Contacts of the strand formed by residues 176 - 180 (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 SER 176 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E CYS* 3.2 15.7 - - - +
32E VAL* 4.1 11.9 - - - +
51E ILE* 5.6 1.0 - - - +
171E ARG 4.7 0.5 + - - -
172E ALA* 3.5 17.3 - - - -
173E ASP* 2.8 43.4 + - - +
174E ASP 4.6 2.6 - - - +
175E ALA* 1.3 78.3 - - - +
177E VAL* 1.3 73.7 + - - +
178E VAL 4.3 0.2 - - - -
221E ILE* 3.9 6.0 - - - +
222E PRO* 3.7 14.6 - - - +
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Residues in contact with VAL 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E LEU* 4.5 9.0 - - + -
26E PRO* 3.7 33.7 - - + +
27E LYS 3.6 29.4 - - - +
28E GLY* 3.9 8.7 - - - +
30E CYS 2.9 11.4 + - - +
31E LEU* 2.7 34.8 - - + +
32E VAL 3.3 7.8 + - - -
47E PHE* 4.6 2.2 - - + -
176E SER* 1.3 80.1 - - - +
178E VAL* 1.3 60.8 + - - +
222E PRO* 3.4 31.6 - - + +
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Residues in contact with VAL 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E LEU* 5.4 0.2 - - - -
32E VAL* 3.6 21.3 - - + +
34E PRO* 4.0 11.9 - - + -
169E MET* 4.3 10.3 - - + +
172E ALA* 3.8 28.7 - - + -
177E VAL* 1.3 75.5 - - - +
179E TYR* 1.3 62.2 + - - +
180E CYS* 3.7 25.4 - - - -
216E LEU* 4.0 13.5 - - + -
221E ILE* 4.2 7.4 - - + -
222E PRO 3.1 10.5 + - - +
223E VAL* 3.2 12.0 - - + +
224E LEU* 2.9 26.3 + - - +
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Residues in contact with TYR 179 (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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14E LYS* 4.6 2.9 - - - +
21E ILE* 3.2 39.2 - - + +
25E LEU* 4.0 17.7 - - + -
31E LEU* 4.4 9.2 - - + -
32E VAL 3.1 12.1 + - - +
33E GLU* 3.7 25.1 - - + +
34E PRO* 3.3 15.8 - - - +
41E VAL* 3.3 28.3 - - + +
177E VAL 3.8 0.6 + - - -
178E VAL* 1.3 73.4 - - - +
180E CYS* 1.3 68.9 + - - +
181E ASP* 3.5 34.6 + - + +
224E LEU* 3.4 27.6 - - + +
226E SER* 3.6 15.6 + - - -
265E LEU* 5.6 0.2 - - + -
302E SAH 4.5 2.5 - - - -
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Residues in contact with CYS 180 (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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34E PRO* 3.7 15.7 - - - -
35E PHE* 4.0 7.2 - - + -
169E MET* 4.0 15.9 - - - -
178E VAL* 3.7 25.8 - - - -
179E TYR* 1.3 77.3 - - - +
181E ASP* 1.3 59.8 + - - +
182E PRO* 3.3 3.0 - - + +
209E LEU* 4.0 22.9 - - + -
223E VAL* 4.4 8.3 - - - -
224E LEU 2.8 11.0 + - - +
225E ILE* 3.3 17.0 - - + -
226E SER 2.9 26.9 + - - -
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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