Contacts of the strand formed by residues 242 - 246 (chain D) in PDB entry 4ZZ7
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 ARG 242 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C TYR* 4.6 9.4 - - - +
458C GLY* 4.3 14.2 + - - +
459C ASP* 3.7 40.7 + - + +
461C HIS* 5.2 5.9 + - - -
139D MET* 3.2 23.4 - - + +
218D LYS 3.3 15.2 + - - +
219D ALA* 3.4 9.3 - - + -
220D VAL 3.1 21.8 + - - -
240D GLY 3.9 1.4 + - - -
241D LYS* 1.3 76.0 - - - +
243D CYS* 1.3 61.6 + - - +
469D ARG 3.4 9.7 + - - -
470D PHE* 2.8 46.9 + - + +
472D THR 2.9 22.0 + - - -
473D LYS* 3.7 18.4 - - - +
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Residues in contact with CYS 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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233C TYR* 5.0 3.6 + - - -
459C ASP* 4.3 7.3 + - - +
220D VAL* 3.4 15.9 - - + +
232D ILE* 4.2 13.2 - - - -
233D TYR* 3.5 50.5 + - + +
236D ALA* 3.8 22.9 - - + -
237D SER* 4.9 2.7 - - - +
241D LYS 4.6 0.9 - - - +
242D ARG* 1.3 77.4 - - - +
244D GLN* 1.3 76.0 + - - +
245D ALA* 4.3 1.6 - - - -
457D PHE 4.3 0.5 - - - +
458D GLY* 4.4 5.0 - - - -
459D ASP 5.3 0.2 + - - -
460D LEU 6.0 0.2 + - - -
470D PHE* 3.5 10.3 - - - -
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Residues in contact with GLN 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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158D MET* 5.6 0.3 - - - +
220D VAL 3.2 5.1 + - - +
221D SER* 2.9 28.3 + - - +
222D PHE 2.9 26.0 + - - +
243D CYS* 1.3 76.7 - - - +
245D ALA* 1.3 61.3 + - - +
246D LEU* 4.6 11.0 - - + +
456D LEU* 5.9 0.7 - - + -
457D PHE 3.7 6.7 - - - +
458D GLY* 5.1 0.9 - - - -
460D LEU 2.8 38.6 + - - +
461D HIS 3.2 20.9 + - - +
462D ALA* 4.6 8.9 - - - +
463D TYR 5.3 1.0 + - - -
467D ALA* 5.5 2.2 - - - +
470D PHE* 3.7 34.9 - - + +
471D TYR* 3.8 6.6 + - - -
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Residues in contact with ALA 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D PHE* 3.3 18.6 - - + -
229D ALA* 3.6 28.9 - - + +
233D TYR* 4.3 1.8 - - + +
243D CYS* 4.3 10.5 - - - -
244D GLN* 1.3 76.5 - - - +
246D LEU* 1.3 65.4 + - - +
456D LEU* 3.5 1.8 - - - +
457D PHE* 2.8 47.5 + - + +
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Residues in contact with LEU 246 (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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157D TRP* 4.3 3.4 - - + -
222D PHE* 2.8 18.8 + - - +
223D VAL* 4.2 8.3 - - + -
224D GLY 3.0 24.2 + - - +
229D ALA* 3.5 10.8 - - - +
244D GLN* 4.6 12.6 - - + -
245D ALA* 1.3 82.5 - - - +
247D GLY* 1.3 57.5 + - - +
449D PHE* 3.6 26.9 - - + +
450D GLY* 4.3 1.6 - - - -
451D GLY 5.2 0.7 - - - +
455D SER 3.7 5.4 - - - +
456D LEU* 3.8 25.1 - - + -
461D HIS 5.4 0.2 - - - -
462D ALA* 3.8 26.0 - - + +
501D NAD 3.3 32.3 - - - +
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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