Contacts of the helix formed by residues 355 - 361 (chain U) in PDB entry 3FKS
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 GLU 355 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172U ASP* 5.6 0.7 - - - -
175U THR* 4.6 1.6 - - - -
353U PHE* 3.3 32.5 + - + -
354U LEU* 1.3 71.7 - - - +
356U ALA* 1.3 65.4 + - - +
357U GLU* 4.2 15.5 - - + +
358U LEU* 3.1 40.1 + - + +
366U ALA* 3.2 24.1 + - - +
368U ASN* 4.1 22.2 + - + +
371U LEU* 4.5 4.3 - - - +
400U ARG* 5.1 5.3 + - - -
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Residues in contact with ALA 356 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172U ASP* 4.8 12.9 + - + +
173U ARG 5.4 1.3 - - - +
174U GLN 5.8 0.7 - - - +
175U THR* 3.9 22.9 - - + +
354U LEU 3.8 2.6 + - - -
355U GLU* 1.3 73.0 - - - +
357U GLU* 1.3 62.4 + - - +
359U PHE* 3.0 22.5 + - - +
360U TYR* 3.3 26.5 - - + -
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Residues in contact with GLU 357 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355U GLU* 3.1 16.9 - - + +
356U ALA* 1.3 80.8 - - - +
358U LEU* 1.3 60.7 + - + +
360U TYR 3.9 0.2 + - - -
361U LYS* 3.2 31.4 + - + +
379X GLN* 3.7 30.4 + - + +
382X LYS* 6.2 1.1 - - - +
383X SER* 3.9 19.6 + - - -
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Residues in contact with LEU 358 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355U GLU* 3.1 37.6 + - + +
357U GLU* 1.3 81.2 - - + +
359U PHE* 1.3 60.9 + - - +
361U LYS* 3.8 17.3 + - + +
362U GLY 3.8 0.2 + - - -
363U ILE* 2.8 57.2 + - + +
366U ALA* 3.8 12.1 - - + -
367U ILE 4.1 6.7 - - - +
368U ASN* 3.8 35.4 - - + +
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Residues in contact with PHE 359 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174U GLN 4.5 10.8 - - - -
175U THR* 4.2 22.4 - - - +
176U GLY* 5.6 2.2 - - - -
355U GLU 3.3 3.8 + - - +
356U ALA* 3.0 15.8 + - - +
358U LEU* 1.3 77.5 - - - +
360U TYR* 1.3 85.0 + + + +
362U GLY* 3.2 14.6 + - - -
363U ILE 3.6 8.3 - - - +
364U ARG* 3.0 56.5 + - + -
366U ALA* 3.8 12.3 - - + -
354X LYS* 3.2 44.4 - - + -
375X GLN* 5.2 0.7 - - - -
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Residues in contact with TYR 360 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174U GLN* 5.2 5.2 + - - +
356U ALA* 3.3 35.2 + - + -
359U PHE* 1.3 86.2 - + - +
361U LYS* 1.3 57.0 + - - +
362U GLY 3.0 10.3 + - - -
364U ARG* 5.3 1.3 - - - +
350X PRO 4.4 0.2 - - - -
351X LEU* 2.9 39.9 - - + -
352X ASP* 3.1 29.1 + - - -
353X SER 4.8 0.4 - - - -
354X LYS* 3.5 22.6 - - + +
375X GLN* 3.3 56.8 - - - +
376X GLU* 3.4 9.9 + - - +
379X GLN* 3.6 27.6 - - + +
382X LYS* 6.2 0.4 - - - -
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Residues in contact with LYS 361 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357U GLU* 3.2 24.3 + - + +
358U LEU* 4.0 16.0 - - + +
359U PHE 3.2 1.0 - - - -
360U TYR* 1.3 77.3 - - - +
362U GLY* 1.3 56.7 + - - +
363U ILE* 3.5 26.4 - - + +
431U LYS* 4.4 3.5 + - - -
376X GLU* 3.9 14.9 - - - +
379X GLN* 4.0 16.3 - - + +
380X THR* 5.2 10.8 - - - +
383X SER* 6.1 3.8 - - - -
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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