Contacts of the strand formed by residues 352 - 356 (chain B) 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 352 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536A SER* 4.7 0.9 - - - -
344B VAL* 5.3 2.9 - - + -
345B PHE* 3.6 1.6 - - - -
346B ASN* 3.0 36.2 + - + +
349B ASP 5.4 0.9 - - - +
350B GLY 4.3 0.2 - - - -
351B LEU* 1.3 77.6 - - - +
353B THR* 1.3 81.9 + - - +
354B TYR* 3.6 24.0 - - + +
6I LYS* 4.0 19.1 + - - +
7I THR 3.9 11.4 - - - -
8I LEU* 3.5 27.6 - - + +
9I THR* 3.8 17.7 - - - +
10I GLY* 3.5 25.8 - - - -
68I HIS* 3.5 29.1 + - - -
69I LEU 5.7 3.1 - - - -
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Residues in contact with THR 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A PHE* 4.8 7.2 - - + -
527A TYR* 3.8 7.0 - - - +
534A GLN 5.0 0.2 + - - -
535A THR* 4.3 3.8 - - - -
536A SER* 2.5 49.1 + - - +
343B LEU* 4.6 17.3 - - + -
344B VAL 3.1 11.7 - - - +
345B PHE* 3.5 25.6 - - + -
352B TYR* 1.3 93.9 - - - +
354B TYR* 1.3 61.4 + - - +
355B THR* 5.1 1.0 + - - -
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Residues in contact with TYR 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B TYR 4.0 0.3 - - - +
343B LEU* 3.3 2.4 - - - -
344B VAL* 2.9 44.9 + - + +
352B TYR* 3.6 21.6 - - + +
353B THR* 1.3 73.7 - - - +
355B THR* 1.3 78.4 + - - +
356B PHE* 3.7 35.9 + + + +
44I ILE* 4.7 8.1 + - + +
46I SER 6.0 0.2 + - - -
68I HIS* 3.2 63.9 + + + +
69I LEU 5.3 2.0 - - - +
70I VAL* 3.9 12.8 - - + -
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Residues in contact with THR 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A SER 4.4 6.3 - - - +
534A GLN 2.8 26.0 + - - +
535A THR* 4.0 15.5 - - + +
339B LEU* 3.4 24.0 - - + -
340B ASN 5.2 1.8 - - - +
342B TYR 3.2 15.0 - - - +
343B LEU* 3.8 8.3 - - - +
353B THR* 4.3 1.4 + - - -
354B TYR* 1.3 91.3 + - - +
356B PHE* 1.3 67.4 + - - +
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Residues in contact with PHE 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B THR* 5.9 0.2 - - + -
227B LEU* 4.7 5.2 - - + -
340B ASN 2.9 15.0 - - - +
341B ASN* 3.1 1.2 - - - +
342B TYR* 2.9 67.3 + + + +
344B VAL* 4.7 0.2 - - + -
354B TYR* 3.7 36.1 - + + +
355B THR* 1.3 77.5 - - - +
357B GLU* 1.3 65.4 + - - +
358B ALA* 3.7 26.9 - - + -
44I ILE* 3.8 39.0 - - + -
47I GLY* 4.5 5.6 - - - +
70I VAL* 3.7 22.7 - - + -
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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