Contacts of the helix formed by residues 338 - 346 (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 ALA 338 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293U ARG* 4.7 2.9 + - - -
294U GLU* 4.7 8.5 - - - +
332U GLN* 6.2 1.3 - - + +
335U ASP* 3.3 33.0 + - + +
336U VAL 3.2 2.2 - - - -
337U SER* 1.3 78.5 - - - +
339U TYR* 1.3 62.5 + - - +
341U PRO* 3.7 16.4 - - + -
342U THR* 2.6 30.8 + - - -
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Residues in contact with TYR 339 (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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293U ARG* 3.5 61.4 + - + +
294U GLU* 3.5 26.2 + - - +
296U TYR* 3.4 43.1 - + + -
297U PRO 3.9 5.8 + - - -
298U GLY* 4.6 5.4 + - - -
300U VAL* 3.1 22.6 - - + +
301U PHE* 4.8 2.3 + - - +
338U ALA* 1.3 74.7 - - - +
340U ILE* 1.3 69.3 + - + +
342U THR* 3.2 12.9 + - - -
343U ASN* 3.2 40.3 + - - +
263V GLN* 5.9 1.3 - - - -
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Residues in contact with ILE 340 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273U LEU* 5.8 0.4 - - + -
274U SER* 5.0 8.1 - - - -
277U ALA* 4.1 12.8 - - + -
294U GLU* 5.0 1.1 + - - +
296U TYR* 3.5 57.7 - - + +
300U VAL* 4.0 17.0 - - + -
304U HIS* 5.3 5.6 - - + +
329U ILE* 4.4 19.1 - - + -
339U TYR* 1.3 84.6 - - + +
341U PRO* 1.3 74.4 - - + +
343U ASN* 3.0 19.6 + - + +
344U VAL* 3.2 19.8 + - + +
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Residues in contact with PRO 341 (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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168U LEU* 5.0 0.2 - - - +
170U ILE* 4.2 16.2 - - + -
329U ILE* 3.7 29.8 - - + -
330U GLU 5.3 0.4 - - - +
331U THR* 4.4 8.1 - - + -
335U ASP 3.9 7.9 - - - +
336U VAL* 3.9 13.5 - - - +
338U ALA* 3.7 24.2 - - + -
339U TYR 3.5 3.8 - - - -
340U ILE* 1.3 95.8 - - + +
342U THR* 1.3 56.6 + - - +
344U VAL* 3.4 2.3 + - + +
345U ILE* 2.9 36.8 + - + +
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Residues in contact with THR 342 (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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293U ARG* 5.9 2.2 - - - +
336U VAL 3.3 14.2 + - - -
337U SER* 3.6 7.6 + - - -
338U ALA 2.6 24.3 + - - -
339U TYR* 3.2 5.0 + - - -
341U PRO* 1.3 75.3 - - - +
343U ASN* 1.3 70.0 + - - +
345U ILE* 3.9 7.5 - - + +
346U SER* 3.3 23.6 + - - -
259V PHE* 5.8 4.7 - - + -
311V TYR* 6.0 2.5 - - + -
313V PRO* 4.3 15.5 - - + -
314V ALA* 4.1 23.3 - - + +
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Residues in contact with ASN 343 (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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300U VAL* 3.8 16.5 + - - +
301U PHE* 3.4 34.7 - - + +
304U HIS* 6.3 2.2 - - + -
339U TYR* 3.2 49.8 + - - +
340U ILE* 3.0 14.4 + - + +
342U THR* 1.3 81.0 - - - +
344U VAL* 1.3 61.4 + - + +
346U SER* 2.9 19.9 + - - -
347U ILE* 3.1 15.8 - - - +
263V GLN* 3.9 11.3 + - - +
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Residues in contact with VAL 344 (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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168U LEU* 3.6 29.6 - - + -
273U LEU* 4.4 6.3 - - + -
304U HIS* 4.2 28.5 - - + +
308U LEU* 4.2 21.3 - - + -
327U PRO* 4.4 4.3 - - + -
329U ILE* 5.1 7.4 - - + -
340U ILE* 3.2 25.1 + - + +
341U PRO* 4.1 4.3 - - + +
343U ASN* 1.3 77.5 - - + +
345U ILE* 1.3 65.6 + - - +
346U SER 3.3 0.7 - - - -
347U ILE* 3.1 14.6 + - - +
348U THR* 3.2 16.2 + - + -
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Residues in contact with ILE 345 (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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168U LEU* 3.6 19.5 - - + -
170U ILE* 4.0 18.8 - - + -
336U VAL* 4.2 22.9 - - + +
341U PRO 2.9 29.1 + - - +
342U THR* 3.9 7.4 - - + +
343U ASN 3.4 0.2 - - - -
344U VAL* 1.3 78.3 - - - +
346U SER* 1.3 60.6 + - - +
347U ILE 3.4 0.2 + - - -
348U THR* 3.6 7.8 + - - +
351U GLN* 2.8 46.0 + - + +
190V ARG* 4.6 1.7 + - - -
311V TYR* 4.2 14.6 + - - +
314V ALA* 6.4 2.9 - - + -
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Residues in contact with SER 346 (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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301U PHE* 3.8 5.2 - - - -
342U THR* 3.3 11.4 + - - -
343U ASN* 2.9 22.0 + - - -
345U ILE* 1.3 78.2 - - - +
347U ILE* 1.3 60.3 + - - +
190V ARG* 3.1 23.7 + - - +
222V MET* 4.2 2.3 - - - +
259V PHE* 5.2 4.2 - - - -
260V ARG* 3.2 40.8 + - - +
263V GLN* 5.1 1.4 + - - -
311V TYR* 4.0 24.7 - - - -
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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
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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