Contacts of the helix formed by residues 96 - 101 (chain B) in PDB entry 2ORY
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 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A PHE* 3.0 29.6 - - - -
67B ILE* 5.2 4.9 - - - +
93B ASN* 3.8 14.6 + - - +
94B PRO 3.4 1.0 - - - -
95B VAL* 1.3 82.7 - - - +
97B ILE* 1.3 63.5 + - - +
98B SER 3.3 2.7 - - - -
99B ASP* 3.0 25.7 + - - +
100B TRP* 3.1 18.4 + - - +
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Residues in contact with ILE 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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65A PHE 4.2 0.4 + - - -
94B PRO 3.4 16.6 - - - +
95B VAL 2.9 10.0 + - - +
96B SER* 1.3 71.1 - - - +
98B SER* 1.3 64.7 + - - +
100B TRP* 3.6 10.5 - - - +
101B LEU* 2.9 45.0 + - + -
102B PHE* 3.2 13.7 + - + -
237B ILE* 3.9 23.3 - - + -
238B VAL* 3.7 23.6 - - + -
305B LEU* 5.4 4.0 - - + +
308B ALA* 3.9 28.7 - - + +
309B ALA* 4.2 3.1 - - - +
312B HIS* 3.8 20.4 - - + -
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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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65A PHE 4.5 1.0 + - - -
66A THR* 4.0 14.4 + - - -
69A ASN* 5.0 0.2 + - - -
96B SER 3.3 1.0 - - - -
97B ILE* 1.3 77.9 - - - +
99B ASP* 1.3 60.9 + - - +
102B PHE* 3.0 35.2 - - - +
103B ASN* 3.1 13.9 + - - -
267B GLN* 2.8 27.7 + - - -
270B LEU* 3.6 14.4 - - - +
305B LEU* 3.9 25.8 - - - +
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Residues in contact with ASP 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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66A THR* 2.9 28.8 + - - -
67A ILE* 3.0 33.2 + - - +
68A PHE* 3.5 35.8 - - + +
67B ILE* 4.6 5.4 - - + -
68B PHE* 3.4 7.9 - - - -
96B SER* 3.0 19.9 + - - +
98B SER* 1.3 77.0 - - - +
100B TRP* 1.3 64.8 + - - +
101B LEU 3.4 0.2 + - - -
103B ASN* 3.3 28.6 + - - +
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Residues in contact with TRP 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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67B ILE* 3.9 18.3 - - + +
68B PHE* 3.3 26.5 - - + -
92B THR* 4.6 16.8 - - - +
93B ASN 3.3 19.5 - - - -
94B PRO* 3.0 23.6 + - + +
96B SER* 3.1 28.6 + - - -
97B ILE* 3.6 7.3 - - + +
99B ASP* 1.3 79.3 - - - +
101B LEU* 1.3 80.0 + - + +
104B ASP* 3.6 10.8 - - - +
174B SER* 3.1 27.8 - - - -
175B LYS* 4.1 34.3 - - + -
209B PRO* 4.8 3.6 - - + -
238B VAL* 3.9 28.9 - - + -
312B HIS* 3.9 10.1 - - - -
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Residues in contact with LEU 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 ILE* 2.9 33.6 + - + +
100B TRP* 1.3 105.5 - - + +
102B PHE* 1.3 77.3 + - + +
103B ASN 3.2 1.8 - - - -
104B ASP* 3.1 9.5 + - + +
209B PRO* 4.0 21.5 - - + -
237B ILE 4.9 1.6 - - - +
238B VAL* 4.0 26.7 - - + -
241B ALA* 4.1 13.0 - - + -
242B TRP* 3.0 45.1 - - + +
250B LEU* 6.3 0.4 - - + -
274B MET* 4.7 0.4 - - + -
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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