Contacts of the helix formed by residues 82 - 93 (chain O) in PDB entry 1YHQ
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 SER 82 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6590 A 3.4 29.8 - - - -
6600 A 2.7 29.4 + - - -
63O LYS* 3.8 1.2 - - - +
64O VAL 3.0 10.9 + - - -
65O LEU* 4.1 7.6 - - - -
66O GLY 3.5 0.9 + - - -
81O PHE* 1.3 80.3 - - - +
83O GLY* 1.3 65.5 + - - +
84O THR 3.8 2.3 + - - -
85O ALA* 3.1 21.3 + - - +
86O GLU* 3.1 18.4 + - - +
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Residues in contact with GLY 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6590 A 2.9 18.0 + - - -
81O PHE 3.9 0.4 + - - -
82O SER* 1.3 71.1 - - - +
84O THR* 1.3 62.0 + - - +
86O GLU* 4.1 6.9 - - - +
87O THR* 3.1 26.5 + - - -
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Residues in contact with THR 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6590 A 4.8 0.8 + - - -
6600 A 3.4 25.5 + - - +
66O GLY* 4.1 7.4 - - - +
82O SER* 3.2 1.4 + - - -
83O GLY* 1.3 74.8 - - - +
85O ALA* 1.3 67.4 + - - +
87O THR* 3.0 8.3 + - - -
88O LYS* 3.0 49.7 + - + +
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Residues in contact with ALA 85 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O LEU* 4.6 5.8 - - + -
64O VAL* 3.3 30.3 - - + +
65O LEU 3.6 14.6 - - - +
66O GLY* 4.1 7.8 - - - -
81O PHE* 4.1 2.7 - - + -
82O SER* 3.1 24.0 + - - +
84O THR* 1.3 78.1 - - - +
86O GLU* 1.3 63.5 + - - +
87O THR 3.0 0.3 + - - -
88O LYS* 3.1 1.4 + - - +
89O ILE* 2.9 31.1 + - + +
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Residues in contact with GLU 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81O PHE* 3.9 25.6 - - + +
82O SER 3.1 12.2 + - - +
83O GLY* 4.1 7.2 - - - +
85O ALA* 1.3 79.5 - - - +
87O THR* 1.3 60.0 + - - +
89O ILE* 4.1 1.3 - - - +
90O ASP* 3.3 36.2 + - - +
95O ALA* 4.0 25.5 - - + +
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Residues in contact with THR 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83O GLY 3.1 14.1 + - - -
84O THR* 3.0 12.8 + - + +
86O GLU* 1.3 76.8 - - - +
88O LYS* 1.3 66.1 - - + +
90O ASP* 3.5 5.7 + - - +
91O GLN* 3.0 42.6 + - + +
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Residues in contact with LYS 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71L GLU 5.5 2.0 + - - -
72L ASN* 4.7 5.5 + - - -
75L LEU* 4.4 26.3 - - + +
45O LEU* 3.4 29.6 - - + -
66O GLY 2.9 23.7 + - - +
68O GLY 3.2 18.3 + - - +
69O VAL* 5.7 1.7 - - - +
70O LEU* 5.1 5.5 - - + +
84O THR* 3.0 31.6 + - + +
85O ALA 3.8 0.4 - - - +
87O THR* 1.3 77.6 - - + +
89O ILE* 1.3 63.7 + - - +
91O GLN* 3.1 33.0 + - - +
92O VAL* 3.8 9.5 + - - +
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Residues in contact with ILE 89 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O LEU* 3.6 29.8 - - + -
48O ILE* 4.7 0.7 - - + -
64O VAL* 3.9 17.0 - - + -
70O LEU* 3.8 19.5 - - + -
74O VAL 4.7 1.3 - - - +
76O VAL* 4.3 22.0 - - + -
81O PHE* 4.1 16.8 - - + -
85O ALA 2.9 17.8 + - - +
86O GLU 4.3 2.7 - - - +
88O LYS* 1.3 76.8 - - - +
90O ASP* 1.3 52.2 + - - +
91O GLN 3.2 0.3 + - - -
92O VAL* 3.3 2.8 + - - +
93O GLY 2.7 32.9 + - - -
94O GLU 3.6 31.2 - - - +
95O ALA* 3.7 6.1 - - + +
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Residues in contact with ASP 90 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O GLU* 3.3 30.8 + - - +
87O THR* 4.0 4.7 - - - +
88O LYS 3.3 1.0 - - - -
89O ILE* 1.3 77.2 - - - +
91O GLN* 1.3 61.1 + - - +
92O VAL 3.3 0.2 - - - -
93O GLY 3.5 13.4 - - - +
94O GLU* 3.4 8.7 - - - +
95O ALA* 2.9 29.8 + - - +
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Residues in contact with GLN 91 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L LEU* 5.6 8.4 - - - +
87O THR* 3.0 37.4 - - + +
88O LYS* 3.1 23.6 + - - +
90O ASP* 1.3 78.0 - - - +
92O VAL* 1.3 68.0 + - + +
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Residues in contact with VAL 92 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70O LEU* 3.5 37.9 - - + +
71O GLN* 3.8 14.6 - - - +
72O LYS 3.5 16.2 - - - +
73O ASP* 2.9 29.8 - - - +
88O LYS 4.1 4.5 - - - +
89O ILE 3.9 6.3 - - - +
91O GLN* 1.3 88.8 - - + +
93O GLY* 1.3 60.0 + - - +
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Residues in contact with GLY 93 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70O LEU* 6.1 0.2 - - - -
73O ASP* 3.5 11.7 - - - -
74O VAL* 3.5 14.6 - - - -
89O ILE 2.7 14.9 + - - +
90O ASP* 3.5 14.6 - - - +
91O GLN 3.8 0.4 - - - -
92O VAL* 1.3 82.7 - - - +
94O GLU* 1.3 63.0 + - - +
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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