Contacts of the helix formed by residues 384 - 392 (chain X) 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 LEU 384 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407U GLN* 4.1 23.8 - - + +
380X THR* 3.4 31.3 + - + +
381X TYR* 3.5 6.9 + - + +
382X LYS 3.2 0.4 - - - -
383X SER* 1.3 83.0 - - - +
385X GLN* 1.3 67.5 + - - +
386X ASP 3.4 2.5 - - - -
387X ILE* 3.2 17.9 + - + +
388X ILE* 3.0 33.5 + - + +
396X LEU* 4.0 24.5 - - + -
400X ASP* 4.3 18.4 - - + +
404X VAL* 4.2 22.7 - - + -
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Residues in contact with GLN 385 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381X TYR* 3.4 48.6 + - - +
382X LYS* 3.4 29.4 - - + +
383X SER 3.7 0.6 - - - -
384X LEU* 1.3 77.3 - - - +
386X ASP* 1.3 65.2 + - - +
388X ILE* 3.3 6.5 + - - +
389X ALA* 2.9 29.1 + - - +
411X GLN* 5.8 1.6 - - - +
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Residues in contact with ASP 386 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384X LEU 3.4 0.4 - - - -
385X GLN* 1.3 82.0 - - - +
387X ILE* 1.3 73.5 + - + +
389X ALA* 2.9 7.5 + - - +
390X ILE* 2.9 33.7 + - + +
13Y ILE* 4.7 5.3 - - + +
247Y MET* 3.6 27.9 - - + +
250Y ARG* 4.9 5.2 + - - -
251Y TYR* 3.3 22.1 + - - -
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Residues in contact with ILE 387 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404U ALA* 5.5 9.0 - - + -
407U GLN* 4.5 31.4 - - + +
383X SER 5.0 2.5 - - - +
384X LEU* 3.2 27.3 + - + +
386X ASP* 1.3 81.3 - - + +
388X ILE* 1.3 62.5 + - + +
390X ILE* 4.9 4.0 - - + -
391X LEU* 3.3 45.0 + - + +
392X GLY 4.0 4.3 - - - +
395X GLU* 6.4 1.3 - - + -
396X LEU* 4.7 16.4 - - + -
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Residues in contact with ILE 388 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381X TYR* 5.6 9.2 - - + +
384X LEU* 3.0 48.2 + - + +
385X GLN* 3.6 4.9 - - - +
387X ILE* 1.3 74.5 - - - +
389X ALA* 1.3 68.1 + - - +
390X ILE 3.1 1.1 + - - -
392X GLY* 3.6 22.7 + - - -
393X MET* 3.9 35.0 - - + -
396X LEU* 3.6 40.2 - - + -
404X VAL* 5.0 7.4 - - + -
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Residues in contact with ALA 389 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385X GLN 2.9 16.9 + - - +
386X ASP* 2.9 6.6 + - - +
388X ILE* 1.3 79.9 - - + +
390X ILE* 1.3 62.3 + - - +
243Y ASN* 3.8 18.0 + - - +
247Y MET* 3.7 21.8 - - + +
250Y ARG* 5.1 5.6 - - - +
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Residues in contact with ILE 390 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386X ASP* 2.9 23.6 + - + +
387X ILE* 5.1 4.5 - - + +
388X ILE 3.1 1.6 - - - -
389X ALA* 1.3 81.3 - - - +
391X LEU* 1.3 74.9 + - + +
392X GLY 3.2 8.4 + - - -
13Y ILE* 4.5 16.2 - - + -
16Y ILE* 4.8 18.2 - - + -
20Y THR* 5.5 2.7 - - + -
239Y ASN* 5.7 0.2 + - - -
240Y ALA* 3.8 30.2 - - + +
243Y ASN* 3.8 19.1 - - - +
244Y ALA* 4.0 17.7 - - + +
247Y MET* 3.9 27.6 - - + -
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Residues in contact with LEU 391 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407U GLN 4.8 6.5 - - - +
408U PHE* 4.6 26.2 - - + -
387X ILE* 3.3 36.9 + - + +
390X ILE* 1.3 90.6 - - + +
392X GLY* 1.3 60.0 + - - +
394X ASP* 3.8 1.2 - - - +
395X GLU* 3.1 50.5 - - + +
16Y ILE* 5.6 7.0 - - + -
20Y THR* 5.6 5.8 - - + -
237Y MET* 6.2 3.1 - - - -
240Y ALA* 4.3 15.9 - - + -
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Residues in contact with GLY 392 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387X ILE* 4.0 9.4 - - - +
388X ILE* 3.6 16.3 + - - -
390X ILE 3.2 8.1 + - - -
391X LEU* 1.3 83.3 - - - +
393X MET* 1.3 63.4 + - - -
394X ASP* 3.3 7.8 + - - -
395X GLU* 3.8 7.6 + - - +
396X LEU* 4.8 3.6 + - - +
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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