Contacts of the helix formed by residues 59 - 69 (chain A) in PDB entry 2WA2
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 GLY 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A SER* 3.1 8.2 + - - -
58A ARG* 1.3 75.9 - - - +
60A THR* 1.3 64.0 + - - +
62A LYS* 3.4 7.3 + - - +
63A LEU 3.1 10.9 + - - -
88A TRP* 3.0 31.5 + - - -
147A ASP* 5.3 2.2 - - - -
1248A SAM 3.7 20.4 - - - -
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Residues in contact with THR 60 (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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56A VAL 4.9 9.0 - - - +
57A SER* 3.3 22.2 + - - -
59A GLY* 1.3 76.8 - - - +
61A ALA* 1.3 59.3 + - - +
63A LEU* 3.3 1.0 + - - +
64A ALA* 2.9 35.5 + - + +
87A SER* 3.4 28.5 + - - -
88A TRP* 5.0 1.8 - - - -
91A TYR* 4.2 24.4 - - + -
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Residues in contact with ALA 61 (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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35A GLU* 4.6 19.1 - - - +
56A VAL 5.9 2.5 - - - +
57A SER 3.0 17.5 + - - +
58A ARG* 3.3 7.2 + - - +
60A THR* 1.3 77.5 - - - +
62A LYS* 1.3 57.0 + - - +
64A ALA* 3.7 5.7 - - - +
65A TRP* 3.0 29.8 + - - +
213A LEU* 3.4 21.1 - - + +
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Residues in contact with LYS 62 (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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58A ARG* 3.0 32.9 + - + +
59A GLY* 3.9 6.4 - - - +
61A ALA* 1.3 73.7 - - - +
63A LEU* 1.3 66.1 + - - +
65A TRP* 3.3 3.3 + - - +
66A ILE* 3.1 30.2 + - + +
88A TRP* 4.9 5.2 - - + +
147A ASP* 4.6 7.5 + - - -
184A LYS* 5.0 2.2 - - - +
211A VAL* 4.2 20.0 - - + +
213A LEU* 4.3 18.2 - - + +
214A SER* 4.1 8.7 - - - +
220A GLU* 2.7 32.3 + - - +
222A TYR* 2.8 34.8 + - - -
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Residues in contact with LEU 63 (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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59A GLY 3.1 8.2 + - - +
60A THR 4.1 2.2 - - - +
62A LYS* 1.3 76.2 - - - +
64A ALA* 1.3 57.3 - - - +
66A ILE* 3.3 5.4 + - + +
67A ASP* 2.8 28.4 + - - +
72A VAL* 4.3 16.2 - - + -
74A LEU* 4.5 5.8 - - + -
88A TRP* 3.6 60.7 - - + +
91A TYR* 3.6 28.5 - - + -
145A LEU* 4.0 15.7 - - + -
182A CYS* 4.3 24.5 - - - -
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Residues in contact with ALA 64 (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 THR* 2.9 22.2 + - + +
61A ALA* 3.7 7.2 - - - +
63A LEU* 1.3 78.0 - - - +
65A TRP* 1.3 55.9 + - - +
67A ASP* 3.3 0.9 + - - +
68A GLU* 2.9 48.3 + - - +
91A TYR* 3.7 31.7 - - + +
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Residues in contact with TRP 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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34A VAL* 6.0 2.9 - - + +
61A ALA 3.0 17.3 + - - +
62A LYS 3.3 5.4 + - - +
64A ALA* 1.3 75.8 - - - +
66A ILE* 1.3 68.2 + - - +
68A GLU* 4.8 2.7 - - - -
69A ARG* 2.7 86.1 + - + +
209A ILE* 4.2 21.1 - - + -
210A ARG 4.0 13.0 - - - -
211A VAL* 3.8 19.7 - - + -
212A PRO* 3.2 39.2 - - + +
213A LEU* 4.0 18.8 - - + -
227A ILE* 6.1 0.2 - - + -
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Residues in contact with ILE 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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62A LYS 3.1 19.0 + - - +
63A LEU* 3.7 9.4 - - + +
65A TRP* 1.3 82.5 - - + +
67A ASP* 1.3 57.8 + - - +
69A ARG* 3.3 6.5 + - - +
71A GLY* 2.8 48.8 + - - -
72A VAL* 3.9 16.8 - - + -
88A TRP* 5.2 1.6 - - + -
182A CYS* 3.6 22.2 - - - -
209A ILE* 4.2 7.4 - - + -
211A VAL* 3.6 28.0 - - + -
222A TYR* 3.8 21.5 - - + -
224A VAL* 3.9 14.1 - - + -
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Residues in contact with ASP 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 LEU 2.8 17.5 + - - +
64A ALA 3.6 0.9 - - - +
65A TRP 3.2 0.4 - - - -
66A ILE* 1.3 76.4 - - - +
68A GLU* 1.3 59.5 + - - +
70A GLY* 3.0 19.9 + - - -
72A VAL* 3.2 24.3 - - + +
73A GLU* 5.2 0.7 - - - +
74A LEU* 3.9 20.9 + - + +
91A TYR* 2.7 33.8 + - + +
95A GLN* 3.6 13.2 - - - +
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Residues in contact with GLU 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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64A ALA* 2.9 32.8 + - - +
65A TRP* 4.7 1.9 + - - -
67A ASP* 1.3 77.1 - - + +
69A ARG* 1.3 74.9 + - - +
70A GLY 3.2 1.2 + - - -
91A TYR* 3.7 14.8 + - - +
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Residues in contact with ARG 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 TRP* 2.7 88.1 + - + +
66A ILE* 3.7 6.3 - - - +
67A ASP 3.2 0.2 - - - -
68A GLU* 1.3 90.3 + - - +
70A GLY* 1.3 59.3 + - - +
71A GLY 3.7 1.5 + - - +
227A ILE* 4.2 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