Contacts of the helix formed by residues 90 - 102 (chain B) in PDB entry 1YA8
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 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B GLN* 1.3 72.9 - - - +
91B PRO* 1.3 59.8 - - - +
92B LYS* 2.9 23.4 + - - +
93B ALA* 2.9 26.1 + - + +
94B GLY* 2.5 37.6 + - - -
145B MET 4.6 0.4 + - - -
146B VAL* 4.1 6.1 - - + +
295B LEU* 4.4 1.9 - - - +
298B THR* 5.5 4.3 - - + +
299B LEU* 3.3 33.6 - - + +
304B LEU* 4.6 8.9 - - + +
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Residues in contact with PRO 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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86B MET* 4.6 6.7 - - + +
89B GLN 3.0 11.5 - - - +
90B ASP* 1.3 89.1 - - - +
92B LYS* 1.3 65.4 + - + +
94B GLY 4.4 0.2 - - - +
95B GLN* 2.9 32.1 + - - +
112B LEU* 4.2 28.3 - - + -
295B LEU* 4.7 9.4 - - + -
299B LEU* 5.3 5.8 - - + -
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Residues in contact with LYS 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 ASP* 2.9 11.0 + - - +
91B PRO* 1.3 81.5 - - + +
93B ALA* 1.3 65.7 + - - +
95B GLN* 4.0 3.0 - - - +
96B LEU* 3.2 22.6 + - - +
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Residues in contact with ALA 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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90B ASP* 2.9 29.7 + - + +
92B LYS* 1.3 75.5 - - - +
94B GLY* 1.3 65.3 + - - +
96B LEU* 3.4 9.3 + - - +
97B LEU* 3.3 21.0 + - - +
146B VAL* 4.3 7.0 - - + +
304B LEU* 3.8 21.1 - - + -
363B LEU* 6.0 0.9 - - - +
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Residues in contact with GLY 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 MET* 4.7 7.4 - - - +
89B GLN* 3.2 28.0 - - - -
90B ASP 2.5 19.5 + - - -
91B PRO 3.9 0.9 - - - -
93B ALA* 1.3 74.7 - - - +
95B GLN* 1.3 62.6 + - - +
96B LEU 3.1 0.3 + - - -
97B LEU* 3.3 2.8 + - - +
98B SER* 3.1 21.1 + - - -
146B VAL* 4.2 6.7 - - - +
147B GLY* 5.0 3.4 + - - -
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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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86B MET* 4.5 8.2 - - + +
91B PRO 2.9 21.9 + - - +
92B LYS* 4.0 3.6 - - - +
94B GLY* 1.3 71.4 - - - +
96B LEU* 1.3 61.2 + - - +
98B SER* 3.3 8.3 + - - -
99B GLU* 2.8 61.1 + - + +
107B ASN* 4.7 3.6 - - - +
109B PRO* 5.1 18.1 - - + +
110B LEU 6.2 0.2 - - - +
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Residues in contact with LEU 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 LYS 3.2 12.8 + - - +
93B ALA* 3.6 11.9 - - - +
94B GLY 3.1 0.8 - - - -
95B GLN* 1.3 75.3 - - - +
97B LEU* 1.3 66.0 + - - +
99B GLU* 3.0 24.3 + - - +
100B LEU* 3.0 39.7 + - + +
361B MET* 5.0 7.2 - - + -
363B LEU* 3.3 30.7 - - + -
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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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93B ALA 3.3 9.7 + - - +
94B GLY 3.9 5.6 - - - +
96B LEU* 1.3 78.3 - - - +
98B SER* 1.3 58.0 + - - +
100B LEU* 4.5 7.4 - - + +
101B PHE* 2.9 77.4 + - + +
141B GLY 4.4 4.3 - - - +
142B GLY* 3.6 32.5 - - - +
146B VAL* 3.8 16.8 - - + +
147B GLY* 5.1 5.8 - - - +
358B LEU* 4.7 2.0 - - + -
363B LEU* 4.3 23.3 - - + +
4002B SMB 4.5 11.0 - - + +
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Residues in contact with SER 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 MET* 6.1 3.4 - - - -
94B GLY 3.1 12.6 + - - -
95B GLN* 3.4 15.3 - - - -
96B LEU 3.1 0.4 - - - -
97B LEU* 1.3 76.7 - - - +
99B GLU* 1.3 53.5 + - - +
102B THR* 2.8 38.6 + - - -
107B ASN* 3.1 21.9 + - - -
108B ILE 4.4 6.2 + - - -
110B LEU* 5.3 5.7 - - - +
148B ALA* 6.2 0.4 - - - -
151B THR* 3.0 29.5 + - - +
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Residues in contact with GLU 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* 2.8 49.8 + - + +
96B LEU* 3.0 26.4 + - + +
98B SER* 1.3 76.5 - - - +
100B LEU* 1.3 65.8 + - + +
102B THR* 3.0 19.6 - - - +
107B ASN* 2.9 26.1 - - + +
482B LYS* 5.0 2.9 + - - -
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Residues in contact with LEU 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 LEU* 3.0 43.0 + - + +
97B LEU* 4.0 6.3 - - - +
99B GLU* 1.3 79.2 - - + +
101B PHE* 1.3 66.0 + - + +
357B TRP* 4.4 10.3 - - + -
358B LEU* 3.3 33.4 - - + -
361B MET* 4.1 11.2 - - + -
363B LEU* 4.3 5.8 - - + -
455B PHE 5.1 1.7 - - - +
457B SER* 4.1 26.2 - - - +
473B PHE* 3.3 24.9 - - - -
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Residues in contact with PHE 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 47.4 + - + +
100B LEU* 1.3 78.1 - - + +
102B THR* 1.3 71.2 + - - +
103B ASN* 3.5 3.5 + - - +
141B GLY 5.4 5.4 - - - -
151B THR* 4.1 4.9 - - + -
152B TYR* 3.3 35.5 - - - +
220B GLU* 3.3 32.1 - - - -
358B LEU* 3.2 36.6 - - + -
468B HIS* 3.9 13.9 - + - -
469B GLY* 4.2 6.7 - - - -
472B LEU* 3.6 22.4 - - + +
473B PHE* 4.4 8.9 - + - -
4002B SMB 4.7 5.6 - - - -
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Residues in contact with THR 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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98B SER 2.8 22.2 + - - +
99B GLU* 3.0 24.7 - - - +
100B LEU 4.4 0.7 - - - +
101B PHE* 1.3 81.0 - - - +
103B ASN* 1.3 67.3 + - - +
104B ARG* 3.0 31.2 + - - +
107B ASN* 3.9 21.0 + - + +
151B THR* 3.3 20.9 + - - +
473B PHE* 3.5 9.5 - - - -
482B LYS* 3.5 20.3 + - - +
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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