Contacts of the helix formed by residues 97 - 110 (chain D) 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 THR 97 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D PHE* 1.3 87.6 - - - +
98D ASP* 1.3 64.7 + - - +
99D ASP* 4.1 4.3 + - - +
100D ASP* 3.2 35.2 + - - +
101D PHE 3.0 18.9 + - - -
119D SER* 3.6 3.8 - - - -
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Residues in contact with ASP 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D THR* 1.3 72.9 - - - +
99D ASP* 1.3 63.3 + - - +
101D PHE* 3.2 4.2 + - - +
102D LYS* 2.9 33.6 + - + +
116D SER* 3.1 23.4 + - - -
117D PRO* 3.5 20.7 - - + +
118D GLU* 3.1 13.8 + - - -
119D SER* 2.7 39.3 + - - +
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Residues in contact with ASP 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D THR* 3.4 4.6 + - - +
98D ASP* 1.3 83.4 - - - +
100D ASP* 1.3 59.4 + - - +
102D LYS* 3.9 8.7 - - - +
103D ARG* 3.0 31.5 + - - +
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Residues in contact with ASP 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D PHE* 5.7 2.2 - - + -
97D THR* 3.2 30.9 + - - +
98D ASP 3.3 0.4 - - - -
99D ASP* 1.3 77.1 - - - +
101D PHE* 1.3 64.3 + - - +
103D ARG* 3.4 4.9 + - - +
104D ALA* 3.0 24.6 + - - +
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Residues in contact with PHE 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ALA 3.9 15.9 - - - -
73C ILE* 3.8 20.6 - - + -
76C ARG* 4.1 15.3 - - + -
77C LEU* 3.5 44.0 - - + -
96D PHE* 3.7 14.3 - + + +
97D THR 3.0 17.1 + - - +
98D ASP 3.2 4.5 + - - +
100D ASP* 1.3 77.3 - - - +
102D LYS* 1.3 61.0 - - + +
104D ALA* 3.4 6.6 + - + +
105D ILE* 3.1 48.1 + - + +
115D TRP* 3.8 18.8 - + - -
117D PRO* 3.7 20.9 - - + -
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Residues in contact with LYS 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ASP* 2.9 19.7 + - - +
99D ASP* 3.9 9.4 - - - +
101D PHE* 1.3 74.0 - - - +
103D ARG* 1.3 62.7 + - - +
105D ILE* 3.4 3.7 + - - +
106D GLN* 3.0 29.3 + - - +
112D ARG* 3.8 29.5 - - + +
113D PRO* 2.8 39.4 + - + +
114D THR* 3.8 7.9 + - - +
115D TRP 2.9 28.6 + - - -
116D SER* 4.3 1.7 - - - +
117D PRO* 3.7 21.5 - - + -
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Residues in contact with ARG 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ASP 3.0 19.2 + - - +
100D ASP* 3.8 5.8 - - - +
102D LYS* 1.3 74.4 - - - +
104D ALA* 1.3 60.8 + - - +
106D GLN* 3.2 10.6 + - - +
107D ASP* 2.7 77.7 + - - +
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Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ARG* 3.8 16.6 - - - +
100D ASP 3.0 18.0 + - - +
101D PHE* 3.7 7.9 - - + +
102D LYS 3.4 0.2 - - - -
103D ARG* 1.3 75.5 - - - +
105D ILE* 1.3 62.9 + - - +
107D ASP* 3.3 11.0 + - - +
108D GLU* 3.2 26.0 + - - +
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Residues in contact with ILE 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ALA* 4.7 0.7 - - + -
76C ARG* 3.4 36.3 - - - +
139C PHE* 3.4 35.9 - - + -
101D PHE* 3.1 43.5 + - + +
102D LYS 3.7 7.0 - - - +
103D ARG 3.3 0.2 - - - -
104D ALA* 1.3 77.0 - - - +
106D GLN* 1.3 58.1 + - - +
108D GLU* 3.3 2.4 + - - -
109D THR* 2.9 38.7 + - + +
111D ILE 3.5 9.4 - - - +
113D PRO* 3.7 21.1 - - + -
115D TRP* 4.1 8.3 - - + -
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Residues in contact with GLN 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D LYS 3.0 17.4 + - - +
103D ARG* 3.2 10.5 + - + +
105D ILE* 1.3 76.9 - - - +
107D ASP* 1.3 62.2 + - - +
110D GLY* 2.8 37.1 + - - -
111D ILE 3.4 23.1 - - - +
112D ARG* 3.1 45.4 + - - +
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Residues in contact with ASP 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ARG* 2.7 62.5 + - - +
104D ALA* 3.5 9.3 - - - +
106D GLN* 1.3 81.8 - - - +
108D GLU* 1.3 61.2 + - + +
110D GLY 4.7 0.7 + - - -
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Residues in contact with GLU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ARG* 2.6 42.2 + - - +
142C LYS* 4.0 16.3 + - - -
104D ALA 3.2 9.1 + - - +
105D ILE 3.8 5.8 - - - +
107D ASP* 1.3 81.6 - - + +
109D THR* 1.3 67.0 + - + +
110D GLY 3.7 0.2 - - - -
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Residues in contact with THR 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ARG* 5.7 4.0 - - - +
138C PRO* 3.6 28.0 - - - +
139C PHE* 4.0 2.9 - - + -
141C THR* 5.9 1.8 - - - +
105D ILE* 2.9 31.3 + - + +
108D GLU* 1.3 86.1 - - + +
110D GLY* 1.3 59.4 + - - +
111D ILE* 3.0 35.3 + - - +
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Residues in contact with GLY 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D GLN* 2.8 28.2 + - - +
107D ASP 4.6 0.6 + - - -
108D GLU 3.7 0.8 - - - -
109D THR* 1.3 75.8 - - - +
111D ILE* 1.3 62.8 + - - +
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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