Contacts of the helix formed by residues 144 - 156 (chain E) 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 PRO 144 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7E PHE* 3.3 44.2 - - + +
81E PHE* 4.3 5.2 - - + -
112E LEU* 4.1 17.3 - - + -
116E ARG* 4.1 8.1 - - - +
142E TYR* 3.2 21.7 - - + +
143E PHE* 1.3 85.8 - - + +
145E GLU* 1.3 58.0 + - - +
147E GLU* 3.4 19.4 + - + +
148E LEU* 2.8 31.2 + - + +
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Residues in contact with GLU 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E VAL* 3.7 6.3 - - - +
78E ARG* 2.9 36.8 + - - -
142E TYR* 4.3 0.4 + - - -
143E PHE* 2.7 35.7 + - + +
144E PRO* 1.3 70.1 - - - +
146E ALA* 1.3 72.9 + - - +
147E GLU* 4.0 0.2 + - - -
148E LEU* 3.1 10.5 + - - +
149E TYR* 3.2 47.0 + - + -
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Residues in contact with ALA 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E TYR* 4.6 4.4 + - - +
144E PRO 3.5 0.4 - - - -
145E GLU* 1.3 81.7 - - - +
147E GLU* 1.3 76.7 + - - +
149E TYR* 3.4 7.2 + - - +
150E HIS* 3.1 20.7 + - - +
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Residues in contact with GLU 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ARG* 3.3 38.7 + - + +
6E ALA 4.0 9.2 - - - +
7E PHE* 3.6 20.0 - - + +
43E LEU* 5.7 0.7 - - - +
142E TYR* 2.4 34.9 + - + -
144E PRO* 3.4 15.3 - - + +
145E GLU 3.1 0.2 - - - -
146E ALA* 1.3 83.3 - - - +
148E LEU* 1.3 67.0 + - - +
150E HIS* 3.0 8.9 + - - +
151E PHE* 2.8 22.7 + - - +
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Residues in contact with LEU 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PHE* 3.8 31.4 - - + +
66E VAL* 3.7 36.7 - - + +
70E THR* 5.5 0.9 - - - -
73E TYR* 3.9 18.4 - - + -
74E VAL* 4.6 17.9 - - + -
112E LEU* 3.9 23.1 - - + -
143E PHE* 4.3 17.3 - - + -
144E PRO* 2.8 25.6 + - + +
145E GLU 3.6 4.3 - - - +
147E GLU* 1.3 71.2 - - - +
149E TYR* 1.3 66.2 + - - +
151E PHE* 3.0 4.7 + - - +
152E ALA* 2.8 24.4 + - - +
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Residues in contact with TYR 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E THR* 4.0 12.8 - - + -
71E ASP* 3.3 28.1 + - - -
74E VAL* 3.6 36.1 - - + +
78E ARG* 5.1 2.4 + - - -
145E GLU* 3.2 48.1 + - + -
146E ALA* 3.7 8.1 - - - +
148E LEU* 1.3 77.2 - - - +
150E HIS* 1.3 65.2 + - - +
152E ALA* 3.1 5.0 + - - +
153E GLU* 2.8 25.3 + - - +
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Residues in contact with HIS 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ASN* 2.9 53.5 + - + +
5E ARG 5.5 2.8 + - - +
43E LEU* 3.7 18.7 - - + +
146E ALA 3.1 12.1 + - - +
147E GLU* 3.0 12.1 + - - +
149E TYR* 1.3 74.7 - - - +
151E PHE* 1.3 64.2 + - - +
153E GLU* 3.0 9.6 + - + +
154E LYS* 2.8 43.4 + - + +
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Residues in contact with PHE 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PHE* 3.4 26.0 - + + -
36E VAL* 6.2 0.2 - - + -
38E ALA 4.6 7.0 - - - -
39E GLY* 5.0 1.3 - - - -
42E PHE* 4.0 16.3 - + - -
43E LEU* 3.7 31.4 - - + +
52E LEU* 5.7 0.2 - - + -
63E TYR* 3.3 56.3 - + + -
66E VAL* 4.0 10.1 - - + -
147E GLU 2.8 11.9 + - - +
148E LEU 3.3 8.1 - - - +
150E HIS* 1.3 77.0 - - - +
152E ALA* 1.3 53.9 + - - +
154E LYS* 3.4 1.2 + - - +
155E ALA* 2.6 40.9 + - + +
160E PHE* 3.6 32.3 - + - -
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Residues in contact with ALA 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E VAL* 3.6 15.5 - - + +
67E LYS* 4.9 0.9 - - - +
70E THR* 3.4 42.2 - - + +
148E LEU 2.8 17.2 + - - +
149E TYR 3.6 3.4 - - - +
151E PHE* 1.3 71.8 - - - +
153E GLU* 1.3 66.4 + - - +
155E ALA* 3.3 17.1 + - - +
156E GLN* 3.5 18.2 + - - +
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Residues in contact with GLU 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E TYR 2.8 13.6 + - - +
150E HIS* 3.0 15.5 + - + +
152E ALA* 1.3 76.8 - - - +
154E LYS* 1.3 61.9 + - - +
156E GLN* 3.5 20.3 + - - +
157E ASN* 4.8 3.1 - - - +
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Residues in contact with LYS 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E PHE* 3.0 43.7 - - + +
43E LEU* 4.3 11.7 - - + +
45E THR 3.0 28.6 + - - -
46E ASP* 4.3 7.1 - - - +
47E PHE 4.7 2.8 + - - -
50E TYR* 3.3 17.5 + - + -
150E HIS* 2.8 35.5 + - + +
151E PHE* 3.9 3.6 - - - +
153E GLU* 1.3 72.6 - - - +
155E ALA* 1.3 63.1 + - - +
156E GLN 3.0 6.1 + - - -
157E ASN* 3.2 20.7 + - - +
158E ALA 4.3 0.2 + - - -
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Residues in contact with ALA 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E PHE* 3.8 10.3 - - - -
67E LYS* 2.9 34.4 - - + -
151E PHE* 2.6 30.3 + - + +
152E ALA* 3.5 13.0 - - - +
153E GLU 3.3 0.4 - - - -
154E LYS* 1.3 73.3 - - - +
156E GLN* 1.3 59.8 + - - +
158E ALA* 3.0 14.0 + - - +
160E PHE* 3.9 22.2 - - + -
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Residues in contact with GLN 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E LYS* 3.3 54.8 + - - +
68E MET* 5.5 0.2 - - - +
70E THR* 5.1 1.4 + - - -
152E ALA 3.6 18.2 + - - +
153E GLU* 3.5 13.7 - - - +
154E LYS 3.0 1.2 + - - -
155E ALA* 1.3 78.6 - - - +
157E ASN* 1.3 67.7 + - - +
158E ALA 3.3 2.6 + - - +
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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