Contacts of the strand formed by residues 242 - 246 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TYR* 4.4 9.0 - - - +
458A GLY* 4.1 17.0 + - - +
459A ASP* 3.6 38.7 + - + +
461A HIS* 5.1 5.5 + - - -
139B MET* 3.5 17.3 - - + +
218B LYS 3.6 5.7 + - - +
219B ALA* 3.5 20.4 - - + -
220B VAL 3.1 21.3 + - - -
240B GLY 4.1 0.4 + - - -
241B LYS* 1.3 76.1 - - - +
243B CYS* 1.3 65.9 + - - +
469B ARG 3.1 8.9 + - - -
470B PHE* 2.7 49.7 + - + +
472B THR 2.9 24.7 + - - -
473B LYS* 3.6 21.2 - - - +
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Residues in contact with CYS 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TYR* 4.8 4.8 + - - +
459A ASP* 4.4 5.7 + - - +
220B VAL* 3.4 19.1 - - - +
232B ILE* 4.2 10.5 - - - -
233B TYR* 3.4 54.3 - - + +
236B ALA* 4.0 21.5 - - + -
237B SER* 5.0 2.0 - - - +
241B LYS 4.0 1.3 + - - +
242B ARG* 1.3 80.4 - - - +
244B GLN* 1.3 72.1 + - - +
245B ALA* 4.4 1.3 - - - -
457B PHE 3.9 1.2 - - - +
458B GLY* 4.0 6.2 - - - -
459B ASP 5.1 0.2 + - - -
470B PHE* 3.6 9.6 - - - -
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Residues in contact with GLN 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B MET* 5.5 0.7 - - - +
220B VAL 3.0 8.0 + - - +
221B SER* 2.6 32.8 + - - +
222B PHE* 2.8 27.6 + - - +
243B CYS* 1.3 75.6 - - - +
245B ALA* 1.3 60.6 + - - +
246B LEU* 4.2 10.1 - - + +
456B LEU* 6.0 1.3 - - + -
457B PHE 3.6 5.4 - - - +
458B GLY* 5.1 0.7 - - - -
460B LEU 2.7 38.7 + - - +
461B HIS 3.0 21.1 + - - +
462B ALA* 4.6 11.3 - - - +
463B TYR 5.3 1.0 + - - -
467B ALA* 5.5 1.6 - - - +
470B PHE* 3.5 28.3 - - + +
471B TYR* 4.0 7.3 + - - -
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Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B PHE* 3.4 13.2 - - + -
229B ALA* 3.5 33.4 - - + +
233B TYR* 4.3 8.1 - - + +
243B CYS* 4.4 4.7 - - - -
244B GLN* 1.3 74.3 - - - +
246B LEU* 1.3 65.1 + - - +
456B LEU* 3.6 0.4 - - - -
457B PHE* 2.9 49.7 + - + +
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Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B TRP* 4.3 7.2 - - + -
222B PHE* 3.0 19.4 + - - +
223B VAL* 4.2 17.0 - - + -
224B GLY 3.1 24.4 + - - +
229B ALA* 3.6 7.8 - - - +
244B GLN* 4.7 11.7 - - + -
245B ALA* 1.3 81.8 - - - +
247B GLY* 1.3 60.6 + - - +
410B ASN* 5.5 1.6 - - - +
449B PHE* 3.5 47.3 - - + +
450B GLY* 4.3 4.3 - - - -
451B GLY 5.1 1.6 - - - +
455B SER 3.5 6.5 - - - +
456B LEU* 4.0 21.1 - - + +
461B HIS 5.5 0.2 - - - -
462B ALA* 4.2 18.4 - - + +
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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
------------------------------------------------------------
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