Contacts of the strand formed by residues 70 - 77 (chain B) in PDB entry 3WYR
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 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LYS* 4.2 6.5 - - - -
43B ASP* 4.1 5.8 - - - -
44B GLY 4.3 0.4 - - - -
68B HIS 3.4 1.6 + - - -
69B ALA* 1.3 74.6 - - - +
71B THR* 1.3 65.4 + - - -
72B TYR* 3.5 9.5 - - - -
93B VAL* 4.4 1.1 - - - -
94B ILE 2.9 33.9 + - - -
181B TYR* 3.5 21.4 - - - +
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LYS* 3.4 6.8 - - - +
42B LYS* 2.7 37.6 + - + -
43B ASP* 3.1 39.8 + - - +
70B GLY* 1.3 73.2 - - - -
72B TYR* 1.3 65.0 + - - +
73B ARG* 4.6 6.5 - - - +
91B PRO* 4.0 27.1 - - + -
92B LEU 3.7 6.1 - - - +
93B VAL* 3.8 17.2 - - + +
181B TYR* 3.9 4.9 + - - -
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Residues in contact with TYR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.3 13.5 - - + -
39B LEU* 3.6 28.3 - - + -
40B TYR 3.2 3.8 - - - +
41B LYS* 3.2 33.0 - - + +
42B LYS* 5.2 0.7 - - - -
50B LEU* 3.5 29.5 - - + +
61B ILE* 4.3 7.8 - - + +
68B HIS* 2.7 40.3 + - - +
70B GLY 3.5 18.4 - - - -
71B THR* 1.3 74.3 - - - +
73B ARG* 1.3 66.5 + - - +
74B CYS* 5.4 2.5 - - - -
90B ASN 3.9 0.7 - - - +
91B PRO* 3.8 0.3 - - - +
92B LEU* 2.9 48.4 + - + +
94B ILE* 3.8 18.8 - - + -
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Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 3.9 0.2 - - - +
40B TYR* 2.7 45.8 + - + +
42B LYS* 3.6 42.8 - - + +
71B THR* 4.6 6.0 - - + +
72B TYR* 1.3 79.1 - - - +
74B CYS* 1.3 65.3 + - - +
88B PRO* 3.7 27.2 - - + +
89B SER* 3.6 21.6 + - - +
90B ASN 4.3 0.2 - - - +
91B PRO* 3.4 38.3 - - + +
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Residues in contact with CYS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PRO* 3.9 5.4 - - - +
10B CYS* 3.7 19.1 - - - -
26B LEU* 5.6 4.7 - - - -
28B CYS* 3.7 22.0 - - - -
37B PHE* 4.5 11.0 - - + -
38B THR 3.4 6.5 - - - +
39B LEU* 3.7 20.6 - - - -
55B PHE* 4.0 11.9 - - - -
72B TYR* 5.4 2.5 - - - -
73B ARG* 1.3 83.6 - - - +
75B ARG* 1.3 62.1 + - - +
88B PRO* 4.3 0.4 - - - -
89B SER* 2.8 37.0 + - - +
92B LEU* 6.4 1.1 - - - -
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Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PHE* 3.3 5.6 - - - -
38B THR* 2.9 43.8 + - + +
40B TYR* 3.6 30.2 + - + -
74B CYS* 1.3 74.9 - - - +
76B GLY* 1.3 60.3 + - - +
83B THR* 5.9 0.2 + - - -
85B TRP* 3.7 13.2 + - + -
86B SER 2.8 42.1 + - - +
87B ALA* 3.6 6.4 - - - +
88B PRO* 3.3 41.7 - - + +
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Residues in contact with GLY 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PRO* 3.7 5.7 - - - +
30B TYR* 3.9 15.5 - - - -
37B PHE* 3.7 19.3 - - - -
75B ARG* 1.3 73.5 - - - +
77B PHE* 1.3 64.2 - - - -
78B HIS 3.2 0.3 + - - -
85B TRP* 3.5 4.5 - - - -
86B SER* 2.9 40.4 + - - -
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B TYR* 4.2 0.2 - - - -
33B GLY* 3.6 2.3 - - - -
34B PHE* 2.9 48.0 + + + +
36B ILE* 2.8 40.4 + - + +
76B GLY* 1.3 68.7 - - - -
78B HIS* 1.3 57.7 + - - +
79B PRO* 3.5 35.6 - - + +
84B GLU* 3.3 34.3 - - + -
85B TRP* 3.6 31.6 - + + -
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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