
72B LEU 3.2 0.4 - - - -
73B LEU* 1.3 76.0 - - - +
75B LEU* 1.3 57.0 + - - +
77B LYS* 3.4 23.0 + - - +
78B SER* 2.8 30.0 + - - -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 5.4 0.4 - - + -
10B ASP* 3.7 21.5 - - - +
12B ALA* 3.7 5.6 - - + +
13B TYR* 3.8 33.9 - - + +
16B LEU* 4.0 19.7 - - + -
71B LEU 3.1 11.7 + - - +
72B LEU* 3.0 10.1 + - + +
74B ASN* 1.3 78.2 - - - +
76B ALA* 1.3 57.0 + - - +
78B SER* 3.2 0.3 + - - -
79B ARG* 2.9 46.5 + - + +
325B LEU* 4.6 5.4 - - + -
328B VAL* 4.5 19.3 - - + -
333B PHE* 5.3 1.3 - - + -
507B ILE* 4.1 20.9 - - + -
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LEU 3.2 4.6 + - - +
73B LEU 3.1 9.0 + - - +
75B LEU* 1.3 76.4 - - - +
77B LYS* 1.3 62.8 + - - +
80B ASN 3.3 2.9 + - - -
81B VAL* 3.1 47.1 + - + +
315B LEU* 4.1 15.5 - - + -
321B VAL* 4.3 9.2 - - + -
325B LEU* 4.1 27.5 - - + +
503B THR* 5.5 0.4 - - + -
507B ILE* 4.7 3.4 - - + -
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Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU* 3.1 14.9 + - + +
74B ASN* 3.6 27.5 + - - +
75B LEU 3.2 0.2 - - - -
76B ALA* 1.3 73.9 - - - +
78B SER* 1.3 65.7 + - - +
80B ASN* 2.9 22.1 + - - +
82B GLU* 5.0 6.3 - - - +
315B LEU* 3.7 21.1 - - + +
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LYS* 6.1 0.2 - - - +
10B ASP* 2.6 38.9 + - - +
11B PRO* 4.4 7.1 - - - +
12B ALA* 3.7 10.6 + - - +
74B ASN 2.8 20.6 + - - -
75B LEU 3.2 4.7 + - - -
77B LYS* 1.3 74.3 - - - +
79B ARG* 1.3 61.1 + - - +
80B ASN* 3.1 11.0 + - - -
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Residues in contact with ARG 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LYS* 2.4 54.2 + - - +
5B VAL* 2.9 32.3 + - - +
7B LEU* 3.7 19.1 - - - +
10B ASP* 3.7 33.2 + - - +
75B LEU* 2.9 35.0 + - + +
76B ALA 3.6 1.8 + - - +
77B LYS 3.1 0.2 - - - -
78B SER* 1.3 75.1 - - - +
80B ASN* 1.3 64.8 + - - +
81B VAL* 3.3 2.5 + - + -
376B TYR* 4.9 0.6 + - - -
506B VAL* 3.5 2.3 - - - +
507B ILE* 2.8 53.9 + - + +
508B TRP 4.5 0.2 - - - -
509B ASP* 3.7 23.0 - - - +
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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