Contacts of the helix formed by residues 59 - 66 (chain D) in PDB entry 5WUA
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 VAL 59 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TRP* 4.8 12.6 - - + +
176A ARG* 6.0 5.8 - - + -
58D ASP* 1.3 83.1 - - + +
60D PHE* 1.3 91.5 + - + +
61D THR* 3.5 2.5 + - + +
62D THR* 4.2 9.8 + - - -
63D LEU* 4.6 7.2 + - - +
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Residues in contact with PHE 60 (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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68A TRP* 3.9 29.4 - + - -
170A LYS 3.9 2.5 - - - -
171A THR* 1.1 106.6 - - + -
173A GLN* 5.9 0.4 - - - -
174A ALA* 5.8 4.7 - - + -
59D VAL* 1.3 93.0 - - + +
61D THR* 1.3 72.9 + - + +
62D THR 3.1 2.8 + - - -
63D LEU* 3.6 34.6 - - + +
64D VAL* 4.0 7.1 - - - +
162D ILE* 5.0 16.6 - - + -
166D CYS* 5.3 7.5 - - + +
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Residues in contact with THR 61 (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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171A THR 5.9 0.2 - - - +
172A ALA 5.8 1.8 - - - +
173A GLN* 5.2 9.9 - - - +
176A ARG 5.7 4.0 - - - +
177A ARG* 6.1 1.8 - - - -
178A ALA* 5.9 6.5 - - + +
206A ARG* 5.1 15.0 + - - -
293A THR* 4.7 6.2 - - - +
58D ASP* 3.4 26.3 - - + +
59D VAL* 3.5 1.1 - - + +
60D PHE* 1.3 85.5 - - + +
62D THR* 1.3 70.1 + - - +
64D VAL* 3.1 25.0 - - - +
65D ASP* 4.0 5.2 + - - +
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Residues in contact with THR 62 (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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206A ARG* 5.6 7.4 + - - +
55D PHE 5.6 1.7 + - - -
56D LEU* 5.2 5.0 + - - +
58D ASP* 5.1 4.6 + - - +
59D VAL 4.2 8.1 + - - -
60D PHE* 3.1 0.8 - - - +
61D THR* 1.3 84.0 + - - +
63D LEU* 1.3 67.6 + - - +
64D VAL 3.1 2.5 - - - -
65D ASP* 2.9 19.1 + - + +
66D LEU* 3.2 34.6 + - + +
51H TRP 5.7 3.6 - - - +
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Residues in contact with LEU 63 (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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59D VAL 4.6 4.5 + - - +
60D PHE* 3.6 32.9 + - + +
62D THR* 1.3 77.3 - - - +
64D VAL* 1.3 84.7 + - + +
66D LEU* 3.0 35.2 + - + +
71D THR* 4.5 24.7 - - - +
74D ILE* 5.7 7.9 - - + -
75D PHE* 4.5 18.4 - - + -
162D ILE* 6.3 2.2 - - + -
166D CYS* 3.9 31.4 - - + -
167D ILE* 5.9 0.7 - - + -
170D LYS* 5.7 2.4 - - + +
51H TRP* 6.5 1.3 - - + -
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Residues in contact with VAL 64 (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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293A THR* 4.4 21.3 + - + +
60D PHE 4.0 6.5 - - - +
61D THR* 3.1 22.4 - - - +
63D LEU* 1.3 92.6 - - + +
65D ASP* 1.3 63.0 + - - +
66D LEU 3.1 7.3 + - - +
71D THR* 5.9 0.2 - - - -
166D CYS* 4.5 3.6 - - + +
169D MET* 3.7 20.2 - - + +
170D LYS* 3.5 51.0 - - + +
173D GLN 4.7 6.6 - - - +
174D ALA* 5.3 4.0 - - - +
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Residues in contact with ASP 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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206A ARG* 2.9 29.8 + - - +
208A SER* 3.8 8.7 - - - -
292A GLU* 5.0 4.4 - - - +
293A THR* 4.5 23.1 + - + -
61D THR 4.3 7.4 - - - +
62D THR* 2.9 12.4 + - + +
64D VAL* 1.3 76.6 - - - +
66D LEU* 1.3 68.8 + - + +
174D ALA* 6.0 1.9 - - - +
175D HIS* 5.3 11.7 + - - +
177D ARG* 5.9 1.2 + - - -
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Residues in contact with LEU 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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62D THR* 3.2 28.9 - - + +
63D LEU* 3.0 30.0 + - + +
64D VAL 3.6 6.2 - - - +
65D ASP* 1.3 86.9 - - + +
67D LYS* 1.3 76.0 + - - +
70D HIS* 4.5 22.7 - - + -
71D THR* 5.4 1.1 - - - +
170D LYS* 5.1 4.2 - - - -
174D ALA* 5.6 2.6 - - - +
175D HIS* 5.2 7.4 + - - +
51H TRP 4.8 12.6 - - - +
53H SER* 5.3 9.4 - - - -
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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