Contacts of the strand formed by residues 184 - 188 (chain R) in PDB entry 2X1X
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 GLY 184 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148R ILE 3.4 8.3 - - - -
150R CYS 3.5 17.3 - - - -
151R LEU* 3.8 3.6 - - - +
179R TRP* 3.2 14.8 - - - -
180R ASP 2.8 29.4 + - - -
182R LYS 3.8 0.6 - - - -
183R LYS* 1.3 82.9 - - - +
185R PHE* 1.3 63.1 + - - -
186R THR* 3.9 5.8 + - - -
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Residues in contact with PHE 185 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146R VAL 3.9 0.2 - - - +
147R VAL* 3.3 6.9 - - - +
148R ILE* 2.7 42.1 + - + +
150R CYS 4.1 0.8 - - - +
159R VAL* 3.7 19.5 - - + -
160R SER 4.3 3.6 - - - -
161R LEU* 3.6 54.3 - - + -
170R PHE 3.7 11.2 - - - -
172R PRO* 4.4 6.3 - - + -
177R ILE* 3.5 33.2 - - + -
178R SER 3.6 3.4 - - - -
179R TRP* 3.4 24.6 - + + -
184R GLY* 1.3 68.6 - - - -
186R THR* 1.3 84.3 + - - +
187R ILE* 4.1 6.7 - - + -
200R CYS* 3.7 22.0 - - - -
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Residues in contact with THR 186 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145R THR* 4.2 20.0 - - + +
146R VAL 3.6 4.3 - - - +
147R VAL* 3.9 24.7 - - + +
176R ARG 3.8 5.6 - - - +
177R ILE* 3.4 9.5 - - - +
178R SER* 2.8 47.0 + - - +
180R ASP* 5.5 0.5 + - - +
183R LYS* 5.3 4.5 - - - +
184R GLY 3.9 5.7 + - - -
185R PHE* 1.3 78.6 + - - +
187R ILE* 1.3 63.8 + - - +
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Residues in contact with ILE 187 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145R THR* 3.9 3.1 - - - -
146R VAL* 2.7 54.6 + - + +
148R ILE* 4.3 2.9 - - + -
161R LEU* 3.7 24.0 - - + -
170R PHE* 3.7 41.5 - - + -
177R ILE* 4.4 6.3 - - + -
185R PHE* 4.1 7.6 - - + -
186R THR* 1.3 74.6 - - - +
188R PRO* 1.3 83.6 - - + +
189R SER 3.1 0.5 + - - -
191R MET* 3.8 20.4 - - + -
192R ILE* 4.1 13.2 - - + -
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Residues in contact with PRO 188 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144R LYS* 3.3 8.7 - - + +
145R THR* 3.6 13.9 - - + -
176R ARG* 3.8 40.8 - - + +
177R ILE* 4.0 13.2 - - + -
187R ILE* 1.3 87.6 - - + +
189R SER* 1.3 59.6 + - - +
190R TYR* 3.0 33.6 + - + +
191R MET* 3.1 36.9 + - - +
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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