Contacts of the strand formed by residues 180 - 184 (chain U) in PDB entry 3OY6
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 MET 180 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98U ALA* 3.9 4.3 - - + -
99U HIS 3.3 26.9 - - - +
100U HIS* 3.9 24.5 - - + +
165U HIS* 5.3 2.8 + - - +
175U GLU 3.7 19.3 - - - +
176U VAL* 3.7 11.4 - - + +
177U THR* 3.1 42.3 + - + +
178U THR* 4.1 1.7 - - - +
179U LYS* 1.3 84.7 - - + +
181U LEU* 1.3 67.6 + - - +
182U CYS 4.3 0.2 - - - -
215U TRP* 3.6 16.8 - - + +
227U VAL* 3.8 15.0 - - + -
228U TYR 3.3 8.1 - - - +
229U THR* 5.4 1.8 - - - -
230U ARG* 4.1 9.4 + - - +
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Residues in contact with LEU 181 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129U ASP* 4.4 9.6 - - + +
130U PRO 6.1 0.2 - - - +
162U LEU* 4.8 16.4 - - + -
163U ILE 5.4 5.4 - - - +
180U MET* 1.3 74.5 - - - +
182U CYS* 1.3 66.1 + - - +
199U LEU* 4.4 11.0 - - + -
210U THR* 3.4 42.0 - - + +
211U GLY* 5.1 1.3 - - - -
227U VAL* 3.5 1.4 - - - -
228U TYR* 2.7 52.1 + - + +
230U ARG* 3.7 43.5 - - + +
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Residues in contact with CYS 182 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162U LEU* 3.7 5.5 - - - +
163U ILE* 2.9 39.0 + - + +
168U CYS* 2.0 53.2 - - + -
176U VAL* 3.8 20.0 - - - -
180U MET 4.4 0.2 + - - -
181U LEU* 1.3 75.5 - - - +
183U ALA* 1.3 62.8 + - - +
225U PRO* 4.0 12.1 - - + -
226U GLY 3.3 4.5 - - - -
227U VAL* 4.3 12.3 - - - -
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Residues in contact with ALA 183 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160U VAL* 3.7 23.5 - - + +
161U LYS 3.1 13.5 - - - +
162U LEU* 3.9 17.3 - - + -
163U ILE* 4.3 1.3 - - - -
182U CYS* 1.3 77.3 - - - +
184U ALA* 1.3 61.5 + - - +
189U ASP* 4.5 3.8 - - - +
199U LEU* 4.4 2.7 - - + -
225U PRO* 4.0 2.3 - - - +
226U GLY* 3.0 31.1 + - - +
228U TYR* 3.9 16.7 - - + -
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Residues in contact with ALA 184 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160U VAL* 3.8 10.4 - - - +
161U LYS* 2.8 41.3 + - - +
163U ILE* 3.6 15.1 - - + +
183U ALA* 1.3 76.7 - - - +
185U ASP* 1.3 63.3 + - - +
186U TRP* 3.6 34.5 - - + -
188U THR 5.2 0.9 - - - -
189U ASP* 5.5 3.6 - - - +
225U PRO* 3.9 5.8 - - + -
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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