Contacts of the strand formed by residues 342 - 346 (chain D) in PDB entry 3GZN
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 TYR 342 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D ASN* 3.4 20.6 + - + -
210D ALA 3.6 1.3 - - - -
211D ARG* 3.9 40.2 - - + -
224D THR* 5.1 1.1 - - + -
227D LEU* 4.0 18.3 - - + +
339D LEU* 4.2 3.4 - - - +
340D ASN 3.7 0.8 + - - -
341D ASN* 1.3 81.3 - - + +
343D LEU* 1.3 67.6 + - - +
344D VAL* 4.3 6.1 - - + -
354D TYR 3.8 0.5 - - - +
355D THR* 3.2 10.0 - - - +
356D PHE* 2.9 77.5 + + + +
358D ALA* 4.9 8.3 - - + +
70J VAL* 4.2 3.8 - - + -
71J LEU 2.6 29.8 + - - -
72J ALA* 3.2 20.8 - - - +
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Residues in contact with LEU 343 (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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503C PHE* 5.4 4.3 - - + -
529C TYR* 5.6 1.1 - - + -
534C GLN* 3.4 42.8 - - + +
209D ASN* 3.1 8.1 - - - +
210D ALA 2.8 37.4 + - - +
319D VAL* 6.0 0.4 - - + -
320D ILE* 4.8 7.6 - - + -
323D VAL* 4.2 28.5 - - + -
339D LEU* 4.5 9.8 - - + +
342D TYR* 1.3 77.7 - - - +
344D VAL* 1.3 77.0 + - - +
345D PHE* 4.2 12.8 - - + -
353D THR* 4.4 14.6 - - + -
354D TYR 3.4 4.5 - - - +
355D THR* 4.3 7.4 - - - +
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Residues in contact with VAL 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D LYS* 6.2 0.2 - - + -
208D GLY 3.4 8.1 - - - +
209D ASN* 4.5 2.0 - - + -
342D TYR* 4.3 10.1 - - + -
343D LEU* 1.3 75.7 - - - +
345D PHE* 1.3 66.6 + - - +
352D TYR* 4.1 5.7 - - + +
353D THR* 3.2 9.4 - - - -
354D TYR* 2.9 56.1 + - + +
356D PHE* 5.7 0.2 - - + -
8J LEU* 4.3 18.8 - - + -
69J LEU 5.1 1.6 - - - +
70J VAL* 4.5 13.7 - - + -
71J LEU* 3.8 34.5 - - + +
73J LEU* 4.7 3.4 - - + -
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Residues in contact with PHE 345 (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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503C PHE* 4.8 2.7 - + - -
507C ALA* 5.0 2.7 - - + -
527C TYR* 4.5 3.4 - - - -
206D PHE 4.0 6.7 - - - -
207D LYS* 3.2 7.3 - - - +
208D GLY 2.6 39.1 + - - +
316D THR* 4.3 17.3 - - + -
319D VAL* 3.9 41.1 - - + -
320D ILE* 4.2 12.8 - - + -
343D LEU* 4.2 6.1 - - + -
344D VAL* 1.3 78.5 - - - +
346D ASN* 1.3 65.9 + - - +
347D ASP* 3.5 43.5 - - + -
351D LEU* 4.1 26.2 - - + -
352D TYR* 3.8 2.5 - - - -
353D THR* 3.5 22.7 - - + -
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Residues in contact with ASN 346 (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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184C ASP* 3.7 8.3 + - - -
206D PHE 3.4 3.3 - - - +
207D LYS* 3.3 25.7 - - + +
345D PHE* 1.3 78.6 - - - +
347D ASP* 1.3 68.6 + - - +
348D VAL* 3.5 17.7 - - - +
349D ASP 5.2 1.7 - - - +
351D LEU* 3.4 6.4 - - - +
352D TYR* 3.0 34.8 + - + +
8J LEU* 2.8 49.6 + - + +
9J THR* 3.5 17.9 - - - +
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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