Contacts of the helix formed by residues 89 - 95 (chain D) in PDB entry 2OZL
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 ALA 89 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59D GLU* 3.6 31.4 - - + +
60D MET* 3.0 13.6 - - + +
63D ALA* 3.7 12.8 - - + -
80D PHE* 4.0 14.4 - - + -
85D PHE 4.3 0.2 + - - -
86D SER 2.9 7.9 + - - +
88D GLN* 1.3 78.6 - - - +
90D ILE* 1.3 62.5 + - - +
91D ASP 3.2 3.4 - - - -
92D GLN* 3.1 13.5 + - - +
93D VAL* 3.4 12.4 + - - +
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Residues in contact with ILE 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B MET* 3.7 29.6 - - + +
90B ILE* 4.2 7.4 - - + -
135B TRP* 3.4 32.5 - - + -
86D SER* 2.8 11.4 + - - +
87D MET* 3.5 19.0 + - + +
88D GLN 3.6 0.6 - - - -
89D ALA* 1.3 77.0 - - - +
91D ASP* 1.3 65.3 + - - +
93D VAL* 3.3 5.9 + - - +
94D ILE* 3.0 25.2 + - + +
132D PHE* 5.4 0.2 - - + -
135D TRP* 3.8 22.0 - - + -
136D TYR* 3.7 34.8 - - + +
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Residues in contact with ASP 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ASN 4.5 3.1 - - - +
87B MET* 3.8 21.8 + - + +
88B GLN* 4.4 17.9 - - + +
137C ILE* 3.4 30.4 - - - +
140C ALA* 3.9 14.4 - - - +
174C GLN* 5.5 0.2 + - - -
60D MET* 4.2 10.5 - - + +
88D GLN 5.2 0.4 + - - -
89D ALA 3.2 0.8 + - - -
90D ILE* 1.3 83.0 - - - +
92D GLN* 1.3 60.9 + - - +
95D ASN* 2.7 60.3 + - - +
96D SER* 3.5 0.9 + - - -
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Residues in contact with GLN 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C ALA* 3.1 27.9 + - - +
143C PRO* 3.8 4.8 - - - +
144C LEU* 3.9 8.3 - - - +
174C GLN* 3.1 19.2 + - - -
60D MET* 3.0 37.4 + - + +
63D ALA* 4.5 7.2 - - + -
64D GLY* 3.5 27.5 - - - +
67D VAL* 4.1 6.3 - - + +
89D ALA 3.1 4.9 + - - +
91D ASP* 1.3 77.7 - - - +
93D VAL* 1.3 58.1 + - - +
96D SER* 2.7 39.8 + - - -
97D ALA* 3.0 28.9 + - - +
114D PHE* 6.0 0.2 - - + -
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Residues in contact with VAL 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ALA* 5.5 0.2 - - + -
80D PHE* 4.5 11.0 - - + -
86D SER 5.5 0.2 - - - +
89D ALA 3.6 14.8 - - - +
90D ILE* 3.7 9.9 - - - +
91D ASP 3.3 0.6 - - - -
92D GLN* 1.3 78.7 - - + +
94D ILE* 1.3 58.7 + - + +
97D ALA* 3.3 8.2 - - - +
98D ALA* 3.0 26.2 + - - +
114D PHE* 3.9 43.7 - - + -
136D TYR* 3.8 31.0 - - + +
142D LEU* 4.0 18.4 - - + +
168D VAL* 4.4 2.7 - - + -
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Residues in contact with ILE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B MET* 4.2 15.3 - - + -
130B GLN* 3.7 26.9 - - - +
135B TRP* 4.3 5.2 - - + -
266B TRP* 5.0 0.2 - - + -
90D ILE* 3.0 29.0 + - + +
93D VAL* 1.3 77.9 - - + +
95D ASN* 1.3 64.2 + - - +
98D ALA* 3.4 6.4 + - + +
99D LYS* 3.3 38.0 + - + +
136D TYR* 4.4 11.2 - - + -
139D CYS* 3.5 35.9 - - + -
142D LEU* 3.9 19.5 - - + -
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Residues in contact with ASN 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ASN* 4.4 2.2 + - - +
87B MET* 3.0 20.3 - - - +
127B GLN* 2.8 48.0 + - - +
137C ILE* 3.6 19.2 - - + +
91D ASP* 2.7 40.7 + - - +
94D ILE* 1.3 76.6 - - - +
96D SER* 1.3 59.6 + - - +
99D LYS* 2.8 38.6 + - - +
100D THR* 4.2 0.7 + - - -
103D MET* 3.9 12.5 - - - +
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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