Contacts of the strand formed by residues 68 - 75 (chain D) in PDB entry 3QWR
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 TYR 68 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 5.1 5.6 - - + -
36D TYR* 4.9 6.3 - + + -
37D GLY* 3.4 25.1 - - - +
38D GLU* 3.7 14.3 - - + +
39D THR* 3.4 4.9 + - - -
46D GLN* 5.9 2.7 - - - -
61D GLY 4.8 0.2 + - - -
62D LEU* 3.4 47.9 - - + -
63D LYS* 2.7 48.4 + - - +
66D VAL* 3.2 29.0 - - + +
67D ASP* 1.4 71.6 - - - +
69D THR* 1.3 61.5 + - - +
70D ILE* 3.7 15.4 + - + +
90D ILE 3.8 0.2 - - - +
91D ASN* 3.4 0.9 - - - -
92D TYR 2.8 40.2 + - - +
93D ARG* 4.0 4.5 - - - -
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Residues in contact with THR 69 (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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35D THR 3.7 1.2 - - - +
36D TYR* 3.3 21.5 - - - -
37D GLY 2.7 16.4 + - - -
38D GLU 5.3 0.2 - - - -
39D THR* 2.7 32.6 + - - +
68D TYR* 1.3 70.4 - - - +
70D ILE* 1.3 61.0 + - - +
71D THR* 4.1 15.7 + - - +
89D SER* 4.3 9.2 - - - +
90D ILE 3.3 11.7 - - - +
91D ASN* 3.5 15.9 + - - +
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Residues in contact with ILE 70 (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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8D LEU* 3.7 8.1 - - + +
10D VAL* 4.6 0.9 - - + -
18D LEU* 3.5 32.3 - - + -
20D ILE* 3.8 34.3 - - + -
34D ILE* 4.2 4.0 - - + -
35D THR 3.4 8.5 - - - +
36D TYR* 4.4 7.0 - - + -
59D ILE* 3.6 27.6 - - + -
62D LEU* 5.8 0.4 - - + -
68D TYR* 4.1 10.8 - - + +
69D THR* 1.3 73.3 - - - +
71D THR* 1.3 65.1 + - - +
89D SER* 3.0 18.7 - - - -
90D ILE* 2.8 36.9 + - + +
92D TYR* 4.7 3.6 - - + -
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Residues in contact with THR 71 (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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33D ARG 4.3 0.9 - - - -
34D ILE* 3.2 6.9 - - - +
35D THR* 2.8 47.8 + - - +
69D THR* 4.2 10.2 + - - +
70D ILE* 1.3 73.2 - - - +
72D VAL* 1.3 70.0 + - - +
73D TYR* 3.7 16.3 + - + +
87D PRO* 3.6 27.6 - - + -
88D ILE 3.3 10.8 - - - +
89D SER* 3.4 17.5 - - - +
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Residues in contact with VAL 72 (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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8D LEU* 3.6 32.1 - - + -
20D ILE* 4.4 5.4 - - + -
22D TRP* 4.0 25.8 - - + +
32D TYR* 3.9 28.9 - - + -
33D ARG 3.3 6.5 - - - +
34D ILE* 4.0 14.8 - - + -
70D ILE* 5.0 0.2 - - + -
71D THR* 1.3 79.9 - - - +
73D TYR* 1.3 63.8 + - - +
86D SER 5.0 0.2 - - - +
87D PRO* 3.7 1.6 - - - +
88D ILE* 2.8 36.9 + - + +
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Residues in contact with TYR 73 (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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98A GLN 5.4 0.2 + - - -
99A LYS* 3.2 24.6 + - - +
100A GLU* 2.8 30.8 + - - -
101A PRO 4.3 7.2 - - - +
32D TYR* 3.1 14.3 - - - +
33D ARG* 2.8 82.0 + - + +
35D THR* 4.0 17.6 + - + +
71D THR* 3.7 23.9 - - + +
72D VAL* 1.3 74.6 - - - +
74D ALA* 1.3 59.7 + - - +
75D VAL* 3.6 8.0 + - + -
85D TYR 5.3 2.7 - - - +
86D SER 5.5 0.7 - - - -
87D PRO* 3.3 24.7 - - + +
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Residues in contact with ALA 74 (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 TYR* 4.1 28.7 - - + +
29D ARG* 4.2 18.2 - - + -
31D TYR 4.0 4.5 - - - -
32D TYR* 4.1 16.2 - - + -
73D TYR* 1.3 71.5 - - - +
75D VAL* 1.3 63.3 + - - +
76D THR* 3.4 10.7 + - - +
85D TYR* 4.3 18.7 + - + +
86D SER 5.5 3.4 + - - +
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Residues in contact with VAL 75 (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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35B MET* 4.0 7.4 - - + -
29D ARG 3.6 0.7 - - - -
30D ARG* 2.6 35.9 + - - -
31D TYR* 2.9 60.8 + - + +
33D ARG* 3.9 27.6 - - + +
73D TYR* 3.6 6.9 + - + +
74D ALA* 1.3 70.6 - - - +
76D THR* 1.3 68.2 + - - +
77D SER 4.1 7.0 - - - +
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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