Contacts of the helix formed by residues 87 - 101 (chain D) in PDB entry 2ORE
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 CYS 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D PRO 5.8 0.2 - - - -
84D GLU 4.6 4.3 - - - -
85D THR 3.4 1.8 + - - +
86D ASN* 1.3 81.6 - - - +
88D ALA* 1.3 68.4 + - - +
89D GLU* 3.9 16.2 - - + +
90D VAL* 2.9 38.6 + - - +
91D TYR* 3.0 10.4 + - - +
135D PHE* 3.6 12.7 - - - -
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Residues in contact with ALA 88 (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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87D CYS* 1.3 70.4 - - - +
89D GLU* 1.3 65.6 + - - +
91D TYR* 2.9 12.4 + - - -
92D TYR* 3.0 32.7 + - + -
135D PHE* 3.4 39.6 - - + -
137D ARG* 4.7 7.9 - - - +
238F GLN 4.7 8.7 - - - +
242F LEU* 6.4 1.1 - - + -
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Residues in contact with GLU 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D CYS* 3.9 17.4 - - + +
88D ALA* 1.3 80.4 - - - +
90D VAL* 1.3 63.4 + - + +
92D TYR* 4.0 4.4 + - - +
93D GLN* 3.8 18.3 + - - +
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Residues in contact with VAL 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D GLU 3.6 16.8 - - - +
85D THR* 3.9 17.9 - - + +
87D CYS* 2.9 28.2 + - - +
89D GLU* 1.3 73.7 - - + +
91D TYR* 1.3 60.0 + - - +
92D TYR 3.2 2.0 - - - -
93D GLN* 2.7 35.3 + - + +
94D PHE* 2.9 51.3 + - + +
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Residues in contact with TYR 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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87D CYS 3.0 4.6 + - - -
88D ALA* 2.9 6.1 + - - +
90D VAL* 1.3 77.2 - - - +
92D TYR* 1.3 67.1 + + - +
94D PHE* 3.5 1.9 + - - +
95D ARG* 3.0 33.5 + - - +
113D TYR* 3.4 17.8 + + - +
114D LEU* 3.7 20.1 + - + +
117D TYR* 3.6 15.3 - - + -
118D GLY* 3.4 38.3 - - - -
131D PHE* 3.8 18.4 - - - -
133D VAL* 3.3 23.4 + - - +
134D PRO 3.6 2.3 + - - -
135D PHE* 3.3 57.9 - + + -
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Residues in contact with TYR 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ALA* 3.0 44.6 + - + +
89D GLU* 4.5 3.8 - - - +
91D TYR* 1.3 83.6 - + - +
93D GLN* 1.3 61.7 + - - +
95D ARG* 3.7 40.9 + - - +
96D GLU* 3.3 21.8 + - - +
134D PRO* 3.6 11.4 - - + +
135D PHE* 3.1 28.8 + - + +
234F ARG* 3.6 5.5 + - - +
235F GLU* 4.4 1.1 - - - -
238F GLN* 3.2 57.0 - - + +
242F LEU* 6.0 0.7 - - - +
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Residues in contact with GLN 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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89D GLU* 3.8 14.3 + - - +
90D VAL* 2.7 22.7 + - - +
92D TYR* 1.3 77.0 - - - +
94D PHE* 1.3 77.7 + - - +
96D GLU* 3.2 6.7 + - - +
97D GLU* 2.9 32.1 + - + +
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Residues in contact with PHE 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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80D LEU* 3.7 31.9 - - + -
85D THR* 3.9 22.2 - - + -
90D VAL* 2.9 33.5 + - + +
93D GLN* 1.3 94.2 - - - +
95D ARG* 1.3 59.6 + - - +
97D GLU* 3.2 20.1 + - - +
98D PHE* 2.9 29.5 + - - +
106D ARG* 5.0 7.0 - - - -
110D LEU* 3.8 13.0 - - + +
113D TYR* 3.3 44.4 - + + -
114D LEU* 4.8 2.2 - - + -
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Residues in contact with ARG 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D TYR* 3.0 24.9 + - + +
92D TYR* 3.7 25.8 + - - +
94D PHE* 1.3 77.2 - - - +
96D GLU* 1.3 57.5 + - - +
98D PHE* 3.2 5.5 + - - +
99D ASN* 2.9 35.2 + - - +
114D LEU* 4.0 14.1 - - + +
131D PHE* 3.6 40.1 + - + +
132D ASN* 3.4 9.7 - - - +
133D VAL 2.2 43.0 + - - -
134D PRO* 3.9 2.2 - - - +
235F GLU* 2.7 41.2 + - - -
238F GLN* 3.9 3.2 + - - +
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Residues in contact with GLU 96 (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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92D TYR 3.3 15.7 + - - +
93D GLN* 3.2 6.7 + - - +
95D ARG* 1.3 78.3 - - - +
97D GLU* 1.3 66.3 + - - +
99D ASN* 3.3 7.6 + - - +
100D LYS* 3.1 60.0 + - + +
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Residues in contact with GLU 97 (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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93D GLN* 2.9 18.4 + - + +
94D PHE* 3.2 21.7 + - - +
96D GLU* 1.3 77.7 - - - +
98D PHE* 1.3 57.2 + - - +
100D LYS* 3.7 4.5 - - - +
101D SER* 2.9 28.8 + - - -
106D ARG* 2.6 54.3 + - + +
110D LEU* 3.9 6.2 - - + +
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Residues in contact with PHE 98 (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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58D ASP* 3.5 16.6 - - - -
94D PHE 2.9 13.4 + - - +
95D ARG 3.4 7.0 - - - +
97D GLU* 1.3 72.3 - - - +
99D ASN* 1.3 77.7 + - - +
100D LYS 3.0 2.8 + - - -
101D SER* 3.0 11.7 + - - -
107D ARG* 2.7 92.2 + - + -
110D LEU* 3.6 21.1 - - + +
111D PHE* 4.4 19.5 - + + -
114D LEU* 3.9 16.6 - - + -
125D TYR* 5.0 2.5 - + - -
131D PHE* 3.7 24.9 - + + -
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Residues in contact with ASN 99 (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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95D ARG* 2.9 28.9 + - - +
96D GLU* 3.3 6.9 + - - +
98D PHE* 1.3 85.4 - - - +
100D LYS* 1.3 60.7 + - + +
101D SER 4.6 1.0 - - - +
102D GLN* 5.5 1.2 - - - +
107D ARG* 4.2 7.5 + - - +
129D GLY 4.8 0.2 - - - +
130D GLU* 3.2 29.6 - - + +
131D PHE* 2.6 51.3 + - - +
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Residues in contact with LYS 100 (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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96D GLU* 3.1 55.4 + - + +
97D GLU* 3.7 5.4 - - - +
98D PHE 3.0 0.8 - - - -
99D ASN* 1.3 80.3 - - + +
101D SER* 1.3 65.6 + - - +
102D GLN* 3.7 14.0 + - - +
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Residues in contact with SER 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D GLU* 2.9 19.1 + - - -
98D PHE* 3.0 4.1 + - - -
99D ASN 4.6 1.2 - - - +
100D LYS* 1.3 79.2 - - - +
102D GLN* 1.3 69.1 + - - +
103D ASP* 3.1 25.6 + - - +
106D ARG* 4.1 15.9 - - - +
107D ARG* 3.4 36.4 + - - +
110D LEU* 5.3 0.2 - - - -
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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