Contacts of the strand formed by residues 92 - 99 (chain F) in PDB entry 3KYM
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 ALA 92 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F ARG* 4.1 20.0 - - - -
39F GLN 3.2 31.4 - - - +
40F ALA* 3.6 2.7 - - + +
41F PRO* 3.9 8.3 - - - -
90F ASP 3.3 4.4 + - - +
91F THR* 1.3 76.5 - - - +
93F THR* 1.3 66.0 + - - +
94F TYR* 3.7 3.3 - - + -
114F LEU* 3.8 2.9 - - - -
115F VAL* 2.8 35.9 + - - +
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Residues in contact with THR 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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38F ARG* 3.4 3.6 - - - -
39F GLN* 3.2 31.8 + - - +
41F PRO* 5.8 2.7 - - + -
92F ALA* 1.3 78.0 - - - +
94F TYR* 1.3 59.5 + - - +
95F TYR* 3.4 30.0 + - - -
112F GLY* 5.2 1.3 - - - -
113F THR 2.9 17.9 - - - +
114F LEU* 3.7 23.6 - - + -
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Residues in contact with TYR 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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6F GLU* 2.9 15.1 - - - +
20F LEU* 3.7 22.9 - - + -
36F TRP* 4.3 9.7 - + + -
37F VAL 3.4 7.2 - - - +
38F ARG* 2.8 50.5 + - + -
48F VAL* 4.2 10.5 - - + -
68F PHE* 4.2 12.6 - + - -
81F LEU* 4.5 9.0 - - + -
83F MET* 4.5 9.5 - - - -
86F LEU* 5.5 0.2 - - - +
90F ASP* 2.7 29.4 + - - +
92F ALA* 3.7 12.1 - - + -
93F THR* 1.3 73.9 - - - +
95F TYR* 1.3 61.9 + - - +
112F GLY* 3.2 0.7 - - - -
113F THR* 2.9 24.1 + - - +
115F VAL* 3.5 39.2 - - + +
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Residues in contact with TYR 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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38E GLN* 3.4 22.0 + - - -
42E GLN 4.9 1.4 + - - -
44E PRO* 3.9 16.6 - - + -
6F GLU* 3.2 4.9 - - - +
36F TRP* 3.1 12.2 - - - -
37F VAL* 2.7 44.5 + - + +
39F GLN* 4.2 10.4 + - + -
45F LEU* 4.0 27.4 - - + -
93F THR* 3.4 31.2 + - - -
94F TYR* 1.3 72.0 - - - +
96F CYS* 1.3 60.3 + - - +
109F TRP* 4.0 24.0 - + + -
110F GLY 3.4 18.8 - - - +
111F ARG 3.1 23.7 + - - -
112F GLY* 3.8 8.1 - - - -
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Residues in contact with CYS 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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4F LEU* 3.8 10.5 - - - -
6F GLU* 2.8 27.9 + - - -
22F CYS* 2.0 52.9 - - + -
34F MET* 4.9 0.2 - - + -
35F PHE 3.5 6.1 - - - +
36F TRP* 3.6 8.0 - - + -
79F LEU* 3.8 16.2 - - + -
95F TYR* 1.3 76.8 - - - +
97F ALA* 1.3 63.7 + - - +
109F TRP* 3.6 2.6 - - - +
110F GLY 3.2 23.6 + - - -
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Residues in contact with ALA 97 (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* 3.9 3.8 - - - -
34F MET* 3.4 11.3 - - - +
35F PHE* 2.8 38.7 + - + -
37F VAL* 4.8 4.5 - - + -
96F CYS* 1.3 79.0 - - - +
98F ARG* 1.3 58.2 + - - +
106F PHE* 4.0 24.7 - - + -
108F LEU 3.2 17.7 - - - +
109F TRP* 4.1 13.2 - - + -
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Residues in contact with ARG 98 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2F VAL* 5.0 9.8 - - - +
27F PHE* 3.5 41.7 - - - +
32F TYR* 3.5 46.7 + - + -
33F PRO 3.8 0.2 - - - -
34F MET* 3.6 24.0 - - + -
97F ALA* 1.3 75.7 - - - +
99F GLU* 1.3 71.4 + - - +
106F PHE* 3.5 5.5 - - - -
107F ASP* 2.9 61.0 + - - +
108F LEU* 3.3 29.0 + - + +
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Residues in contact with GLU 99 (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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102B ASN* 4.2 8.1 + - - +
32F TYR* 4.2 3.6 - - - -
33F PRO* 3.1 38.6 + - + +
35F PHE* 4.6 12.1 - - + -
50F TRP* 3.2 28.4 + - - -
97F ALA 4.3 0.4 + - - -
98F ARG* 1.3 80.0 - - - +
100F GLY* 1.3 75.5 + - - +
101F HIS 4.1 5.5 - - - +
102F ASN 4.2 4.5 - - - +
103F ASP 2.9 26.8 - - - +
104F TRP* 3.5 23.4 + - - +
105F TYR 3.6 5.6 - - - +
106F PHE* 4.7 0.2 - - - +
107F ASP* 3.4 9.6 - - - +
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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