Contacts of the strand formed by residues 240 - 244 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D 2FF 3.8 15.5 - - - -
177D TYR* 5.0 0.2 - - - -
196D CYS* 3.3 5.7 - - - -
197D ALA 2.9 41.2 + - - -
203D ASP* 3.5 22.1 + - - -
229D TRP 4.0 0.4 - - - -
230D GLY* 5.2 0.2 - - - -
239D PRO* 1.3 71.9 - - - +
241D ILE* 1.3 59.6 + - - +
242D TYR* 3.4 10.0 - - - -
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Residues in contact with ILE 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D 2FF 5.3 0.5 - - - -
173D CYS* 3.9 1.1 - - - -
177D TYR* 3.7 21.1 - - + +
190D VAL* 4.0 9.9 - - + -
194D MET* 3.7 31.9 - - + -
195D LEU 3.6 2.9 - - - +
196D CYS* 3.5 24.7 - - - -
227D VAL* 5.1 0.9 - - - +
228D SER* 3.1 20.7 + - - -
229D TRP* 2.8 66.8 + - + +
239D PRO 3.6 14.6 - - - +
240D GLY* 1.3 72.8 - - - -
242D TYR* 1.3 67.6 + - - +
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Residues in contact with TYR 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D VAL* 3.6 24.2 - - + +
165D VAL* 4.7 4.7 - - - +
194D MET* 3.1 11.1 - - - +
195D LEU* 2.8 51.0 + - + +
197D ALA* 3.9 22.2 + - + -
203D ASP* 4.4 1.7 + - - -
204D SER* 3.4 21.5 + - - -
213D LEU* 3.8 30.7 - - + -
225D GLY* 4.2 1.8 - - - -
226D VAL 3.3 11.4 - - - +
227D VAL* 3.4 41.1 - - + -
228D SER* 4.1 3.6 - - - -
240D GLY* 3.4 25.1 - - - -
241D ILE* 1.3 77.5 - - - +
243D THR* 1.3 62.2 + - - +
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Residues in contact with THR 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D ASP* 2.8 47.3 + - - +
107D ILE* 4.3 7.4 - - + -
193D ASP* 3.7 7.2 - - - +
194D MET* 4.6 1.6 - - - +
225D GLY* 3.1 8.7 - - - -
226D VAL* 2.8 38.0 + - - -
228D SER* 3.7 7.9 - - - -
242D TYR* 1.3 72.2 - - - +
244D ARG* 1.3 64.1 + - - +
245D VAL* 3.3 1.9 + - - +
248D TYR* 3.7 33.2 - - + -
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Residues in contact with ARG 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D GLU 4.8 1.8 + - - -
133D THR* 3.1 35.6 + - - +
134D PHE* 4.8 4.1 + - + -
167D ILE* 6.3 0.6 - - - +
168D MET 5.7 0.6 + - - -
169D GLU* 6.1 0.6 - - - +
170D ASN* 2.9 29.9 + - - +
192D ASP 3.7 15.0 + - - -
193D ASP* 2.8 25.8 + - - +
194D MET 3.0 18.6 + - - -
195D LEU* 3.7 27.9 - - + +
224D ALA 3.9 7.6 - - - +
242D TYR 3.6 1.8 + - - -
243D THR* 1.3 69.6 - - - +
245D VAL* 1.3 68.4 + - - +
246D THR* 3.6 21.1 + - + +
247D TYR* 3.1 21.3 + - + +
248D TYR* 3.8 7.6 - - - -
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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