Contacts of the helix formed by residues 90 - 105 (chain B) in PDB entry 1Y8G
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 ASN 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A GLN* 6.0 0.2 - - - +
261A ARG* 5.4 4.2 - - - +
88B GLN 4.0 2.4 + - - -
89B LEU* 1.3 76.6 - - - +
91B SER* 1.3 64.5 + - - +
92B SER* 3.2 13.4 + - - -
93B SER* 2.5 35.0 + - - -
94B LEU* 3.1 21.9 + - - +
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Residues in contact with SER 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 ASN* 1.3 77.1 - - - +
92B SER* 1.3 64.5 + - - +
94B LEU* 3.3 9.5 + - - +
95B GLN* 3.1 35.9 + - - +
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Residues in contact with SER 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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253A GLN* 4.1 3.3 + - - -
257A GLU* 2.9 27.3 + - - -
261A ARG* 3.4 21.2 + - - -
90B ASN* 3.2 12.0 + - - -
91B SER* 1.3 80.5 + - - +
93B SER* 1.3 57.3 + - - +
95B GLN* 3.2 15.2 + - - +
96B LYS* 3.0 33.7 + - - -
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Residues in contact with SER 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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253A GLN* 3.1 32.7 + - - +
89B LEU* 4.1 26.5 - - - +
90B ASN* 2.5 34.4 + - - -
92B SER* 1.3 73.6 + - - +
94B LEU* 1.3 54.7 + - - +
96B LYS* 3.1 3.1 + - - +
97B LEU* 2.7 36.4 + - - +
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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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86B LYS* 4.2 26.0 - - + +
89B LEU* 3.3 44.9 - - + +
90B ASN 3.1 8.3 + - - +
91B SER* 3.6 9.2 - - - +
93B SER* 1.3 77.7 - - - +
95B GLN* 1.3 58.4 + - + +
97B LEU* 3.2 5.1 + - + -
98B PHE* 2.8 60.6 + - + +
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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 SER* 3.1 28.3 + - - +
92B SER* 3.2 14.6 + - - +
94B LEU* 1.3 76.0 - - - +
96B LYS* 1.3 61.8 + - + +
98B PHE* 3.9 4.7 - - - +
99B ARG* 3.0 28.1 + - - +
102B ARG* 5.4 0.2 + - - -
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Residues in contact with LYS 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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253A GLN* 3.4 21.0 - - + +
254A ASN* 4.8 14.8 - - - +
257A GLU* 2.9 45.5 + - - +
92B SER* 3.0 18.8 + - - +
93B SER* 3.1 10.3 + - - +
95B GLN* 1.3 77.3 - - + +
97B LEU* 1.3 61.8 + - - +
99B ARG* 3.2 17.1 + - - +
100B GLU* 2.8 49.8 + - + +
174B ARG* 6.2 2.0 - - - +
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Residues in contact with LEU 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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84B ILE* 4.1 24.2 - - + -
86B LYS* 4.0 18.6 - - + -
89B LEU* 3.9 23.8 - - + -
93B SER 2.7 20.2 + - - +
94B LEU* 3.6 9.4 - - + +
96B LYS* 1.3 73.5 - - - +
98B PHE* 1.3 61.2 + - + +
100B GLU* 3.1 15.5 + - + +
101B VAL* 2.9 38.0 + - + +
125B LEU* 3.8 32.5 - - + -
127B LEU* 4.7 5.4 - - + -
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Residues in contact with PHE 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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86B LYS* 4.7 14.6 - - + -
94B LEU* 2.8 47.5 + - + +
95B GLN* 4.1 4.0 - - - +
97B LEU* 1.3 83.4 - - + +
99B ARG* 1.3 62.7 + - - +
101B VAL* 3.4 7.1 + - + +
102B ARG* 3.1 35.8 + - - +
120B GLU* 5.4 8.7 - - - -
125B LEU* 5.4 4.7 - - + -
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Residues in contact with ARG 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 3.0 19.4 + - - +
96B LYS* 3.5 18.4 - - - +
97B LEU 3.2 0.2 - - - -
98B PHE* 1.3 75.2 - - - +
100B GLU* 1.3 74.6 + - + +
102B ARG* 3.3 21.1 + - - +
103B ILE* 3.0 49.3 + - + +
171B ILE* 4.8 1.4 - - - +
172B VAL 3.0 30.5 + - - +
173B HIS* 4.9 5.1 + - - +
174B ARG* 3.0 38.6 - - - +
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Residues in contact with GLU 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 LYS* 2.8 38.1 + - + +
97B LEU* 3.1 15.1 + - + +
99B ARG* 1.3 88.4 + - - +
101B VAL* 1.3 58.0 + - + +
103B ILE* 3.4 8.5 + - + +
104B MSE 3.0 31.8 + - - +
127B LEU* 6.1 3.4 - - + -
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Residues in contact with VAL 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 LEU* 2.9 20.7 + - + +
98B PHE* 3.8 7.9 - - + +
99B ARG 3.2 0.2 - - - -
100B GLU* 1.3 75.2 - - - +
102B ARG* 1.3 66.1 + - - +
104B MSE 3.3 4.6 + - - +
105B LYS* 3.1 50.7 + - + +
115B LEU* 5.4 0.7 - - + -
118B VAL* 4.4 16.4 - - + -
120B GLU* 6.0 0.9 - - - +
125B LEU* 4.1 25.4 - - + -
127B LEU* 4.2 21.3 - - + -
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Residues in contact with ARG 102 (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 5.4 0.2 + - - -
98B PHE* 3.1 18.7 + - - +
99B ARG* 3.6 32.1 + - - +
101B VAL* 1.3 79.3 - - - +
103B ILE* 1.3 63.0 + - + +
105B LYS* 3.6 16.0 + - - +
106B VAL* 3.7 14.9 + - + +
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Residues in contact with ILE 103 (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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99B ARG* 3.0 64.5 + - + +
100B GLU* 3.7 7.6 - - + +
102B ARG* 1.3 77.4 - - + +
104B MSE 1.3 67.0 + - - +
106B VAL* 3.1 14.9 + - - +
107B LEU* 3.3 38.4 + - + +
171B ILE* 4.1 39.7 - - + -
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Residues in contact with MSE 104 (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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100B GLU 3.0 18.3 + - - +
101B VAL* 3.3 5.4 + - - +
103B ILE* 1.3 78.2 - - - +
105B LYS* 1.3 62.7 + - - +
106B VAL 3.0 1.4 + - - -
107B LEU* 3.3 23.7 + - - +
112B ILE* 4.8 10.8 - - - -
113B VAL* 3.2 49.4 - - + +
114B LYS* 4.6 2.4 + - - -
115B LEU* 3.6 35.6 + - + +
127B LEU* 6.0 4.5 - - + -
129B MSE 4.2 22.2 - - + -
192B ALA 5.4 9.6 - - - -
351B TYR* 4.2 0.9 + - - -
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Residues in contact with LYS 105 (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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101B VAL* 3.1 40.7 + - + +
102B ARG* 3.8 9.4 - - - +
103B ILE 3.3 0.2 - - - -
104B MSE 1.3 76.2 - - - +
106B VAL* 1.3 60.7 + - + +
107B LEU 3.5 0.6 - - - +
115B LEU* 3.8 9.2 - - + -
118B VAL* 3.8 17.6 - - - +
120B GLU* 4.8 11.1 + - - -
349B GLN* 4.1 12.9 + - + +
350B ARG 5.3 3.4 + - - -
351B TYR* 2.6 57.2 + - + +
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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