Contacts of the strand formed by residues 89 - 94 (chain F) in PDB entry 5DK3
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 VAL 89 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F GLN* 3.5 3.8 - - - -
42F GLN* 2.8 42.4 + - + +
88F ALA* 1.3 79.2 - - - +
90F TYR* 1.3 68.1 + - - +
91F TYR* 3.5 37.7 - - + +
105F GLY* 4.3 2.2 - - - -
106F THR 3.4 15.3 - - - +
107F LYS* 4.3 22.2 - - + +
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Residues in contact with TYR 90 (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 8.9 + - - -
21F LEU* 3.3 23.6 - - + -
39F TRP* 4.9 1.8 - - + -
40F TYR 3.2 6.1 - - - -
41F GLN* 3.0 32.3 + - + -
51F LEU* 3.6 33.0 - - + -
66F PHE* 3.6 13.9 - + - -
77F LEU* 3.8 12.3 - - + -
79F ILE* 3.7 11.0 - - + +
86F ASP* 2.6 33.6 + - - -
88F ALA 3.6 17.5 - - - -
89F VAL* 1.3 74.6 - - - +
91F TYR* 1.3 61.9 + - - +
105F GLY* 3.3 2.6 - - - -
106F THR 2.8 31.1 + - - +
108F VAL* 3.8 23.1 - - + -
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Residues in contact with TYR 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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6F GLN* 3.6 1.8 - - - -
39F TRP* 3.3 8.7 - - - -
40F TYR* 2.8 51.1 + - + +
42F GLN* 3.4 31.2 + - + -
48F PRO* 5.4 0.4 - - + -
89F VAL* 3.5 25.5 - - + +
90F TYR* 1.3 72.8 - - - +
92F CYS* 1.3 62.6 + - - +
102F PHE* 4.4 12.6 - - + -
103F GLY 3.3 23.6 - - - -
104F GLY 3.8 7.6 + - - -
105F GLY* 3.7 20.0 - - - -
39G GLN* 3.4 19.7 + - - -
43G GLN 3.7 2.6 + - - -
44G GLY* 3.7 18.5 - - - -
45G LEU* 3.7 24.0 - - + -
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Residues in contact with CYS 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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4F LEU* 3.8 5.6 - - - -
6F GLN* 3.3 21.9 + - - -
23F CYS* 2.6 49.4 - - + -
37F LEU* 4.1 6.1 - - + -
38F HIS 3.2 9.2 - - - +
39F TRP* 3.9 13.7 - - + -
91F TYR* 1.3 72.9 - - - +
93F GLN* 1.3 59.9 + - - +
102F PHE* 3.2 7.2 - - - +
103F GLY* 2.8 36.2 + - - -
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Residues in contact with GLN 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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4F LEU* 3.8 0.9 - - - -
37F LEU* 3.2 9.3 - - - +
38F HIS* 2.8 45.1 + - + +
40F TYR* 2.7 44.3 + - + -
92F CYS* 1.3 75.0 - - - +
94F HIS* 1.4 80.8 + - - +
95F SER* 3.8 12.5 - - - -
100F LEU* 4.1 7.6 - - + +
101F THR 3.4 14.8 - - - +
102F PHE* 3.7 22.4 - - + -
104G ASP* 5.6 0.2 + - - -
107G PHE* 3.9 27.3 - - - -
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Residues in contact with HIS 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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2F ILE* 3.4 40.9 + - + +
4F LEU* 3.5 11.4 - - + +
29F VAL* 3.9 16.8 - - + -
36F TYR 3.2 10.8 - - - +
37F LEU* 4.1 4.3 - - + -
93F GLN* 1.4 90.4 + - - +
95F SER* 1.4 65.1 - - - +
96F ARG 3.7 8.5 - - - -
97F ASP* 3.1 28.9 + - - +
99F PRO 3.1 17.9 + - - -
100F LEU* 3.7 9.7 - - - +
101F THR* 3.0 43.4 + - - -
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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