Contacts of the helix formed by residues 322 - 345 (chain U) in PDB entry 6FF7
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 THR 322 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320U ALA 3.8 2.8 + - - -
321U LEU* 1.3 77.7 - - - +
323U GLU* 1.3 66.7 + - - +
324U ASN* 3.2 10.3 - - - -
325U GLU* 3.4 12.8 + - - +
326U MET* 3.1 21.1 + - - +
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Residues in contact with GLU 323 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322U THR* 1.3 74.5 - - - +
324U ASN* 1.3 61.4 + - - +
326U MET* 3.4 7.8 + - - +
327U THR* 3.1 23.7 + - - -
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Residues in contact with ASN 324 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322U THR* 4.0 6.6 - - - -
323U GLU* 1.3 80.8 - - - +
325U GLU* 1.3 56.4 + - - +
327U THR* 3.3 6.8 + - - -
328U THR* 2.9 29.5 + - - -
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Residues in contact with GLU 325 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321U LEU* 4.4 9.9 - - + -
322U THR* 3.4 23.9 + - - +
323U GLU 3.3 0.4 - - - -
324U ASN* 1.3 75.3 - - - +
326U MET* 1.3 59.7 + - - +
328U THR* 3.4 7.0 + - - -
329U ILE* 3.0 29.3 + - - +
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Residues in contact with MET 326 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312U GLU* 6.3 2.7 - - + -
321U LEU* 4.9 7.5 - - + +
322U THR 3.1 13.4 + - - +
323U GLU* 3.5 12.1 - - - +
324U ASN 3.3 0.2 - - - -
325U GLU* 1.3 77.2 - - - +
327U THR* 1.3 62.1 + - - +
329U ILE* 3.3 8.1 + - - +
330U HIS* 3.0 23.3 + - - +
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Residues in contact with THR 327 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274M LYS* 4.9 18.6 - - - -
277M ASP* 6.3 2.5 - - - -
323U GLU 3.1 14.4 + - - -
324U ASN* 3.6 7.4 - - - -
326U MET* 1.3 78.1 - - - +
328U THR* 1.3 52.2 + - - +
330U HIS* 3.3 7.1 + - - +
331U TYR* 2.8 36.4 + - - +
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Residues in contact with THR 328 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274M LYS* 6.1 0.2 - - - +
324U ASN 2.9 17.2 + - - -
325U GLU* 3.6 8.5 - - - -
326U MET 3.3 0.2 - - - -
327U THR* 1.3 74.8 - - - +
329U ILE* 1.3 56.3 + - - +
331U TYR* 3.6 6.2 - - - +
332U ASP* 2.7 37.7 + - - +
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Residues in contact with ILE 329 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325U GLU 3.0 14.4 + - - +
326U MET* 3.5 11.4 - - - +
328U THR* 1.3 75.9 - - - +
330U HIS* 1.3 63.2 + - - +
332U ASP* 3.8 5.6 - - - +
333U ARG* 3.2 22.3 + - - +
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Residues in contact with HIS 330 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326U MET 3.0 12.8 + - - +
327U THR* 3.6 9.6 - - - +
329U ILE* 1.3 76.7 - - - +
331U TYR* 1.3 61.8 + - - +
333U ARG* 3.4 7.6 + - - +
334U ILE* 3.3 21.7 + - - +
411U HIS 5.4 5.6 - - - +
412U GLU 5.9 3.4 - - - +
413U ARG* 6.3 2.9 - - - -
414U ARG 6.3 0.4 - - - +
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Residues in contact with TYR 331 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272M PHE* 6.6 0.2 - - + -
273M GLU* 5.3 13.7 - - + +
274M LYS* 5.5 7.9 - - + +
327U THR 2.8 21.0 + - - +
328U THR* 3.7 7.4 - - - +
330U HIS* 1.3 70.6 - - - +
332U ASP* 1.3 60.4 + - - +
334U ILE* 3.5 6.8 + - - +
335U THR* 2.9 29.7 + - - -
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Residues in contact with ASP 332 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328U THR 2.7 21.7 + - - +
329U ILE* 3.8 6.3 - - - +
330U HIS 3.3 0.2 - - - -
331U TYR* 1.3 73.7 - - - +
333U ARG* 1.3 57.5 + - - +
335U THR* 3.4 7.7 + - - -
336U SER* 3.0 29.5 + - - -
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Residues in contact with ARG 333 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329U ILE 3.2 13.2 + - - +
330U HIS* 3.6 10.8 - - - +
331U TYR 3.3 0.2 - - - -
332U ASP* 1.3 73.9 - - - +
334U ILE* 1.3 65.0 + - - +
336U SER* 3.3 5.6 + - - -
337U LEU* 3.0 23.4 + - - +
410U ARG 4.9 12.8 - - - +
411U HIS* 5.4 8.3 - - + -
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Residues in contact with ILE 334 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330U HIS 3.3 10.1 + - - +
331U TYR* 3.8 9.4 - - - +
333U ARG* 1.3 77.6 - - - +
335U THR* 1.3 58.3 + - - +
337U LEU* 3.1 9.3 + - - +
338U GLN* 2.8 30.7 + - - +
356U VAL* 4.9 16.8 - - + +
360U ASP* 5.3 11.9 - - + -
411U HIS* 5.6 9.8 - - + +
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Residues in contact with THR 335 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331U TYR 2.9 18.6 + - - -
332U ASP* 3.5 9.9 - - - -
334U ILE* 1.3 77.7 - - - +
336U SER* 1.3 57.4 + - - +
338U GLN* 3.3 8.2 + - - +
339U ARG* 3.0 27.0 + - - +
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Residues in contact with SER 336 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332U ASP 3.0 17.1 + - - -
333U ARG* 4.0 4.7 - - - -
335U THR* 1.3 73.7 - - - +
337U LEU* 1.3 65.2 + - - +
339U ARG* 3.6 7.9 - - - +
340U ALA* 3.2 22.5 + - - +
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Residues in contact with LEU 337 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333U ARG 3.0 14.2 + - - +
334U ILE* 3.1 12.1 + - - +
336U SER* 1.3 77.2 - - - +
338U GLN* 1.3 56.6 + - - +
340U ALA* 3.5 6.5 + - - +
341U ALA* 2.9 28.1 + - - +
384U LEU* 6.5 1.3 - - - -
411U HIS* 5.9 5.6 - - + -
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Residues in contact with GLN 338 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307M ILE* 5.1 7.3 - - + +
308M ALA* 5.2 0.2 - - + -
334U ILE 2.8 16.6 + - - +
335U THR* 3.3 8.0 + - - +
337U LEU* 1.3 75.8 - - - +
339U ARG* 1.3 59.1 + - - +
341U ALA* 4.0 7.0 - - - -
342U PHE* 2.8 31.9 + - - +
351U PHE 5.1 1.8 - - - +
352U ALA* 3.5 29.8 - - - +
354U SER 6.1 0.2 - - - +
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Residues in contact with ARG 339 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307M ILE* 5.9 1.8 - - - +
335U THR 3.0 13.8 + - - +
336U SER* 3.6 13.0 - - - +
337U LEU 3.3 0.2 - - - -
338U GLN* 1.3 77.1 - - - +
340U ALA* 1.3 61.6 + - - +
342U PHE* 3.9 5.2 - - - +
343U ALA* 3.2 25.5 + - - +
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Residues in contact with ALA 340 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336U SER 3.2 12.7 + - - +
337U LEU* 3.8 5.8 - - - +
339U ARG* 1.3 76.7 - - - +
341U ALA* 1.3 66.0 + - - +
343U ALA* 4.9 2.9 - - - -
344U HIS* 3.2 28.1 + - + +
345U PHE* 4.1 1.6 + - - +
380U VAL* 5.4 3.8 - - - +
383U TYR* 4.1 29.4 - - + +
384U LEU* 6.5 0.2 - - + -
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Residues in contact with ALA 341 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337U LEU 2.9 18.4 + - - +
338U GLN* 3.5 7.0 - - - +
339U ARG 3.3 0.2 - - - -
340U ALA* 1.3 77.0 - - - +
342U PHE* 1.3 62.3 + - - +
345U PHE* 3.0 40.2 + - - +
348U LEU* 3.9 19.7 - - + +
351U PHE* 5.5 1.6 - - + -
352U ALA* 3.8 16.8 - - + +
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Residues in contact with PHE 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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307M ILE* 5.0 12.8 - - + +
338U GLN 2.8 20.8 + - - +
339U ARG* 3.9 5.4 - - - +
341U ALA* 1.3 75.0 - - - +
343U ALA* 1.3 61.2 + - - +
344U HIS 3.6 0.3 + - - -
345U PHE 4.6 2.6 + - - +
349U TYR* 5.6 3.8 - - - +
352U ALA* 3.7 15.6 - - + +
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Residues in contact with ALA 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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339U ARG 3.2 16.2 + - - +
340U ALA* 4.3 3.1 - - - +
341U ALA 3.3 0.2 - - - -
342U PHE* 1.3 80.5 - - + +
344U HIS* 1.3 61.0 - - + +
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Residues in contact with HIS 344 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340U ALA* 3.2 14.4 + - + +
343U ALA* 1.3 81.8 - - + +
345U PHE* 1.3 60.9 + - + +
346U PRO 4.1 1.1 - - - -
383U TYR* 6.4 2.2 - - + -
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Residues in contact with PHE 345 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340U ALA 4.9 0.9 - - - +
341U ALA* 3.0 26.0 + - - +
342U PHE 4.6 2.6 + - - -
343U ALA 3.9 0.2 - - - -
344U HIS* 1.3 81.9 - - + +
346U PRO* 1.3 59.3 - - - +
347U GLU* 3.2 5.8 - - + +
348U LEU* 3.0 30.9 + - + +
349U TYR* 3.6 3.3 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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