Contacts of the helix formed by residues 84 - 89 (chain C) in PDB entry 1Y9D
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 84 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A PHE* 3.7 7.9 - - - -
82C SER 3.5 0.4 + - - -
83C ALA* 1.3 67.5 - - - +
85C PRO* 1.3 66.1 - - - +
87C GLY* 3.1 6.2 + - - -
88C THR* 3.0 26.5 + - - +
124C MET* 3.4 26.5 - - - -
126C GLU* 2.8 21.8 + - - +
129C ILE* 5.4 0.4 - - - +
130C TYR* 4.4 1.9 + - - -
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Residues in contact with PRO 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASN* 3.0 30.7 + - - +
419A PHE* 3.3 37.2 - - + +
420A ALA 3.7 13.9 - - - +
421A THR* 3.5 17.0 - - - +
2602A TPP 3.5 19.9 - - + +
83C ALA 3.1 10.3 - - - +
84C GLY* 1.3 80.9 - - - +
86C GLY* 1.3 64.5 + - - +
88C THR* 3.4 10.5 - - - +
89C HIS* 3.4 10.9 + - - +
124C MET* 5.0 0.7 - - + -
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Residues in contact with GLY 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2602A TPP 3.8 2.3 - - - -
59C GLU* 3.4 34.9 - - - +
81C GLY* 3.9 6.5 - - - -
82C SER* 3.4 26.7 + - - -
84C GLY 3.3 0.8 + - - -
85C PRO* 1.3 76.6 - - - +
87C GLY* 1.3 61.5 + - - +
89C HIS* 3.4 16.8 - - - +
90C LEU* 3.7 3.6 + - - +
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Residues in contact with GLY 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLY* 4.1 2.0 - - - -
82C SER 2.8 14.9 + - - -
84C GLY 3.1 2.8 + - - -
86C GLY* 1.3 77.3 - - - +
88C THR* 1.3 57.1 + - - +
90C LEU* 2.9 38.3 + - - +
91C MET* 4.1 1.0 - - - +
108C ILE* 4.3 7.4 - - - -
130C TYR* 3.0 27.9 + - - -
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Residues in contact with THR 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A THR 5.2 0.3 - - - +
91A MET* 4.5 14.4 - - + +
92A ASN* 2.7 29.7 + - - +
95A TYR* 4.1 19.1 - - + -
419A PHE* 3.4 9.0 - - + -
84C GLY 3.0 14.0 + - - +
85C PRO* 3.4 11.8 - - - +
86C GLY 3.4 0.2 - - - -
87C GLY* 1.3 76.2 - - - +
89C HIS* 1.3 60.5 + - - +
91C MET* 3.1 27.3 + - + +
129C ILE* 3.8 37.7 - - + -
130C TYR* 4.2 1.1 - - - +
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Residues in contact with HIS 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A HIS* 6.3 0.2 - + - -
60A GLU* 2.7 28.5 + - + -
92A ASN* 3.2 24.9 + - + -
421A THR* 4.7 0.2 + - - -
422A MET 4.8 4.3 - - - -
452A MET* 3.8 15.3 - - + -
2602A TPP 3.5 20.0 - - + +
58C HIS* 3.2 31.6 + + + -
59C GLU* 2.8 28.5 + - + +
60C GLU* 2.9 30.8 - - - +
85C PRO 3.4 5.7 + - - +
86C GLY 3.4 12.3 - - - +
88C THR* 1.3 78.5 + - - +
90C LEU* 1.3 59.7 + - - +
91C MET* 3.2 1.1 + - - -
92C ASN 4.6 1.7 + - - -
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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
------------------------------------------------------------
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