Contacts of the helix formed by residues 72 - 82 (chain A) in PDB entry 2WSC
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 GLU 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A THR* 5.5 0.9 - - + -
70A ASP* 3.2 32.9 - - + +
71A LEU* 1.4 87.9 - - - +
73A GLU* 1.3 73.2 + - + +
75A SER* 3.0 19.6 + - - -
76A ARG* 2.9 44.7 + - - +
192A LYS* 4.2 7.3 + - - +
193A LEU* 3.4 25.1 - - - +
196A PHE* 4.5 2.9 - - - -
1810A LMU 5.8 2.5 - - - +
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Residues in contact with GLU 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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64A PHE* 5.1 1.0 - - - -
67A HIS* 3.2 35.4 - - - +
68A THR* 3.2 20.0 - - + +
70A ASP 3.8 6.1 - - - +
71A LEU 3.4 8.3 - - - +
72A GLU* 1.3 75.8 - - + +
74A ILE* 1.3 66.5 + - - +
76A ARG* 2.0 60.8 + - - +
77A LYS* 3.9 3.2 - - - +
186A TYR* 2.7 26.1 + - - +
1767A CLA 6.1 0.2 - - - +
1810A LMU 2.9 36.8 + - - +
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Residues in contact with ILE 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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64A PHE* 3.1 57.7 - - + -
67A HIS* 5.4 0.9 - - + -
68A THR 5.0 8.3 - - - +
70A ASP 5.1 0.2 - - - -
71A LEU* 3.1 39.9 + - + +
73A GLU* 1.3 82.1 + - + +
75A SER* 1.3 67.1 + - - +
77A LYS* 2.8 11.4 + - - +
78A VAL* 2.7 35.1 + - + +
354A TRP* 4.8 16.8 - - + +
1761A CLA 5.8 0.9 - - + -
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Residues in contact with SER 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 LEU* 5.6 0.2 - - - +
72A GLU 3.0 14.0 + - - -
73A GLU 2.7 1.8 + - - -
74A ILE* 1.3 80.5 - - - +
76A ARG* 1.3 53.4 + - - -
78A VAL* 4.3 3.6 - - - +
79A PHE* 3.2 32.4 + - - +
196A PHE* 3.0 37.3 - - - -
354A TRP* 3.1 42.4 - - - +
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Residues in contact with ARG 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 GLU* 2.9 51.7 + - - +
73A GLU* 2.0 31.1 + - - +
75A SER* 1.3 68.4 - - - +
77A LYS* 1.3 51.9 + - - -
79A PHE* 4.6 6.1 - - - -
80A SER* 3.3 15.6 + - - -
185A HIS* 4.9 1.2 - - - +
186A TYR* 2.6 31.9 + - + +
190A ALA* 4.1 15.5 - - + -
191A PRO* 3.2 31.7 + - + +
192A LYS* 2.5 48.2 - - - +
193A LEU* 3.2 20.2 - - - +
196A PHE* 5.0 2.0 - - + -
1810A LMU 6.1 2.4 - - - -
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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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61A ALA 5.7 0.7 - - - -
62A HIS* 3.9 17.1 - - - +
64A PHE* 3.2 37.9 - - + -
67A HIS* 6.0 6.7 - - + +
73A GLU* 3.0 3.5 + - + +
74A ILE* 2.8 17.1 + - - +
76A ARG* 1.3 70.8 - - - +
78A VAL* 1.3 57.5 + - - +
79A PHE 3.2 1.8 - - - -
80A SER* 2.7 23.9 + - - -
81A ALA* 2.8 16.1 + - + +
186A TYR* 3.3 14.5 - - + -
1760A CLA 2.8 33.6 + - - -
1761A CLA 3.7 31.6 - - - +
1767A CLA 3.4 26.7 - - + +
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Residues in contact with VAL 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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64A PHE* 4.1 9.4 - - + -
74A ILE 2.7 26.9 + - - +
75A SER 4.3 0.7 - - - +
77A LYS* 1.3 74.4 - - - +
79A PHE* 1.3 51.6 + - - +
80A SER 3.2 0.2 - - - -
81A ALA* 5.2 1.1 - - - -
82A HIS* 2.6 48.7 + - + +
354A TRP* 3.9 27.1 - - + -
1761A CLA 3.4 75.2 - - + +
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Residues in contact with PHE 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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75A SER 3.2 18.6 + - - +
76A ARG* 5.2 4.9 - - - -
77A LYS 3.2 0.8 - - - -
78A VAL* 1.3 76.3 - - + +
80A SER* 1.3 57.1 + - - +
82A HIS* 3.9 6.7 - - - -
83A PHE* 3.7 12.2 - + - -
185A HIS* 2.1 65.3 - + + -
191A PRO* 5.5 8.7 - - + -
195A TRP* 4.9 10.5 - + - -
354A TRP* 5.9 3.4 - - + -
1766A CLA 4.4 29.8 - + + -
1769A CLA 3.5 62.4 - + + +
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Residues in contact with SER 80 (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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76A ARG 3.3 10.8 + - - -
77A LYS* 2.7 15.7 + - - -
79A PHE* 1.3 71.5 - - - +
81A ALA* 1.3 58.8 + - - -
82A HIS 3.1 4.0 - - - -
83A PHE* 2.7 36.9 + - - +
84A GLY 3.5 2.6 + - - -
182A GLY 4.3 9.0 - - - -
185A HIS* 3.1 28.3 - - - +
186A TYR* 3.2 18.5 + - - -
1767A CLA 4.5 16.0 - - - +
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Residues in contact with ALA 81 (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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77A LYS* 2.8 19.7 + - + +
78A VAL* 5.2 1.1 - - - -
80A SER* 1.3 70.8 - - - +
82A HIS* 1.3 67.3 + - - +
84A GLY* 4.4 1.6 - - - +
1760A CLA 2.2 53.2 - - + +
1761A CLA 3.5 36.6 - - + +
1767A CLA 4.4 6.3 - - + -
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Residues in contact with HIS 82 (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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78A VAL* 2.6 37.7 + - + +
79A PHE* 3.9 9.4 - - - +
81A ALA* 1.3 79.2 - - - +
83A PHE* 1.4 55.1 + - - +
84A GLY 2.4 18.6 + - - -
85A GLN* 2.8 18.1 + - - +
86A LEU* 4.2 4.3 - - - -
354A TRP* 5.9 0.8 - - - -
1761A CLA 2.8 99.3 + + + +
1769A CLA 3.5 31.1 + + - +
1780A CLA 5.1 2.9 - - + -
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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