Contacts of the helix formed by residues 110 - 130 (chain C) in PDB entry 1YKI
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 110 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C PHE* 3.3 8.9 - - - +
109C ALA* 1.3 91.9 - - + +
111C PRO* 1.3 72.0 - - + +
112C GLU* 3.3 20.2 + - - +
113C ALA* 3.1 25.0 + - - +
114C LYS* 3.2 16.5 + - - +
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Residues in contact with PRO 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C THR* 1.3 88.3 - - - +
112C GLU* 1.3 65.8 + - - +
114C LYS* 3.3 10.6 + - + +
115C ALA* 2.9 29.1 + - - +
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Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C THR* 3.2 21.8 - - - +
111C PRO* 1.3 86.7 - - - +
113C ALA* 1.3 56.9 + - - +
115C ALA* 3.3 7.4 + - - +
116C ALA* 3.0 29.0 + - - +
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Residues in contact with ALA 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C PHE* 3.9 15.5 - - + -
109C ALA* 4.5 5.2 - - + +
110C THR* 3.1 27.6 + - - +
112C GLU* 1.3 73.3 - - - +
114C LYS* 1.3 66.4 + - - +
116C ALA* 3.4 7.1 + - - +
117C ASN* 3.1 23.7 + - - +
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Residues in contact with LYS 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C VAL* 3.8 20.0 - - + +
100C ASP* 2.9 29.2 + - - +
103C ASP* 2.9 41.6 + - - +
108C PHE* 3.6 30.2 - - + -
110C THR 3.2 9.2 + - - +
111C PRO* 3.6 11.4 - - + +
113C ALA* 1.3 78.3 - - - +
115C ALA* 1.3 58.6 + - - +
117C ASN* 3.4 2.6 + - - +
118C ASP* 3.0 27.1 + - + +
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Residues in contact with ALA 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C PRO 2.9 17.0 + - - +
112C GLU* 3.6 8.5 - - - +
114C LYS* 1.3 75.2 - - - +
116C ALA* 1.3 58.2 + - - +
118C ASP* 3.5 8.4 + - - +
119C LYS* 3.0 28.8 + - - +
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Residues in contact with ALA 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C GLU 3.0 16.5 + - - +
113C ALA* 3.8 7.4 - - - +
115C ALA* 1.3 72.1 - - - +
117C ASN* 1.3 61.8 + - - +
119C LYS* 3.6 9.0 - - - +
120C GLY* 2.9 25.8 + - - -
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Residues in contact with ASN 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C VAL* 3.6 1.7 - - - +
102C GLU* 3.1 23.0 + - - +
107C ARG* 6.0 2.4 - - - +
108C PHE* 3.5 30.3 - - + -
113C ALA 3.1 9.5 + - - +
114C LYS 3.6 2.9 - - - +
116C ALA* 1.3 75.5 - - - +
118C ASP* 1.3 59.7 + - - +
120C GLY* 3.3 1.9 + - - -
121C ARG* 2.9 62.3 + - - +
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Residues in contact with ASP 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C LEU* 4.7 7.8 - - - +
96C LYS* 5.4 1.0 + - - -
99C VAL* 4.2 23.4 - - + +
114C LYS* 3.0 18.1 + - + +
115C ALA* 3.6 8.1 - - - +
117C ASN* 1.3 78.1 + - - +
119C LYS* 1.3 57.2 + - - +
121C ARG* 3.4 12.6 + - - +
122C LYS* 3.0 59.7 + - - +
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Residues in contact with LYS 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ALA 3.0 17.9 + - - +
116C ALA* 3.6 9.0 - - - +
118C ASP* 1.3 74.9 - - - +
120C GLY* 1.3 60.7 - - - +
122C LYS* 3.3 8.5 + - - +
123C PHE* 3.0 26.2 + - - +
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Residues in contact with GLY 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C THR* 5.3 0.2 - - - -
116C ALA 2.9 16.3 + - - -
117C ASN* 3.3 1.8 + - - -
119C LYS* 1.3 73.5 - - - +
121C ARG* 1.3 64.7 + - - +
123C PHE* 3.3 15.2 + - - +
124C PHE* 3.3 25.2 - - - -
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Residues in contact with ARG 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C THR* 2.8 55.2 + - - +
43C SER* 5.1 2.5 - - - +
95C LEU* 3.7 36.1 + - + -
98C VAL* 3.7 18.9 - - - +
99C VAL* 3.6 23.2 - - - +
102C GLU* 3.0 30.3 + - - -
117C ASN* 2.9 37.2 + - - +
118C ASP* 3.7 7.9 + - - +
120C GLY* 1.3 77.1 - - - +
122C LYS* 1.3 57.7 + - + +
124C PHE* 3.2 5.2 + - - +
125C ALA* 2.9 25.7 + - + +
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Residues in contact with LYS 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ASP* 3.6 32.5 + - - +
95C LEU* 4.1 22.8 - - + +
118C ASP* 3.0 48.6 + - - +
119C LYS* 3.7 7.4 - - - +
120C GLY 3.3 0.2 - - - -
121C ARG* 1.3 75.1 - - + +
123C PHE* 1.3 59.1 + - - +
125C ALA* 4.2 5.8 - - - -
126C ASP* 2.8 44.4 + - - +
129C ARG* 4.4 6.7 - - - +
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Residues in contact with PHE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C LYS 3.0 12.7 + - - +
120C GLY* 3.4 12.1 - - - +
121C ARG 3.2 0.4 - - - -
122C LYS* 1.3 75.5 - - - +
124C PHE* 1.3 81.1 + + - +
126C ASP* 4.0 3.4 - - - +
127C MET* 3.0 58.4 + - + +
67D ASN* 3.7 42.6 - - + -
68D TYR* 4.1 15.7 - + - -
4219D NFZ 5.3 0.4 - - - -
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Residues in contact with PHE 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C THR* 3.8 20.2 - - + -
120C GLY* 3.3 22.8 + - - -
121C ARG 3.2 2.1 + - - +
123C PHE* 1.3 100.8 - + - +
125C ALA* 1.3 66.6 + - - +
127C MET* 3.3 17.6 + - + +
128C HIS* 3.2 28.8 - - + -
138C TRP* 4.4 8.5 - - + -
68D TYR* 4.4 3.4 - + - -
165D GLU* 3.9 30.3 - - + -
166D GLY* 3.9 14.1 - - - -
4219D NFZ 3.4 61.5 - + - -
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Residues in contact with ALA 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C MET* 4.3 6.1 - - + -
95C LEU* 4.0 34.3 - - + -
121C ARG 2.9 16.6 + - - +
122C LYS* 4.0 3.8 - - - +
124C PHE* 1.3 77.6 - - - +
126C ASP* 1.3 56.5 + - - +
128C HIS* 3.3 4.0 + - - +
129C ARG* 2.9 39.9 + - - +
138C TRP* 3.8 21.0 - - + -
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Residues in contact with ASP 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C LYS* 2.8 35.8 + - - +
123C PHE* 4.1 3.6 - - - +
125C ALA* 1.3 70.8 - - - +
127C MET* 1.3 65.6 + - - +
129C ARG* 2.9 38.2 + - - -
130C LYS* 2.9 46.5 + - + +
131C ASP* 3.3 10.3 + - - +
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Residues in contact with MET 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C PHE* 3.0 50.7 + - + +
124C PHE* 3.3 14.3 + - + +
126C ASP* 1.3 76.7 - - - +
128C HIS* 1.3 68.4 + - + +
131C ASP* 3.3 18.9 + - + +
132C LEU* 2.9 46.0 + - + +
68D TYR* 3.3 27.8 - - + +
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Residues in contact with HIS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C PHE* 3.2 26.2 + - + -
125C ALA 3.3 5.8 + - - +
126C ASP 3.2 0.2 - - - -
127C MET* 1.3 88.9 - - + +
129C ARG* 1.3 58.9 + - - +
132C LEU* 3.7 16.1 - - + +
133C HIS 2.9 25.1 + - - -
134C ASP* 2.7 39.9 + - - +
135C ASP* 3.9 15.9 - - - -
138C TRP* 3.3 48.5 + + + +
165D GLU* 4.4 6.9 + - - +
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Residues in contact with ARG 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C MET* 3.0 34.6 + - - +
91C ASP* 3.8 5.5 - - - +
92C ASP* 2.9 30.7 + - - +
95C LEU* 3.7 22.8 - - - +
122C LYS* 4.4 8.1 - - - +
125C ALA* 2.9 26.8 + - - +
126C ASP* 2.9 27.1 + - - -
128C HIS* 1.3 75.8 - - - +
130C LYS* 1.3 84.2 + - + +
133C HIS* 3.5 18.6 + - - -
135C ASP* 3.5 32.6 - - + +
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Residues in contact with LYS 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C ASP* 2.9 44.0 + - + +
129C ARG* 1.3 106.2 - - + +
131C ASP* 1.3 70.1 + - - +
133C HIS* 2.9 24.2 - - - -
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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
------------------------------------------------------------
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