Contacts of the strand formed by residues 62 - 68 (chain D) in PDB entry 3U8Z
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 PHE 62 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D PHE* 3.5 14.9 - - + -
56D LEU* 3.7 16.4 - - + -
58D GLU 3.5 25.8 - - - -
59D THR 2.9 11.4 + - - +
60D TRP* 4.3 3.8 - - - +
61D PHE* 1.3 86.5 - - + +
63D GLY* 1.3 58.2 + - - +
96D PHE* 3.6 32.8 - + + -
97D LEU* 3.4 4.5 - - - +
98D ALA* 3.7 29.8 - - + -
99D LYS* 4.7 6.3 - - - +
100D PHE* 5.8 0.9 - - - -
114D THR* 3.5 19.5 - - + -
117D LEU* 4.0 32.8 - - + -
118D PHE* 3.7 21.3 - + - -
121D GLN* 5.3 0.9 - - - -
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Residues in contact with GLY 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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47D PHE* 3.8 11.0 - - - -
62D PHE* 1.3 75.6 - - - +
64D LEU* 1.3 62.1 + - - -
74D TRP* 3.5 18.2 - - - -
77D MET* 5.7 3.4 - - - -
95D HIS 3.6 0.3 - - - +
96D PHE* 3.6 8.1 - - - -
97D LEU 3.0 29.1 + - - -
99D LYS* 5.2 2.0 - - - -
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Residues in contact with LEU 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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26D ILE* 3.8 24.0 - - + -
46D LEU* 4.0 19.3 - - + +
47D PHE* 4.0 33.3 - - + +
50D VAL* 4.6 3.6 - - + -
63D GLY* 1.3 70.5 - - - -
65D GLN* 1.3 60.4 + - - +
66D TYR* 4.2 0.5 + - - -
74D TRP* 3.6 4.8 - - - +
75D LEU* 2.8 65.0 + - + +
77D MET* 5.1 4.5 - - + +
94D PHE* 3.8 14.6 - - + -
95D HIS 3.6 1.1 - - - -
96D PHE* 3.9 32.8 - - + -
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Residues in contact with GLN 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 LEU* 1.3 73.4 - - - +
66D TYR* 1.3 64.6 + - - +
67D THR* 4.9 8.1 - - - +
72D VAL* 3.5 37.4 - - + +
73D ALA 3.3 15.9 - - - +
74D TRP* 3.6 28.2 - - + -
94D PHE* 3.4 7.2 - - - -
95D HIS* 2.8 53.7 + - + +
97D LEU* 3.7 23.3 - - + +
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Residues in contact with TYR 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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65D GLN* 1.3 78.4 - - - +
67D THR* 1.3 71.2 + - - +
68D ILE* 3.7 24.9 - - + +
73D ALA* 2.8 52.9 + - + +
74D TRP 3.7 8.4 + - - -
75D LEU* 3.5 35.0 - - + +
76D LYS 5.4 0.7 + - - -
79D LYS* 6.0 0.7 + - - -
93D THR 4.2 9.2 - - - +
94D PHE* 3.8 29.2 - + + -
95D HIS* 5.6 2.5 - - - -
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Residues in contact with THR 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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65D GLN* 4.9 10.3 - - - +
66D TYR* 1.3 84.3 - - - +
68D ILE* 1.4 63.6 + - - +
69D LYS 4.0 8.7 + - - +
70D ASP* 5.1 4.7 - - - +
71D THR 3.3 19.3 - - - +
72D VAL* 4.5 7.9 - - + -
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Residues in contact with ILE 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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66D TYR* 3.7 35.9 + - + +
67D THR* 1.4 70.6 - - - +
69D LYS* 1.4 60.8 + - + +
70D ASP 2.8 15.2 + - - -
71D THR* 2.9 23.1 + - - +
73D ALA* 3.8 14.1 - - + +
291D ARG* 3.5 44.2 + - + +
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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