Contacts of the strand formed by residues 84 - 99 (chain F) in PDB entry 1KN0
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 TRP 84 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26F PHE* 3.9 2.7 - - - -
72F ILE* 4.3 11.9 - - + -
75F ALA* 3.8 25.1 - - + -
76F ASN* 3.0 24.0 + - - +
79F PHE* 3.7 19.3 - + + -
80F GLY 3.3 16.8 + - - -
81F TYR 4.1 3.0 + - - +
82F ASN 3.5 0.4 - - - -
83F GLY* 1.3 81.4 - - - +
85F ALA* 1.3 73.7 + - - +
86F HIS* 4.3 3.8 - + + -
113F VAL* 3.9 16.4 - - + -
114F GLN 3.3 7.9 - - - +
115F LEU* 4.0 8.1 - - + -
151F LEU* 3.8 38.4 - - + -
155F LEU* 4.0 12.3 - - + -
119G SER* 3.9 9.7 + - - -
121G HIS* 3.2 44.5 + + - -
157G SER* 3.7 18.6 - - - -
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Residues in contact with ALA 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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26F PHE* 3.6 16.8 - - + -
84F TRP* 1.3 80.7 - - - +
86F HIS* 1.3 58.0 + - - +
113F VAL* 3.2 6.8 - - - +
114F GLN 2.7 35.4 + - - +
120G TYR* 2.8 52.5 - - + +
121G HIS* 4.0 4.0 - - - -
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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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84F TRP* 4.3 4.0 - + + -
85F ALA* 1.3 78.1 - - - +
87F SER* 1.3 61.4 + - - +
88F ILE* 5.7 0.6 - - - +
111F VAL* 3.8 20.5 - - + +
112F ARG 3.1 11.4 - - - +
113F VAL* 4.2 2.9 - - + -
147F VAL* 5.2 6.3 - - + -
151F LEU* 3.5 39.5 - - + +
120G TYR* 3.1 20.4 + - - -
121G HIS* 2.8 42.2 - + + +
122G GLU 3.2 42.0 + - - -
123G ASP* 4.7 7.8 - - - +
154G ALA* 6.0 0.2 - - - -
157G SER* 3.5 14.9 + - - -
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Residues in contact with SER 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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86F HIS* 1.3 78.1 - - - +
88F ILE* 1.3 67.0 + - - +
89F THR* 3.6 2.3 + - - -
111F VAL* 3.5 5.9 - - - +
112F ARG* 2.9 44.6 + - - +
112G ARG* 5.0 6.7 - - - -
120G TYR* 3.8 17.7 + - - -
122G GLU* 3.4 18.4 - - - -
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Residues in contact with ILE 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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86F HIS* 5.7 0.2 - - - +
87F SER* 1.3 74.5 - - - +
89F THR* 1.3 68.3 + - - +
90F GLN* 3.7 22.8 - - - +
91F GLN* 4.4 3.4 - - + -
109F ALA* 4.8 0.7 - - + -
110F PHE 3.5 11.2 - - - +
111F VAL* 4.6 6.7 - - + +
147F VAL* 3.5 37.0 - - + -
110G PHE* 3.7 33.7 - - + -
122G GLU* 2.8 34.2 + - + +
123G ASP* 3.9 22.9 - - - -
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Residues in contact with THR 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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88E ILE 5.7 2.5 - - - +
87F SER* 3.6 4.7 + - - -
88F ILE* 1.3 74.3 - - - +
90F GLN* 1.3 67.4 + - + +
110F PHE* 2.8 17.7 + - + -
112F ARG* 3.9 17.2 - - - +
122F GLU* 2.7 27.9 + - - +
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Residues in contact with GLN 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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88F ILE* 3.2 8.0 - - - +
89F THR* 1.3 90.1 - - + +
91F GLN* 1.3 71.6 + - - +
92F ASN* 4.6 9.0 - - + +
109F ALA* 3.4 0.5 - - - -
110F PHE* 2.7 53.5 + - + +
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Residues in contact with GLN 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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88F ILE* 4.3 2.1 - - + +
90F GLN* 1.3 80.7 - - - +
92F ASN* 1.3 64.0 + - - +
107F VAL* 3.9 11.6 - - + +
108F CYS 3.4 12.3 - - - +
109F ALA* 4.0 9.5 - - + +
143F ARG* 2.8 74.5 + - - +
147F VAL* 3.7 11.6 - - - +
110G PHE* 3.0 42.4 - - + -
124G VAL* 3.7 3.0 - - - +
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Residues in contact with ASN 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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143E ARG* 4.4 7.3 - - - +
90F GLN* 4.3 11.6 - - + +
91F GLN* 1.3 75.6 - - - +
93F VAL* 1.3 69.2 + - - +
94F ASP* 3.2 29.1 + - - +
107F VAL* 4.4 2.2 - - - -
108F CYS* 3.0 44.4 + - - -
110F PHE* 5.7 2.0 - - + -
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Residues in contact with VAL 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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91F GLN 4.3 0.2 + - - -
92F ASN* 1.3 79.5 + - - +
94F ASP* 1.3 64.1 + - - +
95F PHE* 4.0 7.4 - - - +
96F VAL* 3.8 29.2 - - + -
106F GLY 3.9 2.7 - - - -
107F VAL* 4.0 21.3 - - + -
139F LEU* 4.4 7.4 - - + -
143F ARG* 3.6 39.7 - - - +
94G ASP* 5.1 0.9 - - - +
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Residues in contact with ASP 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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93E VAL* 5.0 1.3 - - - +
139E LEU* 3.2 25.2 - - + +
143E ARG* 2.5 34.9 + - - -
92F ASN* 3.2 20.3 + - - +
93F VAL* 1.3 73.0 - - - +
95F PHE* 1.3 63.6 + - + +
106F GLY 2.8 15.3 + - - +
108F CYS* 4.5 0.2 - - - -
126F TYR* 2.6 31.0 + - - +
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Residues in contact with PHE 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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135E LYS* 3.3 44.9 - - + +
136E ALA* 3.2 35.7 - - + -
139E LEU* 3.7 23.3 - - + -
93F VAL* 3.4 2.9 - - - +
94F ASP* 1.3 79.4 - - + +
96F VAL* 1.3 71.5 + - - +
97F ASP* 3.4 18.4 - - - +
104F TYR* 3.0 33.2 - - + -
105F VAL* 3.4 3.0 - - - +
106F GLY* 3.1 40.5 + - - +
130F GLU* 5.9 0.2 - - - -
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Residues in contact with VAL 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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93F VAL* 3.8 12.1 - - + -
95F PHE* 1.3 83.0 - - - +
97F ASP* 1.3 61.9 + - - +
98F LEU* 4.2 0.7 + - - +
103F PHE* 4.4 12.0 - - + -
104F TYR 3.7 4.0 - - - -
105F VAL* 3.8 14.4 - - + -
135F LYS* 4.2 27.1 - - + -
139F LEU* 3.7 27.8 - - + -
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Residues in contact with ASP 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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135E LYS* 2.8 40.2 + - - -
95F PHE* 3.4 9.6 - - - +
96F VAL* 1.3 79.7 + - - +
98F LEU* 1.3 60.4 + - - +
99F ASN* 4.1 10.3 - - - +
102F LYS 3.7 0.3 - - - +
103F PHE* 3.4 9.6 - - - -
104F TYR* 2.9 44.3 + - + +
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Residues in contact with LEU 98 (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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96F VAL 4.2 0.6 + - - +
97F ASP* 1.3 74.5 - - - +
99F ASN* 1.3 64.1 + - - +
100F ASN 4.0 2.3 + - - +
101F GLY* 3.6 18.2 - - - +
102F LYS 3.2 31.6 - - - +
103F PHE* 3.7 32.3 - - + -
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Residues in contact with ASN 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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97F ASP* 4.1 10.2 - - - +
98F LEU* 1.3 75.9 - - - +
100F ASN* 1.3 88.1 + - - +
102F LYS* 3.0 21.3 + - - +
104F TYR* 3.7 39.3 - - + +
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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