Contacts of the helix formed by residues 66 - 76 (chain D) in PDB entry 2WJZ
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 LEU 66 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D ILE* 4.2 20.2 - - + -
8D VAL* 4.4 7.0 - - + -
35D VAL* 4.0 9.0 - - + -
36D GLU 4.2 9.2 - - - +
37D SER* 3.8 22.2 - - - -
61D LEU* 3.0 35.2 + - + +
64D ASN* 3.4 26.0 - - + +
65D ASP* 1.3 75.9 - - - +
67D ILE* 1.3 68.6 - - - +
68D ASP 3.1 2.7 - - - -
69D PHE* 2.8 32.0 + - + +
70D VAL* 2.8 30.8 + - + +
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Residues in contact with ILE 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D MET* 5.0 6.7 - - + +
61D LEU* 3.5 21.9 + - + +
62D ARG* 3.6 30.5 - - + -
65D ASP* 3.7 0.9 - - - -
66D LEU* 1.3 78.4 - - - +
68D ASP* 1.3 63.1 + - - +
70D VAL* 3.6 3.5 + - - +
71D ARG* 3.1 22.9 + - - -
103D LEU* 4.5 24.4 - - + +
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Residues in contact with ASP 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D ASP* 4.2 19.0 + - - +
66D LEU 3.1 1.2 - - - +
67D ILE* 1.3 81.0 - - - +
69D PHE* 1.3 60.5 + - - +
70D VAL 3.1 1.6 - - - -
71D ARG* 4.3 2.2 - - - +
72D LYS* 2.8 28.9 + - - -
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Residues in contact with PHE 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 5.7 0.4 - - + -
35D VAL* 4.2 14.8 - - + -
37D SER 4.6 2.2 - - - -
38D PRO* 3.7 23.7 - - + +
39D ARG* 3.6 30.7 - - + -
42D LEU* 4.1 16.5 - - + +
43D TYR* 3.5 29.4 - + - -
46D LEU* 4.4 8.5 - - + -
65D ASP 4.3 1.4 + - - -
66D LEU* 2.8 38.7 + - + +
68D ASP* 1.3 78.6 - - - +
70D VAL* 1.3 55.2 + - + +
72D LYS* 3.8 1.4 + - - -
73D HIS* 2.6 62.9 + + - -
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Residues in contact with VAL 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 4.1 15.5 - - + -
46D LEU* 3.8 19.7 - - + -
48D ILE* 4.2 10.1 - - + -
61D LEU* 5.7 4.9 - - + -
66D LEU* 2.8 19.2 + - + +
67D ILE* 3.9 5.8 - - - +
69D PHE* 1.3 76.5 - - + +
71D ARG* 1.3 65.7 + - - +
72D LYS 3.1 1.3 - - - -
73D HIS* 2.9 19.3 + - - +
74D VAL* 3.1 12.5 + - + +
80D VAL* 4.1 17.5 - - + -
103D LEU* 4.9 9.6 - - + -
105D LEU* 3.8 28.7 - - + -
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Residues in contact with ARG 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ILE 3.1 14.0 + - - -
68D ASP* 3.2 4.2 + - - +
70D VAL* 1.3 81.7 - - - +
72D LYS* 1.3 56.0 + - - +
74D VAL* 3.5 7.4 + - - +
75D GLU* 3.0 30.0 + - - +
105D LEU* 5.2 5.2 - - - -
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Residues in contact with LYS 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU* 3.4 13.8 - - - +
68D ASP 2.8 16.3 + - - -
69D PHE* 4.2 2.5 - - - +
71D ARG* 1.3 72.8 - - - +
73D HIS* 1.3 64.3 + - - +
75D GLU* 3.7 7.6 - - - +
76D ASP* 3.1 25.1 + - - +
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Residues in contact with HIS 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU* 3.7 9.1 - - + +
43D TYR* 2.6 54.7 + + + +
46D LEU* 3.7 21.2 - - + +
69D PHE* 2.6 60.4 + + - -
70D VAL* 2.9 10.4 + - - +
72D LYS* 1.3 74.7 - - - +
74D VAL* 1.3 66.9 + - - +
76D ASP 3.0 5.5 + - - -
78D ARG* 3.0 39.9 + - + +
79D TYR 5.2 0.2 - - - -
80D VAL* 3.7 15.5 - - + -
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Residues in contact with VAL 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D VAL* 3.1 15.5 + - + +
71D ARG 3.8 4.5 - - - +
73D HIS* 1.3 73.3 - - - +
75D GLU* 1.3 64.3 + - - +
77D GLU* 3.1 15.1 + - - -
78D ARG 4.4 4.4 - - - +
80D VAL* 3.8 18.6 - - + +
105D LEU* 3.3 36.8 - - + -
172D ILE* 3.4 31.6 - - + -
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Residues in contact with GLU 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ARG 3.0 16.3 + - - +
72D LYS* 3.7 9.6 - - - +
74D VAL* 1.3 80.3 - - - +
76D ASP* 1.3 56.8 + - - +
77D GLU 3.5 2.6 + - - -
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Residues in contact with ASP 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU* 3.6 19.9 - - + +
72D LYS 3.1 16.3 + - - +
73D HIS 3.0 3.0 + - - -
75D GLU* 1.3 75.1 - - + +
77D GLU* 1.3 68.2 + - - +
78D ARG* 2.9 18.6 + - + +
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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