Contacts of the helix formed by residues 338 - 348 (chain L) 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 ALA 338 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294L GLU* 5.6 1.1 - - - +
335L ASP* 3.5 25.8 + - + +
336L VAL 3.5 2.0 - - - -
337L SER* 1.3 79.3 - - - +
339L TYR* 1.3 65.3 + - - +
340L ILE* 3.2 7.3 + - + +
341L PRO* 3.3 18.3 - - + +
342L THR* 2.6 30.4 + - - -
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Residues in contact with TYR 339 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293L ARG* 3.3 69.5 - - + +
294L GLU* 3.6 23.1 + - - +
296L TYR* 4.8 5.6 - + + -
297L PRO 4.8 0.5 + - - -
298L GLY* 4.4 7.8 + - - -
300L VAL* 3.1 34.3 - - + +
301L PHE* 4.8 2.8 + - - +
337L SER 3.9 0.8 + - - -
338L ALA* 1.3 74.6 - - - +
340L ILE* 1.3 74.5 + - + +
342L THR* 3.8 4.8 - - - -
343L ASN* 3.3 45.0 + - - +
263M GLN* 5.1 5.7 + - - -
313M PRO* 5.6 5.2 - - + -
314M ALA* 4.6 5.5 - - - +
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Residues in contact with ILE 340 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274L SER* 5.6 7.0 - - - +
277L ALA* 4.6 19.7 - - + -
294L GLU* 4.0 25.8 - - - +
296L TYR* 4.0 31.4 - - + +
300L VAL* 5.6 5.2 - - + -
304L HIS* 5.0 6.5 - - + +
329L ILE* 4.3 11.4 - - + -
338L ALA* 4.6 5.6 - - + -
339L TYR* 1.3 86.1 - - + +
341L PRO* 1.3 76.7 - - + +
343L ASN* 3.0 24.2 + - + +
344L VAL* 3.3 13.6 + - + +
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Residues in contact with PRO 341 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170L ILE* 3.9 23.6 - - + -
329L ILE* 3.4 20.4 - - + -
330L GLU 5.1 3.1 - - - +
331L THR* 3.7 20.6 - - + -
335L ASP 4.4 1.6 - - - +
336L VAL 4.7 7.4 - - - +
338L ALA* 3.3 28.0 - - + +
340L ILE* 1.3 98.1 - - + +
342L THR* 1.3 60.9 + - - +
344L VAL* 3.3 2.8 + - - +
345L ILE* 3.0 30.0 + - - +
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Residues in contact with THR 342 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336L VAL 3.8 1.6 + - - -
337L SER* 3.4 21.5 + - - -
338L ALA 2.6 23.6 + - - -
339L TYR 3.8 4.0 - - - -
341L PRO* 1.3 78.7 - - - +
343L ASN* 1.3 63.0 + - - +
345L ILE* 3.4 9.3 + - - +
346L SER* 3.2 21.0 + - - -
159M ALA* 3.5 14.7 - - + +
311M TYR* 2.9 28.7 - - + +
312M VAL 4.7 0.7 - - - +
313M PRO* 4.4 0.7 - - + -
314M ALA* 3.5 23.8 - - - +
315M ASP* 4.6 9.4 + - - +
337M ARG* 5.1 1.3 - - - +
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Residues in contact with ASN 343 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300L VAL* 4.1 10.9 + - - +
301L PHE* 4.1 30.1 - - + +
304L HIS* 5.8 3.8 - - + +
339L TYR* 3.3 50.9 + - - +
340L ILE* 3.0 12.4 + - + +
342L THR* 1.3 79.3 - - - +
344L VAL* 1.3 62.2 - - + +
346L SER* 2.6 23.9 + - - -
347L ILE* 3.1 14.8 - - + +
260M ARG* 5.5 0.9 + - - -
263M GLN* 4.4 6.4 + - - -
311M TYR* 4.5 10.0 + - - -
313M PRO* 6.0 1.4 - - - +
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Residues in contact with VAL 344 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168L LEU* 3.5 29.2 - - + -
273L LEU* 4.8 11.4 - - + -
304L HIS* 4.2 27.4 - - + +
308L LEU* 4.5 13.0 - - + -
327L PRO* 4.9 0.2 - - + -
329L ILE* 3.5 21.8 - - + -
340L ILE* 3.5 15.0 - - + +
341L PRO 3.3 4.8 + - - +
343L ASN* 1.3 73.5 - - + +
345L ILE* 1.3 67.7 + - - +
347L ILE* 3.0 20.5 + - + +
348L THR* 3.3 17.8 + - + +
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Residues in contact with ILE 345 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168L LEU* 3.6 24.0 - - + -
170L ILE* 4.0 18.2 - - + -
336L VAL* 4.0 22.4 - - + +
341L PRO 3.0 24.1 + - - +
342L THR* 3.7 7.4 - - - +
344L VAL* 1.3 74.9 - - - +
346L SER* 1.3 61.9 + - - +
347L ILE 3.2 0.9 + - - -
348L THR* 3.3 19.4 + - - +
350L GLY 5.1 0.5 + - - -
351L GLN* 3.6 31.4 + - + +
159M ALA* 3.7 25.6 - - + +
160M GLY* 5.0 1.6 + - - -
190M ARG* 4.6 1.9 + - - -
337M ARG* 4.5 11.4 - - - +
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Residues in contact with SER 346 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301L PHE* 4.1 2.9 - - - -
342L THR 3.2 8.3 + - - -
343L ASN* 2.6 25.5 + - - -
345L ILE* 1.3 79.6 - - - +
347L ILE* 1.3 58.7 + - - +
159M ALA* 3.6 17.7 - - - +
190M ARG* 2.9 34.1 + - - +
222M MET* 4.5 2.6 - - - +
260M ARG* 3.4 29.8 + - - -
311M TYR* 3.8 12.3 + - - -
609M PO4 5.6 1.3 - - - -
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Residues in contact with ILE 347 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166L ARG* 3.5 23.2 + - - +
301L PHE* 4.0 20.6 - - + +
304L HIS* 3.6 40.2 - - + +
305L SER* 3.8 9.6 - - - +
308L LEU* 4.0 21.3 - - + -
309L GLU* 5.0 0.2 - - - +
343L ASN* 3.1 21.1 - - + +
344L VAL* 3.0 11.1 + - - +
346L SER* 1.3 77.4 - - - +
348L THR* 1.3 67.5 + - - +
190M ARG* 3.4 15.8 + - - +
222M MET* 3.6 22.2 - - - -
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Residues in contact with THR 348 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166L ARG* 3.0 24.2 - - + +
168L LEU* 3.8 22.1 - - + +
308L LEU* 4.1 11.7 - - + -
327L PRO* 4.0 18.8 - - + -
344L VAL* 3.5 13.1 + - + +
345L ILE* 3.3 18.2 + - - +
347L ILE* 1.3 76.3 - - - +
349L ASP* 1.3 61.7 + - - +
350L GLY 2.8 24.3 + - - -
375L ARG* 4.6 0.7 + - - -
190M ARG* 2.9 23.2 + - - -
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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