Contacts of the strand formed by residues 240 - 244 (chain C) in PDB entry 2ZA5
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 240 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C 2FF 3.7 15.5 - - - -
177C TYR* 5.0 0.2 - - - -
196C CYS* 3.4 5.5 - - - -
197C ALA 2.9 39.7 + - - -
203C ASP* 3.7 22.6 + - - -
229C TRP 4.1 0.2 - - - -
238C ARG 3.7 1.0 + - - -
239C PRO* 1.3 72.1 - - - +
241C ILE* 1.3 60.6 + - - +
242C TYR* 3.6 9.7 - - - -
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Residues in contact with ILE 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C 2FF 4.5 0.7 - - - -
177C TYR* 3.5 33.7 - - + +
190C VAL* 4.4 10.3 - - + -
194C MET* 3.8 27.8 - - + -
195C LEU 3.6 3.8 - - - +
196C CYS* 4.1 14.4 - - - -
227C VAL* 5.4 0.3 - - - +
228C SER* 3.2 6.4 + - - -
229C TRP* 2.8 90.0 + - + +
230C GLY* 4.5 0.2 - - - -
239C PRO 3.6 6.5 + - - +
240C GLY* 1.3 76.1 - - - +
242C TYR* 1.3 69.0 + - - +
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Residues in contact with TYR 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C VAL* 3.7 16.7 - - + +
165C VAL* 4.6 2.3 - - - +
194C MET* 3.1 9.4 - - - +
195C LEU* 2.8 45.2 + - + +
197C ALA* 3.8 19.2 + - + +
203C ASP* 4.3 2.6 + - - -
204C SER* 3.2 27.1 + - - -
213C LEU* 3.6 39.8 - - + +
225C GLY* 4.1 6.7 - - - -
226C VAL 3.2 6.5 - - - +
227C VAL* 3.6 38.1 - - + -
228C SER* 4.1 2.9 - - - -
240C GLY* 3.6 26.5 - - - -
241C ILE* 1.3 78.4 - - - +
243C THR* 1.3 67.0 + - - +
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Residues in contact with THR 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C ASP* 2.7 47.4 + - - +
107C ILE* 4.2 8.3 - - + -
193C ASP* 3.6 6.3 - - - +
194C MET* 4.6 2.6 - - - +
225C GLY* 3.2 8.8 - - - -
226C VAL* 2.9 39.8 + - + -
228C SER* 3.6 8.6 + - - -
242C TYR* 1.3 70.8 - - - +
244C ARG* 1.3 64.2 + - - +
245C VAL* 3.4 1.4 + - - +
248C TYR* 3.7 33.9 - - + -
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Residues in contact with ARG 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C GLU 4.9 1.6 + - - -
133C THR* 3.5 27.3 + - - +
134C PHE* 4.7 4.5 + - + -
169C GLU* 6.0 0.2 - - - +
170C ASN* 3.1 33.5 + - - +
192C ASP 3.4 16.7 + - - -
193C ASP* 2.7 23.9 + - - +
194C MET 2.8 20.6 + - - +
195C LEU* 3.8 28.1 - - + +
224C ALA 3.9 4.7 - - - +
242C TYR 3.5 1.4 + - - -
243C THR* 1.3 70.7 - - - +
245C VAL* 1.3 66.1 + - - +
246C THR* 3.5 23.2 + - + +
247C TYR* 3.2 21.8 + - + +
248C TYR* 3.8 7.8 - - - -
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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
------------------------------------------------------------
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