Contacts of the helix formed by residues 117 - 135 (chain C) in PDB entry 4KYI
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 ARG 117 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LYS 4.5 6.7 + - - -
103C LEU* 4.2 24.7 - - + +
104C LEU 4.9 2.0 + - - -
105C ASP* 3.2 36.3 + - - +
115C GLY 3.2 0.8 - - - -
116C ASP* 1.3 78.7 + - - +
118C PHE* 1.3 65.7 + - - +
119C ARG 3.1 1.6 - - - -
120C ASN* 3.1 3.8 + - - +
121C ILE* 3.0 23.3 + - + +
183C VAL* 4.4 13.7 - - - +
186C LEU* 3.9 43.8 + - + +
187C GLU* 3.9 24.6 + - - +
189C LEU* 5.1 1.1 - - + +
190C ASP* 2.9 38.3 + - - +
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Residues in contact with PHE 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C MET* 3.5 37.2 - - + -
98C LEU* 5.8 0.9 - - + -
100C ILE* 4.6 19.7 - - + -
103C LEU* 3.5 45.9 + - + +
115C GLY 3.5 7.0 + - - +
117C ARG* 1.3 78.8 - - - +
119C ARG* 1.3 61.4 + - - +
121C ILE* 3.6 2.4 + - - +
122C LEU* 3.2 49.7 + - + +
265C VAL* 4.3 6.7 - - + -
266C GLN* 3.8 28.9 - - + -
269C GLY* 5.7 5.8 - - - -
275C PHE* 4.3 20.0 - + + -
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Residues in contact with ARG 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C GLY 3.1 17.0 + - - +
116C ASP* 3.0 37.8 + - - +
117C ARG 3.1 0.2 - - - -
118C PHE* 1.3 79.5 - - - +
120C ASN* 1.3 90.8 + - - +
122C LEU* 3.5 2.9 + - - -
123C ASP* 3.3 20.1 + - - +
194C ASN* 3.9 8.1 + - - +
198C THR* 5.7 6.3 - - - +
212C ARG* 4.1 22.5 - - - +
262C ALA* 3.3 54.9 - - - +
263C GLN* 4.0 14.1 - - + +
266C GLN* 4.1 13.8 + - + +
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Residues in contact with ASN 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ASP 2.4 26.3 + - - -
117C ARG 3.1 7.4 + - - +
119C ARG* 1.3 93.5 + - - +
121C ILE* 1.3 64.5 + - - +
123C ASP* 3.3 4.1 + - - +
124C VAL* 3.0 28.3 + - - +
189C LEU* 4.3 10.3 - - + -
190C ASP* 2.8 25.7 + - - +
193C LEU* 3.3 36.4 - - + +
194C ASN* 3.2 16.3 + - - +
212C ARG* 4.1 4.9 + - - -
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Residues in contact with ILE 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU* 3.8 33.2 - - + -
103C LEU* 3.6 25.6 - - + -
117C ARG 3.0 17.0 + - - +
118C PHE* 3.8 7.6 - - + +
119C ARG 3.4 0.2 - - - -
120C ASN* 1.3 76.2 - - - +
122C LEU* 1.3 60.3 + - + +
124C VAL* 3.2 7.7 + - + +
125C ILE* 3.0 39.2 + - + +
176C ILE* 4.5 7.9 - - + +
179C LEU* 4.6 8.3 - - + -
180C THR* 4.1 15.3 - - + -
186C LEU* 4.0 14.4 - - + -
189C LEU* 3.6 23.8 - - + -
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C MET* 4.2 26.2 - - + -
81C ILE* 6.0 0.7 - - + -
118C PHE* 3.2 42.6 + - + +
119C ARG* 3.6 7.2 - - - +
120C ASN 3.2 0.4 - - - -
121C ILE* 1.3 79.4 - - + +
123C ASP* 1.3 56.3 + - - +
125C ILE* 3.1 16.3 + - + +
126C TYR* 2.8 53.7 + - + +
262C ALA* 3.5 30.5 - - + +
265C VAL* 3.7 21.5 - - + -
266C GLN 4.0 1.8 - - - +
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Residues in contact with ASP 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ARG* 3.3 11.5 + - - +
120C ASN* 3.3 11.0 + - - +
122C LEU* 1.3 78.7 - - - +
124C VAL* 1.3 62.6 + - - +
126C TYR* 4.0 7.7 - - - +
127C MET* 3.1 27.4 + - - +
159C TYR* 2.9 38.5 + - + -
193C LEU* 4.6 5.6 - - + +
212C ARG* 3.1 27.6 + - - -
213C LEU* 4.7 6.8 - - - +
260C SER* 4.2 5.0 + - - -
262C ALA* 3.4 22.8 + - - +
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Residues in contact with VAL 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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120C ASN 3.0 19.7 + - - +
121C ILE* 3.4 10.5 - - + +
122C LEU 3.2 0.2 - - - -
123C ASP* 1.3 75.4 - - - +
125C ILE* 1.3 65.0 + - - +
127C MET* 3.3 10.4 - - + +
128C MET* 3.1 23.9 + - - +
159C TYR* 5.5 0.9 - - + -
163C LEU* 4.5 10.5 - - + -
170C ILE* 3.8 24.7 - - + -
176C ILE* 3.7 28.5 - - + -
179C LEU* 5.1 4.7 - - + -
189C LEU* 3.6 28.7 - - + -
193C LEU* 4.1 6.1 - - + -
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Residues in contact with ILE 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C MET* 6.0 0.7 - - - -
81C ILE* 4.5 10.8 - - + -
84C VAL* 5.7 0.8 - - + +
86C MET* 3.6 28.9 - - + -
94C LEU* 3.7 30.1 - - + -
98C LEU* 3.8 17.5 - - + -
121C ILE* 3.0 24.4 + - + +
122C LEU* 3.4 17.0 - - + +
124C VAL* 1.3 77.4 - - - +
126C TYR* 1.3 70.7 + - + +
128C MET* 3.4 3.7 + - + +
129C GLN* 3.2 23.1 + - + +
176C ILE* 3.6 27.6 - - + -
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Residues in contact with TYR 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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80C SER* 2.7 44.2 + - - -
81C ILE* 4.7 10.3 - - + -
84C VAL* 4.6 16.8 - - + -
122C LEU* 2.8 40.2 + - + +
123C ASP* 4.0 6.3 - - - +
125C ILE* 1.3 78.3 - - + +
127C MET* 1.3 60.0 + - - +
129C GLN* 4.2 0.3 - - - +
130C MET* 2.8 40.5 + - - +
213C LEU* 3.8 17.9 - - + -
261C ILE* 3.5 27.8 - - + -
262C ALA* 3.5 32.1 - - + -
265C VAL* 3.4 14.2 - - - +
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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
----------------------------------------------------------
123C ASP 3.1 17.2 + - - +
124C VAL* 3.3 15.3 - - - +
126C TYR* 1.3 76.0 - - - +
128C MET* 1.3 65.8 + - - +
130C MET* 4.0 3.4 - - - -
131C LYS* 3.1 24.9 + - - +
156C ILE* 4.1 16.6 - - + +
159C TYR* 3.5 38.6 - - + -
160C GLU* 3.8 25.8 - - + +
163C LEU* 3.6 31.0 - - + -
170C ILE* 4.1 25.6 - - + +
213C LEU* 3.5 13.4 - - + +
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Residues in contact with MET 128 (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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86C MET* 5.1 6.1 - - + -
124C VAL 3.1 19.4 + - - +
125C ILE* 3.6 5.6 - - - +
126C TYR 3.1 0.2 - - - -
127C MET* 1.3 80.8 - - - +
129C GLN* 1.3 98.6 + - + +
131C LYS* 3.2 14.8 + - - +
132C LYS* 3.2 31.7 + - + +
170C ILE* 3.9 20.9 - - + +
171C ASN* 4.2 15.7 - - - +
172C ASN* 3.7 30.7 - - - +
173C VAL* 3.8 18.2 - - + -
176C ILE* 4.0 12.6 - - + -
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Residues in contact with GLN 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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84C VAL* 3.9 26.2 - - + +
85C GLY 3.5 7.5 + - - -
86C MET* 3.7 31.4 - - + +
87C ASP* 4.3 4.8 - - - +
90C ASP* 4.1 8.1 + - - +
125C ILE 3.2 13.1 + - - +
128C MET* 1.3 93.8 - - + +
130C MET* 1.3 61.3 + - - +
131C LYS 3.0 5.8 + - - -
132C LYS* 3.2 24.1 + - - +
133C HIS* 3.0 54.8 + - - +
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Residues in contact with MET 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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84C VAL* 3.6 19.5 - - + -
126C TYR* 2.8 22.2 + - - +
127C MET* 4.0 4.0 - - - +
129C GLN* 1.3 74.5 - - - +
131C LYS* 1.3 57.5 + - - +
133C HIS* 4.1 2.7 - - - -
134C LEU* 3.3 24.6 + - - +
152C LEU* 4.1 11.9 - - + -
156C ILE* 4.1 8.8 - - + +
213C LEU* 3.7 42.0 - - + -
217C ASP* 4.0 20.9 - - + +
218C LEU* 3.8 19.7 - - + -
221C LEU* 3.6 36.8 - - + +
261C ILE* 4.5 1.3 - - - -
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Residues in contact with LYS 131 (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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127C MET* 3.1 19.4 + - - +
128C MET* 3.4 7.2 - - - +
129C GLN 3.0 0.6 - - - -
130C MET* 1.3 76.2 - - - +
132C LYS* 1.3 54.5 + - + +
133C HIS 3.0 4.3 - - - -
134C LEU* 2.9 6.2 + - + +
135C GLU* 2.3 77.7 + - + +
153C LYS* 4.6 16.8 - - - +
156C ILE* 3.7 21.8 - - + -
160C GLU* 3.2 39.9 - - - +
170C ILE 5.9 0.7 - - - +
171C ASN* 6.5 1.3 - - + -
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Residues in contact with LYS 132 (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 ASP* 4.4 16.4 + - - -
128C MET* 3.4 34.1 - - + +
129C GLN* 3.2 20.8 + - - +
131C LYS* 1.3 75.5 - - + +
133C HIS* 1.3 61.0 + - + +
135C GLU* 3.9 20.2 + - - +
136C SER* 3.8 16.6 + - - -
171C ASN* 4.6 15.8 + - - +
172C ASN* 5.7 4.6 + - - +
173C VAL* 5.6 2.4 - - - +
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Residues in contact with HIS 133 (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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84C VAL 3.5 19.0 + - - -
85C GLY* 3.2 18.0 + - - -
129C GLN* 3.0 48.1 + - - +
130C MET* 4.2 4.3 - - - +
131C LYS 3.0 0.6 - - - -
132C LYS* 1.3 79.4 + - + +
134C LEU* 1.3 63.1 + - - +
135C GLU 3.2 1.3 - - - -
136C SER* 2.7 25.2 + - - -
137C VAL* 3.6 11.8 - - - +
221C LEU* 3.7 20.9 - - + -
225C LEU* 3.7 8.9 - - + +
232C LEU* 3.7 29.9 - - + +
233C ILE* 4.5 7.4 - - + -
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Residues in contact with LEU 134 (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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130C MET 3.3 14.4 + - - +
131C LYS* 2.9 11.1 + - + +
133C HIS* 1.3 79.1 - - - +
135C GLU* 1.3 62.4 + - + +
136C SER 3.3 0.7 + - - -
137C VAL* 3.4 19.7 + - + +
149C TYR* 3.5 32.1 + - + +
152C LEU* 4.0 15.3 - - + -
153C LYS* 3.9 48.9 - - + +
156C ILE* 3.9 14.1 - - + -
221C LEU* 4.9 4.4 - - + +
224C LEU* 3.6 24.7 - - + -
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Residues in contact with GLU 135 (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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131C LYS* 2.3 61.3 + - + +
132C LYS* 3.9 19.5 - - - +
133C HIS 3.2 0.4 - - - -
134C LEU* 1.3 76.9 - - + +
136C SER* 1.3 58.4 + - - +
137C VAL 3.3 5.7 + - - +
153C LYS* 6.1 3.6 - - - +
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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