Contacts of the helix formed by residues 64 - 72 (chain D) in PDB entry 2WWR
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 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62D HIS* 4.4 10.2 - - + +
63D VAL 1.1 73.7 - - - +
65D LYS* 1.3 56.7 + - + +
66D ARG* 2.6 46.0 + - + +
67D ILE* 3.5 22.6 - - - +
68D LEU* 3.0 24.8 + - - +
89D ALA* 3.3 14.4 - - + -
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Residues in contact with LYS 65 (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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64D ASP* 1.3 72.1 - - + +
66D ARG* 1.3 58.6 + - + +
68D LEU* 4.2 3.6 - - - -
69D ASP* 2.7 38.1 - - - +
89D ALA* 3.9 5.8 - - + +
92D GLU* 2.4 57.2 + - + +
95D LYS* 6.0 1.1 - - - +
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Residues in contact with ARG 66 (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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46D GLU* 5.0 13.0 - - - +
64D ASP* 2.6 36.0 + - + +
65D LYS* 1.3 78.7 - - + +
67D ILE* 1.3 59.6 + - + +
68D LEU 3.7 0.4 - - - -
69D ASP* 4.7 2.5 - - - +
70D ALA* 3.1 24.2 + - - +
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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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42D ALA* 5.4 5.8 - - + -
45D LEU* 3.4 25.8 - - + -
46D GLU* 4.1 22.0 - - + +
49D VAL* 3.4 35.2 - - + +
55D LEU* 5.7 0.7 - - + -
62D HIS 3.1 27.8 - - - +
63D VAL* 4.6 11.2 - - + -
64D ASP* 3.5 15.7 + - - +
66D ARG* 1.3 66.9 - - + +
68D LEU* 1.3 61.5 + - - +
69D ASP 3.4 0.2 - - - -
70D ALA* 3.8 3.3 - - + +
71D ALA* 3.4 19.6 + - - +
75D LEU* 5.5 0.7 - - - +
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Residues in contact with LEU 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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63D VAL* 4.3 8.3 - - + +
64D ASP* 3.0 26.0 + - - +
65D LYS* 4.5 1.3 - - - -
67D ILE* 1.3 72.0 - - - +
69D ASP* 1.3 66.2 + - - +
71D ALA* 3.4 5.8 + - - +
72D GLY* 3.1 18.4 + - - +
75D LEU* 5.3 3.8 - - + -
78D ILE* 3.8 20.6 - - + -
89D ALA* 4.1 2.5 - - + +
92D GLU* 3.6 29.2 - - + +
93D ILE* 3.3 39.3 - - + +
96D ARG* 3.8 23.9 + - - +
98D ILE* 3.8 21.3 - - + +
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Residues in contact with ASP 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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65D LYS* 2.7 23.8 + - - +
66D ARG* 4.7 4.5 - - - +
67D ILE 3.4 0.2 - - - -
68D LEU* 1.3 74.6 - - - +
70D ALA* 1.3 65.4 + - - +
72D GLY* 3.0 16.4 + - - +
96D ARG* 1.9 39.7 + - - +
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Residues in contact with ALA 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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46D GLU* 4.1 23.8 - - + +
49D VAL* 4.3 7.9 - - + -
50D ALA* 4.0 16.3 - - - +
51D GLY 4.8 0.5 + - - -
66D ARG 3.1 22.3 + - - +
67D ILE* 3.8 10.1 - - + +
68D LEU 3.3 0.4 - - - -
69D ASP* 1.3 79.1 - - - +
71D ALA* 1.3 59.9 + - - +
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Residues in contact with ALA 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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49D VAL* 4.0 22.6 - - + +
50D ALA* 4.7 0.2 - - - +
51D GLY* 4.0 9.9 + - - -
52D ALA 4.7 1.0 + - - +
67D ILE 3.4 13.2 + - - +
68D LEU* 3.7 5.8 - - - +
69D ASP 3.0 0.6 - - - -
70D ALA* 1.3 80.7 - - - +
72D GLY* 1.3 64.1 + - - +
74D ASN* 3.8 15.4 - - - +
75D LEU* 3.5 36.9 + - + -
98D ILE* 6.4 0.2 - - + -
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Residues in contact with GLY 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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68D LEU 3.1 10.6 + - - +
69D ASP* 3.0 16.0 + - - -
71D ALA* 1.3 78.8 - - - +
73D ALA* 1.3 54.4 + - - -
74D ASN* 2.7 16.1 + - - -
75D LEU* 3.3 12.5 + - - +
96D ARG* 5.4 6.4 - - - -
98D ILE* 5.3 4.0 - - - +
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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