Contacts of the helix formed by residues 122 - 136 (chain C) in PDB entry 1YLK
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 ASP 122 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C LEU* 3.5 2.4 - - - +
120C TYR* 3.5 6.1 - - - -
121C PRO* 1.3 87.2 - - + +
123C ALA* 1.3 61.0 + - - +
124C VAL* 3.3 17.3 + - - +
125C GLU* 3.4 22.5 + - + +
126C ASP* 3.0 30.8 + - - +
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Residues in contact with ALA 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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87C HIS* 3.5 8.7 - - + -
88C HIS 3.8 22.7 - - - +
89C THR* 5.1 2.9 - - + +
91C CYS* 5.8 0.7 - - + -
94C LEU* 4.0 14.0 - - + +
120C TYR* 4.2 13.9 - - + +
122C ASP* 1.3 71.2 + - - +
124C VAL* 1.3 66.3 + - + +
127C VAL* 3.1 27.9 + - - +
150C VAL* 4.2 16.4 - - + -
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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
----------------------------------------------------------
122C ASP* 3.3 8.7 + - - +
123C ALA* 1.3 73.8 - - + +
125C GLU* 1.3 67.4 + - - +
127C VAL* 3.3 12.6 + - - +
128C ARG* 3.3 35.6 + - - +
150C VAL* 4.0 22.9 - - + -
161C VAL* 3.7 22.1 - - + +
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Residues in contact with GLU 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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122C ASP* 3.4 26.1 + - + -
124C VAL* 1.3 78.8 - - - +
126C ASP* 1.3 58.4 + - - +
128C ARG* 2.8 47.6 + - - +
129C GLN* 3.0 24.7 + - + +
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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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61C CYS 5.0 0.5 - - - +
62C VAL* 5.1 3.8 - - - +
87C HIS* 2.8 25.8 + - + +
120C TYR* 3.3 44.6 - - + +
122C ASP 3.0 18.7 + - - +
124C VAL 3.2 0.4 - - - -
125C GLU* 1.3 74.6 - - - +
127C VAL* 1.3 55.7 + - - +
129C GLN* 3.0 29.7 + - - +
130C SER* 2.7 44.2 + - - -
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Residues in contact with VAL 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 5.2 4.9 - - + +
87C HIS* 3.4 33.6 + - + +
123C ALA 3.1 17.3 + - - +
124C VAL 3.3 7.4 + - - +
126C ASP* 1.3 75.7 - - - +
128C ARG* 1.3 57.2 + - - +
130C SER* 3.3 4.5 + - - -
131C LEU* 2.9 39.5 + - + +
148C GLY* 3.6 31.2 - - - -
149C PHE 3.8 10.3 - - - +
150C VAL* 3.9 9.0 - - + -
161C VAL* 3.7 18.4 - - + -
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Residues in contact with ARG 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C VAL* 3.3 36.2 + - - +
125C GLU* 2.8 48.8 + - - +
127C VAL* 1.3 77.7 - - - +
129C GLN* 1.3 61.9 + - - +
131C LEU* 3.2 13.2 + - - +
132C ARG* 3.0 27.7 + - + +
161C VAL* 3.8 6.8 - - + +
162C THR* 5.0 4.8 - - - +
163C PRO* 2.8 51.6 - - + +
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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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62C VAL* 6.2 0.4 - - - +
125C GLU* 3.0 14.8 + - + +
126C ASP* 3.0 30.7 + - - +
128C ARG* 1.3 77.6 - - - +
130C SER* 1.3 59.7 + - - +
132C ARG* 3.2 10.9 + - + +
133C ARG* 2.8 72.6 + - - +
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Residues in contact with SER 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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61C CYS 4.0 4.2 + - - -
62C VAL* 4.9 0.5 - - - -
63C VAL* 3.6 25.7 + - - +
85C LEU* 3.7 12.8 - - - -
87C HIS* 3.6 13.3 - - - -
126C ASP* 2.7 38.7 + - - -
127C VAL 3.7 4.9 - - - -
129C GLN* 1.3 72.9 + - - +
131C LEU* 1.3 65.8 + - - +
133C ARG* 3.4 8.4 + - - +
134C ILE* 3.3 25.6 + - - +
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Residues in contact with LEU 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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85C LEU* 3.6 21.5 - - + -
127C VAL* 2.9 39.0 + - + +
128C ARG* 3.5 6.7 - - - +
130C SER* 1.3 77.0 - - - +
132C ARG* 1.3 56.5 + - + +
134C ILE* 3.4 4.3 + - - +
135C GLU* 2.9 46.1 + - - +
146C LEU* 3.9 27.0 - - + +
147C ARG* 4.1 1.1 - - - -
148C GLY* 3.9 24.5 - - - +
161C VAL* 4.6 9.6 - - + +
162C THR 4.8 0.4 - - - +
163C PRO 4.1 26.7 - - - +
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Residues in contact with ARG 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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128C ARG* 3.0 21.8 + - + +
129C GLN* 3.5 10.8 - - + +
131C LEU* 1.3 73.2 - - - +
133C ARG* 1.3 68.1 + - - +
135C GLU* 3.4 22.5 + - - +
136C VAL* 2.9 57.9 + - + +
163C PRO 6.5 1.1 - - - -
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Residues in contact with ARG 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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62C VAL* 3.5 11.5 - - - +
63C VAL* 2.9 43.6 + - + +
64C THR* 4.5 0.8 - - - +
68C ILE* 4.7 1.1 - - - +
118C GLU* 2.8 42.4 + - - -
129C GLN* 2.8 49.8 + - - +
130C SER* 3.5 11.2 - - - +
132C ARG* 1.3 77.7 - - + +
134C ILE* 1.3 60.8 + - - +
136C VAL* 3.8 8.9 - - - +
137C ASN* 3.4 22.2 + - - +
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Residues in contact with ILE 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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63C VAL* 3.8 19.7 - - + -
68C ILE* 4.5 6.3 - - + -
71C LEU* 4.2 16.8 - - + -
83C ILE* 4.3 4.9 - - + -
85C LEU* 3.7 40.2 - - + -
130C SER 3.3 6.1 + - - +
131C LEU 3.7 6.5 - - - +
132C ARG 3.2 0.4 - - - -
133C ARG* 1.3 74.5 - - - +
135C GLU* 1.3 66.1 + - - +
137C ASN* 3.1 23.3 + - - +
140C VAL* 4.0 18.3 - - + +
143C HIS* 4.0 20.4 - - + +
146C LEU* 3.9 25.6 - - + -
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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 LEU* 2.9 40.6 + - - +
132C ARG* 3.4 30.1 + - - +
134C ILE* 1.3 78.6 - - - +
136C VAL* 1.3 60.0 + - + +
137C ASN 3.5 2.9 + - - +
143C HIS* 6.0 2.2 - - - +
146C LEU* 4.0 15.7 - - + +
163C PRO 4.5 10.6 - - - +
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Residues in contact with VAL 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C ARG* 2.9 54.1 + - + +
133C ARG* 3.8 9.4 - - - +
135C GLU* 1.3 75.6 - - + +
137C ASN* 1.3 65.9 + - - +
138C PRO* 3.5 7.1 - - - +
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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