Contacts of the strand formed by residues 84 - 89 (chain F) in PDB entry 4KJW
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 84 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37F GLN* 3.4 24.1 + - - +
83F ALA* 1.3 73.5 - - - +
85F TYR* 1.3 61.7 + - - +
86F TYR* 3.4 34.1 - - + +
99F GLY 5.3 0.7 - - - +
100F GLY* 4.0 10.8 - - - -
101F THR 3.4 22.0 - - - +
102F LYS* 3.8 29.5 + - + +
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Residues in contact with TYR 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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6F GLN* 3.0 21.7 + - - +
21F MET* 3.6 39.0 - - + -
34F TRP* 4.6 6.3 - - + -
35F TYR 3.3 7.4 - - - +
36F GLN* 3.1 45.7 + - + +
46F TRP* 4.1 4.5 - + - -
61F PHE* 3.3 33.3 - + - -
72F LEU* 4.1 16.6 - - + -
74F ILE* 4.3 1.8 - - + -
81F ASP* 2.6 32.3 + - - +
83F ALA* 3.6 18.2 - - + -
84F THR* 1.3 71.6 - - - +
86F TYR* 1.3 60.7 + - - +
100F GLY* 3.6 0.2 - - - -
101F THR 3.1 18.9 + - - -
103F LEU* 4.3 6.5 - - + -
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Residues in contact with TYR 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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39E GLN* 3.3 22.4 + - - -
43E LYS 3.6 6.4 + - - -
44E GLY* 4.0 15.0 - - - -
45E LEU* 3.9 28.5 - - + -
6F GLN* 3.4 3.4 - - - -
34F TRP* 3.3 6.3 - - - -
35F TYR* 2.6 52.3 + - + +
37F GLN* 3.1 31.6 + - + -
43F PRO* 5.6 0.4 - - + -
84F THR* 3.4 40.4 - - + +
85F TYR* 1.3 73.2 - - - +
87F CYS* 1.3 63.8 + - - +
97F PHE* 4.9 2.9 - - + -
98F GLY 4.1 10.3 - - - -
99F GLY 3.8 18.5 + - - -
100F GLY* 3.8 14.1 - - - -
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Residues in contact with CYS 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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4F LEU* 4.1 3.4 - - - -
6F GLN* 2.9 26.3 + - - -
23F CYS* 2.0 46.7 - - + -
32F ILE* 4.1 4.3 - - + -
33F HIS 3.2 7.2 - - - +
34F TRP* 3.6 21.8 - - + -
86F TYR* 1.3 75.8 - - - +
88F GLN* 1.3 63.2 + - - +
97F PHE* 3.4 3.5 - - - +
98F GLY* 2.7 37.1 + - - -
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Residues in contact with GLN 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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106E TRP 3.5 18.4 + - - -
107E TYR* 4.1 0.2 - - - -
108E PHE* 3.8 18.2 - - + -
4F LEU* 4.0 3.6 - - - -
32F ILE* 3.3 5.8 - - - +
33F HIS* 2.6 54.5 + - - +
35F TYR* 2.7 41.4 + - + -
87F CYS* 1.3 79.3 - - - +
89F GLN* 1.3 83.1 + - - +
90F TRP* 3.7 4.6 - - - +
95F GLN* 4.1 1.0 - - + +
96F THR 3.4 14.8 - - - +
97F PHE* 3.6 22.7 - - + -
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Residues in contact with GLN 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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2F ILE* 3.8 12.5 - - + +
4F LEU* 3.7 14.5 - - + +
29F VAL* 3.6 29.5 - - + +
30F SER 5.6 0.7 - - - +
31F TYR 5.3 0.2 - - - -
32F ILE* 4.3 13.0 - - + +
33F HIS* 5.1 0.4 - - - -
88F GLN* 1.3 82.3 + - - +
90F TRP* 1.3 59.7 + - - +
91F SER* 3.1 11.6 + - - +
92F SER* 3.1 28.0 + - - -
94F PRO 3.5 14.1 + - - -
95F GLN* 3.1 24.5 - - - +
96F THR* 2.9 42.5 + - - +
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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