Contacts of the helix formed by residues 122 - 132 (chain B) in PDB entry 2YDW
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B PHE* 3.6 9.9 - - - +
101B GLN* 3.2 20.1 - - - +
102B PRO* 3.2 35.5 - - + +
103B VAL 5.3 0.4 - - - +
121B MET* 1.3 81.6 - - - +
123B MET* 1.3 64.0 + - - +
124B GLY* 3.0 19.6 + - - -
125B THR* 2.6 29.1 + - - -
126B ILE* 3.2 24.2 + - - +
148B MET* 3.7 13.0 - - - -
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Residues in contact with MET 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B MET* 3.5 12.4 - - + +
90B LEU* 4.0 29.2 - - - +
91B TRP* 3.8 17.7 - - + -
96B ALA* 3.4 47.8 - - + +
99B PHE* 2.7 28.2 + - + +
100B ARG* 4.2 5.8 - - + -
122B ASP* 1.3 70.1 - - - +
124B GLY* 1.3 57.7 + - - +
126B ILE* 4.3 6.3 - - - -
127B LYS* 2.8 32.1 + - - +
145B PHE* 4.5 8.3 - - + -
148B MET* 3.5 29.3 - - + -
169B LEU* 5.4 4.5 - - + -
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Residues in contact with GLY 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B TRP* 3.7 10.5 - - - -
100B ARG 3.3 22.4 + - - -
101B GLN* 5.0 0.4 - - - -
122B ASP* 3.0 8.3 + - - -
123B MET* 1.3 78.2 - - - +
125B THR* 1.3 60.5 + - - +
127B LYS* 3.5 2.8 + - - +
128B ARG* 3.0 26.0 + - - +
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Residues in contact with THR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PRO* 4.5 6.9 - - - +
121B MET* 3.8 19.0 - - + +
122B ASP* 2.6 31.5 + - - -
123B MET 3.3 0.2 - - - -
124B GLY* 1.3 73.2 - - - +
126B ILE* 1.3 65.3 + - - +
128B ARG* 3.4 27.9 + - - +
129B ARG* 3.0 50.1 + - - +
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B MET* 3.4 20.6 - - + -
121B MET* 3.9 7.4 - - + -
122B ASP 3.2 20.0 + - - +
123B MET* 3.3 3.8 + - - +
125B THR* 1.3 76.3 - - - +
127B LYS* 1.3 58.3 + - - +
129B ARG* 3.2 2.6 + - - +
130B LEU* 2.9 30.6 + - + +
135B TYR* 3.6 16.2 - - - +
141B CYS* 3.9 12.1 - - - -
144B ASP* 3.7 21.5 - - + +
145B PHE* 3.6 58.6 - - + +
148B MET* 4.7 2.9 - - - -
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Residues in contact with LYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B HIS* 4.8 6.7 + - - +
87B MET* 3.6 21.5 - - + +
91B TRP* 3.7 48.0 - - + +
123B MET 2.8 18.2 + - - +
124B GLY* 3.7 5.4 - - - +
126B ILE* 1.3 73.1 - - - +
128B ARG* 1.3 65.2 + - - +
130B LEU* 3.3 6.0 + - - +
131B GLU* 3.0 53.9 + - + +
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLY 3.0 18.7 + - - +
125B THR* 3.7 37.4 + - - +
126B ILE 3.4 0.2 - - - -
127B LYS* 1.3 75.6 - - - +
129B ARG* 1.3 64.6 + - - +
131B GLU* 3.2 13.7 + - - +
132B ASN* 2.9 49.3 + - - +
1183B SO4 2.8 29.7 + - - +
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Residues in contact with ARG 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B MET* 3.7 14.9 - - - +
125B THR* 3.0 38.4 + - + +
126B ILE 3.5 0.9 - - - +
128B ARG* 1.3 84.2 - - - +
130B LEU* 1.3 60.3 + - - +
133B ASN* 3.2 3.3 + - - -
134B TYR* 2.9 84.5 + - + -
135B TYR* 3.5 30.5 + - + -
144B ASP* 2.9 23.6 + - - -
1183B SO4 4.1 12.1 + - - +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU* 3.7 46.7 - - + +
82B LEU* 4.1 5.8 - - + +
83B HIS* 3.9 41.7 + - + +
87B MET* 4.3 13.7 - - + -
126B ILE* 2.9 34.7 + - + +
127B LYS 3.7 4.3 - - - +
128B ARG 3.3 0.2 - - - -
129B ARG* 1.3 78.4 - - - +
131B GLU* 1.3 60.5 + - - +
132B ASN 3.4 0.5 + - - -
133B ASN* 3.5 13.2 + - - +
135B TYR* 4.0 12.3 - - + -
141B CYS* 4.0 11.4 - - - -
145B PHE* 5.1 0.9 - - + -
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B HIS* 3.7 26.2 + - + +
127B LYS* 3.0 54.6 + - - +
128B ARG* 3.5 13.0 - - - +
130B LEU* 1.3 77.6 - - - +
132B ASN* 1.3 66.2 + - - +
133B ASN* 3.4 8.8 + - - +
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Residues in contact with ASN 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ARG* 2.9 31.6 + - - +
129B ARG 4.5 0.2 - - - +
130B LEU 3.3 0.2 - - - -
131B GLU* 1.3 88.1 - - - +
133B ASN* 1.3 72.5 + - - +
134B TYR* 3.2 3.5 + - - -
1183B SO4 3.3 36.6 + - - +
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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