Contacts of the helix formed by residues 64 - 77 (chain A) in PDB entry 2WNW
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 SER 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A SER 3.9 0.4 + - - -
63A MET* 1.3 78.3 - - - +
65A GLU* 1.3 64.8 + - - +
66A LYS* 3.5 9.1 + - - +
67A THR* 3.1 17.3 + - - -
68A LYS* 2.9 18.5 + - - +
354A TYR* 3.7 1.4 + - - -
359A ASP* 3.0 32.2 + - - -
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Residues in contact with GLU 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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63A MET 4.6 0.5 - - - +
64A SER* 1.3 73.7 - - - +
66A LYS* 1.3 62.1 + - - +
68A LYS* 3.4 34.8 + - - +
69A ALA* 3.2 21.8 + - - +
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Residues in contact with LYS 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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64A SER* 3.1 8.6 + - - +
65A GLU* 1.3 78.7 - - - +
67A THR* 1.3 64.2 + - - +
69A ALA* 3.3 8.1 + - - +
70A GLN* 3.2 20.5 + - + +
359A ASP* 5.6 1.6 - - - +
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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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63A MET* 3.8 22.0 - - + -
64A SER* 3.1 13.6 + - - -
66A LYS* 1.3 77.8 - - - +
68A LYS* 1.3 59.9 + - - +
70A GLN* 3.1 11.6 + - - +
71A PHE* 2.8 28.9 + - - +
354A TYR* 3.7 24.2 - - + -
359A ASP* 2.8 29.5 + - - -
361A LEU* 4.1 16.2 - - + +
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Residues in contact with LYS 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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60A PHE* 3.4 48.8 - - + -
61A ASN* 3.8 19.5 + - - +
63A MET* 3.3 31.4 - - + -
64A SER 2.9 16.5 + - - +
65A GLU* 3.6 35.9 + - - +
66A LYS 3.3 0.2 - - - -
67A THR* 1.3 75.3 - - - +
69A ALA* 1.3 62.3 + - - +
71A PHE* 3.4 1.4 + - - +
72A LEU* 3.0 32.3 + - + +
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Residues in contact with ALA 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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65A GLU 3.2 10.0 + - - +
66A LYS* 3.5 10.5 - - - +
67A THR 3.2 0.4 - - - -
68A LYS* 1.3 80.6 - - - +
70A GLN* 1.3 62.5 + - - +
72A LEU* 3.5 6.4 + - - +
73A SER* 3.0 29.6 + - - +
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Residues in contact with GLN 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 LYS* 3.2 9.6 + - + +
67A THR* 3.1 14.8 + - - +
69A ALA* 1.3 78.4 - - - +
71A PHE* 1.3 64.5 + - - +
73A SER* 3.3 5.4 + - - -
74A LEU* 3.0 44.0 + - + +
361A LEU* 3.4 27.7 - - + +
363A ARG* 5.9 3.0 - - - +
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Residues in contact with PHE 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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60A PHE* 3.8 20.2 - + - -
63A MET* 4.0 24.2 - - + -
67A THR 2.8 20.6 + - - +
68A LYS 3.6 2.2 - - - +
70A GLN* 1.3 75.7 - - - +
72A LEU* 1.3 70.0 + - + +
74A LEU* 3.3 5.9 + - - +
75A TYR* 3.3 54.2 + + - +
76A PHE* 4.8 3.6 - + - -
126A LEU* 4.0 24.9 - - + -
333A LEU* 4.5 7.2 - - + -
334A LEU* 3.7 35.7 - - + -
352A ILE* 4.1 17.9 - - + -
361A LEU* 4.0 9.4 - - + -
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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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60A PHE* 4.0 21.5 - - + -
68A LYS* 3.0 23.4 + - + +
69A ALA* 4.0 5.2 - - - +
71A PHE* 1.3 90.8 - - + +
73A SER* 1.3 57.9 + - - +
76A PHE* 2.8 46.4 + - + -
126A LEU* 4.1 9.0 - - + +
129A GLY* 3.8 25.8 - - - +
130A ALA 3.9 18.2 - - - +
132A ARG* 5.7 1.3 - - - +
133A LEU* 3.0 24.5 - - + +
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Residues in contact with SER 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 ALA* 3.0 20.8 + - - +
70A GLN* 3.8 5.4 - - - -
72A LEU* 1.3 73.2 - - - +
74A LEU* 1.3 68.5 + - - +
77A SER* 2.8 34.8 + - - -
80A GLU* 3.2 8.7 - - - +
133A LEU* 3.5 13.3 - - - +
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Residues in contact with LEU 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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70A GLN* 3.0 45.4 + - + +
71A PHE* 3.5 6.1 - - - +
73A SER* 1.3 79.1 - - - +
75A TYR* 1.3 56.2 + - - +
80A GLU* 3.3 26.5 - - + +
81A HIS* 3.1 27.9 + - - +
352A ILE* 4.6 9.9 - - + -
361A LEU* 4.1 14.1 - - + -
363A ARG* 4.3 31.2 - - - +
367A TRP* 3.5 22.7 - - + -
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Residues in contact with TYR 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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71A PHE* 3.3 40.4 + + - +
73A SER 3.2 0.2 - - - -
74A LEU* 1.3 81.0 - - - +
76A PHE* 1.3 78.9 + + + +
77A SER 3.7 0.4 - - - -
81A HIS* 3.5 7.0 - - - +
82A ASN 3.3 5.8 + - - -
83A TYR* 2.9 67.2 + + - +
330A ASP* 4.8 0.5 + - - -
333A LEU* 2.7 44.9 + - + -
351A PRO* 3.3 24.8 - - + +
352A ILE* 3.6 10.8 + - + -
367A TRP* 3.5 28.0 - + - -
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Residues in contact with PHE 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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52A PHE* 3.9 4.0 - + - -
71A PHE* 4.8 3.1 - + - -
72A LEU* 2.8 39.9 + - + +
75A TYR* 1.3 90.9 - + + +
77A SER* 1.3 62.8 + - - +
78A ALA* 3.6 1.9 + - - -
82A ASN* 4.4 5.2 - - - +
83A TYR* 3.7 30.7 - + + +
130A ALA* 3.5 31.0 - - + +
133A LEU* 3.7 27.1 - - + +
134A ASN* 4.0 14.6 - - + +
137A MET* 3.7 35.9 - - + -
333A LEU* 3.8 29.8 - - + -
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU 3.8 2.0 + - - -
73A SER* 2.8 34.4 + - - -
76A PHE* 1.3 75.5 - - - +
78A ALA* 1.3 56.9 + - - +
79A GLN* 3.0 29.8 + - - +
80A GLU* 3.0 24.7 + - - +
82A ASN 3.0 17.0 + - - -
133A LEU* 3.9 8.7 - - - +
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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