Contacts of the strand formed by residues 83 - 89 (chain F) in PDB entry 1QZH
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 LEU 83 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ILE* 3.9 23.1 - - + +
33F SER* 4.1 21.3 - - - -
34F GLN* 4.1 15.5 - - + +
45F LEU* 3.8 30.7 - - + -
69F VAL 3.5 1.4 - - - +
70F TYR* 3.2 4.6 - - - -
71F LEU* 2.8 37.6 + - + +
82F GLY* 1.3 71.0 - - - -
84F GLN* 1.3 67.5 + - - +
85F ILE* 3.6 8.9 + - + +
112F LEU* 4.3 8.3 - - + -
119F THR* 3.6 42.8 - - + +
120F GLN* 4.4 2.7 - - - +
121F GLY 5.3 0.4 - - - +
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Residues in contact with GLN 84 (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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34F GLN* 5.7 0.2 - - - +
68F THR* 4.1 9.0 - - + -
69F VAL 3.8 3.1 - - - -
70F TYR* 3.5 40.2 + - + -
82F GLY 3.6 3.4 + - - +
83F LEU* 1.3 76.5 - - - +
85F ILE* 1.3 62.7 + - - +
86F HIS* 3.4 12.3 - - + -
115F TYR* 5.1 4.2 - - - +
119F THR 4.7 5.8 + - - +
120F GLN* 3.0 39.0 - - + +
121F GLY 2.8 23.9 + - - -
6L C 3.2 18.3 + - - +
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Residues in contact with ILE 85 (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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45F LEU* 3.3 31.9 - - + -
67F THR 4.0 0.2 - - - +
68F THR* 3.5 3.3 - - - +
69F VAL* 2.9 41.3 + - + +
71F LEU* 3.7 20.4 - - + -
83F LEU* 3.9 16.6 - - + +
84F GLN* 1.3 79.6 - - - +
86F HIS* 1.3 66.4 + - - +
87F LEU* 3.8 25.9 + - + +
107F LEU* 3.6 17.5 - - + -
110F ILE* 4.0 11.0 - - + -
121F GLY* 3.2 18.2 - - - +
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Residues in contact with HIS 86 (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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66F VAL* 4.5 3.1 - - + +
67F THR 3.9 3.1 - - - -
68F THR* 2.8 41.3 + - + +
84F GLN* 3.4 14.3 + - - -
85F ILE* 1.3 70.7 - - - +
87F LEU* 1.3 62.0 + - - +
88F PHE* 3.4 27.7 - + + -
120F GLN* 3.4 25.0 + - + -
121F GLY 2.7 12.2 + - - +
122F LEU* 3.7 2.4 - - + -
123F SER 3.1 23.6 + - - -
5L A 3.3 39.5 + + + -
6L C 3.3 24.6 + - - -
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Residues in contact with LEU 87 (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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66F VAL* 3.2 6.2 - - - +
67F THR* 3.0 53.4 + - + +
69F VAL* 4.6 17.7 - - + -
85F ILE* 3.9 22.7 - - + +
86F HIS* 1.3 72.1 - - - +
88F PHE* 1.3 61.1 + - - +
95F LEU* 3.7 4.6 - - + +
96F PRO* 3.9 24.0 - - + -
105F LEU* 5.0 1.6 - - + -
107F LEU* 3.9 26.2 - - + -
110F ILE* 4.0 3.1 - - + -
123F SER* 3.7 19.7 - - - -
127F PHE* 4.0 15.3 - - + -
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Residues in contact with PHE 88 (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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58F SER* 4.4 0.9 - - - -
64F ASP* 4.4 8.3 - - + +
65F TRP 3.2 7.0 - - - -
66F VAL* 3.4 28.7 - - + -
86F HIS* 3.4 34.1 - - + -
87F LEU* 1.3 72.6 - - - +
89F SER* 1.3 63.8 + - - +
90F LYS* 6.0 2.2 - - + -
95F LEU* 4.0 1.6 - - - -
122F LEU* 4.6 4.3 - - + -
123F SER* 3.0 16.1 + - - +
124F LYS 5.1 1.2 - - - +
125F ASP* 5.1 4.4 - - - +
127F PHE* 3.6 18.4 - - - -
150F ARG* 3.7 4.5 + - - -
2L G 4.0 18.4 - - - +
4L T 3.7 50.3 - + + +
5L A 3.3 34.5 - + - -
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Residues in contact with SER 89 (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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64F ASP* 3.4 4.6 - - - +
65F TRP* 3.0 35.1 + - - +
88F PHE* 1.3 77.8 - - - +
90F LYS* 1.3 62.0 + - - +
91F GLN* 3.3 2.6 - - - +
92F GLY 2.8 25.5 + - - +
94F ASP* 2.8 25.6 + - - -
95F LEU* 3.7 14.6 - - - -
125F ASP* 6.1 0.4 - - - -
150F ARG* 3.1 14.1 + - - +
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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