Contacts of the strand formed by residues 102 - 115 (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 LYS 102 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98F LEU* 3.2 6.6 - - - +
99F ASN 3.0 30.8 + - - +
100F ASN* 2.9 29.6 + - - +
101F GLY* 1.3 79.5 - - - +
103F PHE* 1.3 61.1 + - - +
104F TYR* 3.5 26.2 + - + +
130F GLU 5.3 1.1 - - - +
131F GLY* 3.3 18.4 - - - +
132F LEU 3.6 4.0 - - - -
133F LYS* 5.1 7.2 - - + +
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Residues in contact with PHE 103 (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* 4.4 11.9 - - + -
97F ASP 3.4 14.6 - - - -
98F LEU* 3.7 36.3 - - + -
101F GLY 4.8 0.9 - - - -
102F LYS* 1.3 72.4 - - - +
104F TYR* 1.3 64.3 + - - +
105F VAL* 4.0 3.8 - - + -
129F SER 3.2 12.0 - - - +
130F GLU 3.3 15.4 - - - -
131F GLY 3.7 1.4 + - - -
132F LEU 2.9 10.4 + - - +
133F LYS 3.3 25.4 - - - -
134F SER 3.6 2.2 - - - -
135F LYS* 3.4 56.8 - - + -
138F SER* 3.5 21.5 + - - +
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Residues in contact with TYR 104 (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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136E ALA* 6.3 0.2 - - - -
95F PHE* 3.0 18.1 - - + -
97F ASP* 2.9 41.0 + - + +
99F ASN* 3.7 35.8 + - + +
100F ASN* 5.0 1.2 + - - -
102F LYS* 3.5 46.7 + - + +
103F PHE* 1.3 76.1 - - - +
105F VAL* 1.3 62.1 + - - +
129F SER 3.4 4.5 - - - -
130F GLU* 3.5 41.7 + - + +
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Residues in contact with VAL 105 (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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136E ALA* 4.8 0.2 - - - -
93F VAL* 4.7 0.2 - - + -
95F PHE* 3.4 13.9 - - - +
96F VAL* 3.8 27.8 - - + -
103F PHE* 4.7 1.8 - - + -
104F TYR* 1.3 79.2 - - - +
106F GLY* 1.3 62.0 + - - +
107F VAL* 3.8 7.6 - - + -
127F GLY 3.9 0.2 - - - +
128F VAL* 3.5 12.0 - - - +
129F SER 2.8 32.6 + - - +
130F GLU* 5.4 0.4 - - - +
135F LYS* 6.0 0.2 - - + -
138F SER* 4.1 28.3 - - - +
139F LEU* 3.7 26.2 - - + -
142F ALA* 3.8 18.6 - - + -
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Residues in contact with GLY 106 (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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136E ALA* 4.4 1.3 - - - -
93F VAL 3.6 0.2 - - - -
94F ASP* 2.8 31.9 + - - +
95F PHE* 3.1 28.2 + - - +
105F VAL* 1.3 75.2 - - - +
107F VAL* 1.3 59.5 + - - +
126F TYR* 3.7 21.8 - - - -
127F GLY 3.8 3.6 - - - -
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Residues in contact with VAL 107 (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* 3.9 20.4 - - + +
92F ASN 3.7 8.3 - - - +
93F VAL* 4.0 20.4 - - + -
94F ASP 4.2 0.7 - - - +
105F VAL* 3.8 9.9 - - + -
106F GLY* 1.3 79.5 - - - +
108F CYS* 1.3 69.7 + - - +
126F TYR* 3.1 12.5 - - - -
127F GLY 2.7 33.2 + - - -
139F LEU* 5.1 0.7 - - + -
142F ALA* 3.6 33.9 - - + +
143F ARG* 4.1 7.6 - - + +
146F ALA* 3.7 16.2 - - + -
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Residues in contact with CYS 108 (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* 3.3 42.2 - - - -
91F GLN* 3.4 5.5 - - - +
92F ASN* 3.0 50.2 + - - +
94F ASP* 4.1 0.2 - - - -
107F VAL* 1.3 75.5 - - - +
109F ALA* 1.3 60.8 + - - +
110F PHE* 3.9 14.4 - - - -
124F VAL* 4.3 4.9 - - + -
125F GLY 3.3 8.1 - - - +
126F TYR* 3.6 19.9 - - + -
146F ALA* 4.0 2.0 - - - -
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Residues in contact with ALA 109 (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* 4.8 3.4 - - + -
90F GLN 3.4 8.7 - - - +
91F GLN* 4.0 13.2 - - + +
108F CYS* 1.3 76.4 - - - +
110F PHE* 1.3 65.8 + - - +
111F VAL* 4.0 3.5 + - + -
123F ASP 3.8 0.2 - - - +
124F VAL* 3.2 4.0 - - - -
125F GLY 2.6 37.2 + - - -
146F ALA* 3.8 28.3 - - + +
147F VAL* 3.9 13.7 - - + +
150F GLY* 4.7 0.3 - - - -
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Residues in contact with PHE 110 (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* 3.7 33.7 - - + -
91E GLN* 3.0 50.5 - - + -
143E ARG* 4.4 5.4 - - - -
88F ILE* 3.5 5.4 - - - +
89F THR* 2.8 44.2 + - + -
90F GLN* 2.7 41.0 + - + +
92F ASN* 5.7 2.2 - - + -
108F CYS* 3.9 21.8 - - - -
109F ALA* 1.3 74.5 - - - +
111F VAL* 1.3 61.9 - - - +
122F GLU* 4.2 6.3 - - - +
123F ASP 3.5 2.7 - - - +
124F VAL* 3.6 14.1 - - + -
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Residues in contact with VAL 111 (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* 3.8 31.2 - - + +
87F SER 3.5 11.9 - - - +
88F ILE* 4.6 11.4 - - + -
89F THR* 4.8 0.2 - - - -
109F ALA* 4.8 1.8 - - + -
110F PHE* 1.3 81.8 - - - +
112F ARG* 1.3 65.0 + - - +
113F VAL* 4.1 2.9 - - + -
122F GLU* 3.1 4.8 - - - +
123F ASP 2.9 32.5 + - - -
147F VAL* 3.7 21.3 - - + +
150F GLY* 3.8 8.7 - - - +
151F LEU* 3.7 33.4 - - - +
154F ALA* 4.1 3.4 - - - +
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Residues in contact with ARG 112 (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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87E SER* 5.0 5.5 - - - -
86F HIS* 3.1 3.6 - - - -
87F SER* 2.9 41.3 + - - +
89F THR* 3.9 17.9 - - - +
110F PHE 4.3 0.2 + - - -
111F VAL* 1.3 74.9 - - - +
113F VAL* 1.3 66.0 + - - +
114F GLN* 2.8 36.0 + - - +
120F TYR* 3.8 41.5 - - + +
121F HIS 3.5 6.1 - - - +
122F GLU* 3.7 22.7 - - + -
120G TYR* 4.9 10.5 + - - -
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Residues in contact with VAL 113 (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* 3.9 12.1 - - + -
85F ALA 3.2 11.0 - - - +
86F HIS* 4.2 2.7 - - + +
111F VAL* 4.6 0.9 - - + -
112F ARG* 1.3 75.4 - - - +
114F GLN* 1.3 67.4 + - - +
120F TYR* 3.1 6.5 - - - +
121F HIS 2.7 38.4 + - - +
151F LEU* 3.6 23.1 - - + -
154F ALA* 3.2 29.6 - - + -
155F LEU* 3.6 27.4 - - + +
158F PHE* 3.9 18.1 - - + -
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Residues in contact with GLN 114 (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* 3.1 28.7 - - + -
27F GLY* 4.5 6.1 - - - -
84F TRP* 3.3 2.4 - - - +
85F ALA 2.7 40.4 + - - +
112F ARG* 2.8 30.3 + - - +
113F VAL* 1.3 76.0 - - - +
115F LEU* 1.3 69.6 + - - +
118F GLY* 3.9 17.8 + - - +
119F SER 3.2 15.7 - - - +
120F TYR* 4.1 4.0 - - + -
120G TYR* 3.7 24.1 + - - +
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Residues in contact with LEU 115 (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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81E TYR* 3.9 23.3 - - + -
82E ASN* 4.5 0.2 - - + -
26F PHE* 3.5 5.9 - - - -
31F TYR* 3.7 14.8 - - - +
79F PHE* 3.7 38.8 - - + -
83F GLY 3.4 9.0 - - - +
84F TRP* 4.0 7.2 - - + -
113F VAL* 5.4 0.2 - - + -
114F GLN* 1.3 83.7 - - - +
116F LYS* 1.3 60.3 + - - +
117F ASP* 3.0 21.7 + - - +
118F GLY* 3.1 10.4 + - - -
119F SER* 2.9 21.2 + - - +
158F PHE* 3.4 37.5 - - + -
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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