Contacts of the strand formed by residues 90 - 96 (chain F) in PDB entry 3QAZ
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 90 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52F TRP* 3.4 21.7 + - - -
54F SER* 4.6 3.1 - - - -
61F THR 4.7 0.3 + - - -
62F ASN* 3.9 19.1 + - + +
63F LEU* 2.9 32.2 + - - +
83F TYR* 3.3 37.7 - - + -
84F LEU 3.5 5.8 - - - -
85F PHE* 3.5 19.1 - - + -
89F ILE* 1.3 79.3 - - - +
91F SER* 1.3 59.2 + - - +
92F GLY 3.4 0.4 - - - -
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Residues in contact with SER 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F THR* 3.3 9.9 - - - -
52F TRP* 2.8 43.0 + - - +
54F SER* 6.1 0.7 - - - +
84F LEU* 2.6 14.3 + - - -
85F PHE 3.8 5.2 - - - -
86F SER* 3.4 34.5 - - - -
89F ILE 3.1 1.8 + - - -
90F THR* 1.3 72.8 - - - +
92F GLY* 1.3 54.6 + - - -
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Residues in contact with GLY 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F CYS 3.2 6.7 - - - -
51F THR* 4.0 2.2 - - - -
52F TRP* 3.0 24.2 - - - -
83F TYR* 3.6 11.6 - - - -
84F LEU* 2.8 32.1 + - - +
90F THR 3.4 2.2 - - - -
91F SER* 1.3 81.9 - - - +
93F CYS* 1.3 63.4 + - - +
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Residues in contact with CYS 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F MET 3.9 0.2 - - - +
49F ASN* 3.7 0.9 - - - -
50F CYS* 2.8 35.2 + - - +
51F THR* 5.7 0.2 - - - +
65F LEU* 3.9 22.4 - - + -
80F CYS* 2.0 44.6 - - - -
82F HIS 3.1 12.6 - - - -
83F TYR* 5.2 0.9 - - + -
84F LEU* 3.6 7.9 - - - +
92F GLY* 1.3 75.6 - - - +
94F GLN* 1.3 62.5 + - - +
95F LEU* 3.5 25.0 + - - +
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Residues in contact with GLN 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F TYR* 3.8 23.7 - - + +
48F MET 3.0 9.6 - - - +
49F ASN* 3.2 24.7 + - - +
81F SER* 5.5 0.3 + - - -
82F HIS* 3.1 47.8 + - - +
84F LEU* 3.3 9.0 - - + +
93F CYS* 1.3 75.4 - - - +
95F LEU* 1.3 69.0 + - - +
96F GLN* 2.8 40.1 - - - +
99F GLU* 5.0 0.3 - - - +
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Residues in contact with LEU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F TYR* 3.5 1.3 - - - -
48F MET* 2.7 68.0 + - + +
50F CYS* 5.9 2.5 - - + -
65F LEU* 5.9 0.4 - - + -
67F TYR* 3.2 47.6 - - + -
80F CYS* 4.7 0.9 - - - -
81F SER* 5.9 2.0 - - - +
82F HIS 6.2 0.2 - - - +
93F CYS* 3.5 28.0 - - - +
94F GLN* 1.3 73.7 - - - +
96F GLN* 1.3 61.6 + - - +
99F GLU* 4.0 23.3 - - + +
100F ILE* 3.7 7.9 - - + +
106F PHE* 3.7 14.4 - - + -
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Residues in contact with GLN 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F GLU 4.9 0.4 - - - +
47F TYR* 3.8 13.0 - - + -
81F SER* 5.3 3.3 + - - -
82F HIS* 3.7 23.2 + - - +
94F GLN* 2.8 39.8 - - - +
95F LEU* 1.3 77.0 - - - +
97F LYS* 1.3 69.5 + - - +
98F LYS* 3.0 6.5 + - + +
99F GLU* 3.1 23.2 + - - +
100F ILE* 3.5 7.7 - - - +
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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