Contacts of the strand formed by residues 71 - 78 (chain B) in PDB entry 3QB4
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 THR 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B ILE* 4.2 19.3 - - + +
64B GLU 3.2 7.6 - - - -
65B GLU* 3.8 21.1 - - + +
66B ASP* 5.0 1.6 - - - -
69B GLY 3.8 10.5 - - - +
70B GLU* 1.3 82.5 - - - +
72B THR* 1.3 65.6 + - - +
115B LEU* 4.2 18.4 - - + -
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Residues in contact with THR 72 (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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62B ILE 3.8 0.5 - - - +
63B ILE* 3.3 5.5 - - - +
64B GLU* 2.8 45.8 + - - +
66B ASP* 3.9 15.3 + - - +
71B THR* 1.3 78.3 - - - +
73B LEU* 1.3 66.1 + - - +
74B ALA* 4.2 2.4 + - - -
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Residues in contact with LEU 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 TYR* 6.4 0.9 - - + -
41B SER* 4.6 9.8 + - - +
61B ALA* 5.3 3.1 - - + -
62B ILE 3.1 14.4 - - - +
63B ILE* 4.2 7.8 - - + +
72B THR* 1.3 80.8 - - - +
74B ALA* 1.3 76.3 + - - +
75B SER* 4.4 9.9 - - - +
111B LEU 3.6 23.6 - - - +
112B GLN* 4.0 19.5 - - + +
113B PRO* 5.3 2.5 - - + -
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Residues in contact with ALA 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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18A ARG* 5.8 1.8 - - - +
41B SER* 3.1 18.8 - - - +
42B GLY* 4.7 3.6 - - - -
43B HIS* 3.6 21.8 - - + +
61B ALA* 3.6 0.5 - - - -
62B ILE* 2.8 40.4 + - + +
72B THR* 4.2 2.4 + - - -
73B LEU* 1.3 80.5 - - - +
75B SER* 1.3 64.5 + - - +
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Residues in contact with SER 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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39B TYR* 3.7 15.5 - - - -
40B CYS* 3.0 2.1 - - - +
41B SER* 2.6 48.6 + - - +
43B HIS* 3.8 5.6 - - - +
60B PHE* 3.2 25.6 - - - -
61B ALA* 4.2 7.0 - - - -
73B LEU* 4.4 7.0 - - - +
74B ALA* 1.3 80.4 - - - +
76B GLY* 1.3 58.1 + - - +
108B ASN* 3.6 15.5 - - - -
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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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38B CYS* 3.9 0.5 - - - +
39B TYR 3.3 15.9 - - - -
40B CYS* 3.7 9.9 - - - -
43B HIS* 4.4 4.9 - - - -
53B CYS* 3.8 1.8 - - - -
59B CYS* 3.4 3.5 - - - -
60B PHE* 3.1 42.6 + - - -
75B SER* 1.3 77.4 - - - +
77B CYS* 1.3 58.6 + - - -
108B ASN* 3.4 6.9 + - - -
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Residues in contact with CYS 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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57A ALA* 3.4 5.9 - - + +
58A SER* 2.9 35.7 + - - +
38B CYS* 3.5 15.0 - - - -
43B HIS 5.1 1.2 + - - -
45B PRO* 5.9 1.1 - - + -
53B CYS* 2.0 66.2 - - + -
54B ILE 3.7 2.7 - - - +
55B THR* 3.8 12.1 - - - -
58B HIS 3.6 4.0 - - - -
60B PHE* 3.3 11.3 - - - -
76B GLY* 1.3 72.6 - - - -
78B MET* 1.3 61.5 + - - +
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Residues in contact with MET 78 (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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55A PRO* 4.7 4.0 - - + -
56A LEU 4.5 3.6 - - - +
58A SER* 3.9 1.6 - - - +
55B THR* 3.4 6.0 + - - -
57B GLY* 3.2 3.8 - - - -
58B HIS* 2.5 47.0 + - + +
60B PHE* 4.0 16.4 - - + -
77B CYS* 1.3 75.4 - - - +
79B LYS* 1.3 71.1 + - - +
83B SER* 3.6 18.6 - - - -
86B GLN* 3.3 44.0 - - + +
87B CYS* 3.4 29.4 - - - -
99B ILE* 3.8 26.5 - - + -
101B CYS* 4.2 1.8 - - - -
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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