Contacts of the helix formed by residues 90 - 101 (chain B) in PDB entry 1DY7
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 GLY 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B THR 2.9 11.8 + - - -
87B ARG 3.6 8.7 + - - -
88B ASP 3.4 1.8 - - - -
89B LEU* 1.3 79.9 - - - +
91B PHE* 1.3 67.5 + - - -
92B ASP 3.4 2.5 - - - -
93B TYR 3.3 2.2 + - - -
94B LEU* 3.2 26.1 + - - +
128B LEU* 4.6 2.7 - - - -
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Residues in contact with PHE 91 (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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90B GLY* 1.3 71.5 - - - -
92B ASP* 1.3 78.8 + - - +
94B LEU* 3.2 5.6 + - - +
95B GLN* 2.9 55.7 + - + +
121B ASP* 3.9 17.0 - - + -
124B ALA* 3.5 26.7 - - + -
125B ASN* 3.4 37.7 - - - -
128B LEU* 4.1 19.2 - - + +
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Residues in contact with ASP 92 (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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90B GLY 3.4 1.0 - - - -
91B PHE* 1.3 92.8 - - - +
93B TYR* 1.3 63.9 + - - +
95B GLN* 3.4 11.3 + - - +
96B SER* 3.0 25.6 + - - -
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Residues in contact with TYR 93 (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 LYS* 5.6 0.5 + - - -
89B LEU* 3.3 63.4 + - + +
90B GLY 3.3 2.1 + - - +
91B PHE 3.2 0.4 - - - -
92B ASP* 1.3 80.5 - - - +
94B LEU* 1.3 66.7 + - + +
96B SER* 3.4 4.6 + - - -
97B PHE* 3.0 44.3 + + - +
601B HEC 2.7 33.3 + - + -
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Residues in contact with LEU 94 (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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81B LEU* 5.1 0.2 - - + -
86B THR* 4.0 23.8 - - + +
89B LEU* 4.1 24.9 - - + -
90B GLY 3.3 12.8 - - - +
91B PHE* 3.2 6.1 + - - +
93B TYR* 1.3 76.6 - - + +
95B GLN* 1.3 64.1 + - - +
97B PHE* 3.3 1.7 + - - +
98B ILE* 3.0 32.3 + - + +
124B ALA* 3.7 31.9 - - + +
127B LEU* 4.3 7.0 - - + -
128B LEU* 3.7 27.8 - - + -
601B HEC 3.6 26.7 - - + -
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Residues in contact with GLN 95 (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 PHE* 2.9 40.8 + - + +
92B ASP* 3.7 13.0 - - - +
94B LEU* 1.3 76.4 - - - +
96B SER* 1.3 55.7 + - - +
99B THR* 2.7 39.6 + - - +
120B VAL* 3.7 13.4 - - + +
121B ASP* 2.7 33.4 + - - +
124B ALA* 3.8 10.7 - - + +
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Residues in contact with SER 96 (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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92B ASP 3.0 17.0 + - - -
93B TYR* 3.7 5.8 - - - -
95B GLN* 1.3 79.3 + - - +
97B PHE* 1.3 61.2 + - - +
99B THR* 3.2 1.2 + - - -
100B TYR* 2.9 47.9 + - - +
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Residues in contact with PHE 97 (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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93B TYR* 3.0 36.6 + + + +
94B LEU 3.3 2.9 + - - +
96B SER* 1.3 75.9 + - - +
98B ILE* 1.3 57.9 + - - +
101B GLY* 2.7 38.4 + - - +
102B SER* 3.6 31.4 - - - -
106B MET* 3.6 26.8 - - + +
601B HEC 3.6 68.4 - + + -
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Residues in contact with ILE 98 (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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94B LEU 3.0 22.0 + - - +
95B GLN 4.0 2.9 - - - +
97B PHE* 1.3 76.8 - - - +
99B THR* 1.3 58.5 + - - +
106B MET* 3.8 6.1 - - - -
109B TRP* 3.1 47.1 + - + +
110B GLY 3.3 0.2 + - - -
115B LEU* 4.2 13.2 - - + -
120B VAL* 3.9 19.7 - - + +
123B MET* 3.9 3.1 - - + -
124B ALA* 3.8 31.0 - - + +
127B LEU* 4.2 8.5 - - + -
601B HEC 3.6 42.8 - - + -
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Residues in contact with THR 99 (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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95B GLN* 2.7 28.5 + - - +
96B SER 3.2 3.6 + - - -
98B ILE* 1.3 76.9 - - - +
100B TYR* 1.3 91.4 + - + +
108B ASN 3.5 5.9 - - - -
110B GLY* 3.1 20.0 + - - +
111B THR* 3.0 32.8 + - + -
120B VAL* 3.3 15.5 - - + +
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Residues in contact with TYR 100 (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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96B SER* 2.9 35.1 + - - +
99B THR* 1.3 92.1 - - + +
101B GLY* 1.3 69.1 + - - +
102B SER 3.8 0.2 + - - -
108B ASN* 3.2 17.8 - - - +
111B THR* 3.6 29.3 + - + -
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Residues in contact with GLY 101 (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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97B PHE* 2.7 35.7 + - - -
99B THR 3.7 0.8 - - - -
100B TYR* 1.3 82.2 - - - +
102B SER* 1.3 65.3 + - - -
106B MET* 3.3 16.6 - - - -
107B PRO 3.3 10.8 - - - -
108B ASN* 3.8 1.6 - - - +
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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