Contacts of the helix formed by residues 329 - 345 (chain T) 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 ASP 329 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A PRO* 5.4 0.2 - - - -
328T ILE* 1.3 76.5 - - - +
330T LYS* 1.3 67.1 + - - +
331T ARG* 3.2 7.6 - - + +
332T VAL* 3.3 8.0 + - + +
333T GLN* 3.1 23.0 + - - +
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Residues in contact with LYS 330 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329T ASP* 1.3 74.7 - - - +
331T ARG* 1.3 57.4 + - - +
333T GLN* 3.3 5.8 + - - +
334T TYR* 2.9 33.6 + - - +
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Residues in contact with ARG 331 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287T ASP* 5.4 11.4 - - + -
329T ASP* 3.2 6.1 - - + +
330T LYS* 1.3 79.1 - - - +
332T VAL* 1.3 61.3 + - - +
334T TYR* 3.9 5.0 - - - +
335T MET* 3.2 22.7 + - - +
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Residues in contact with VAL 332 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ILE 5.7 0.9 - - - +
286T THR 5.9 0.9 - - - +
287T ASP* 5.4 11.6 - - + +
290T VAL* 5.0 16.5 - - + +
328T ILE* 4.2 16.4 - - + -
329T ASP* 3.3 12.4 + - + +
331T ARG* 1.3 75.8 - - - +
333T GLN* 1.3 65.6 + - - +
335T MET* 3.3 5.8 + - - +
336T ILE* 3.1 26.1 + - - +
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Residues in contact with GLN 333 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A ILE 4.9 2.8 - - - +
357A ASN 5.4 0.2 - - - -
358A PRO* 1.9 52.2 - - + +
359A ILE 5.1 0.4 - - - +
328T ILE* 4.9 0.6 - - - +
329T ASP 3.1 14.7 + - - +
330T LYS* 3.8 6.5 - - - +
332T VAL* 1.3 76.7 - - - +
334T TYR* 1.3 59.2 + - - +
336T ILE* 4.1 3.5 - - - +
337T GLU* 3.4 22.0 + - - +
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Residues in contact with TYR 334 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330T LYS 2.9 18.1 + - - +
331T ARG* 3.9 6.3 - - - +
333T GLN* 1.3 75.4 - - - +
335T MET* 1.3 58.9 + - - +
336T ILE 3.2 1.8 - - - -
337T GLU* 3.4 4.9 + - - +
338T VAL* 3.0 27.9 + - - +
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Residues in contact with MET 335 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290T VAL* 5.4 7.6 - - + +
291T GLU* 5.5 7.0 - - + -
294T ILE* 4.3 20.7 - - + +
331T ARG 3.2 15.5 + - - +
332T VAL* 3.3 6.3 + - - +
334T TYR* 1.3 78.7 - - - +
336T ILE* 1.3 58.0 + - - +
338T VAL* 3.5 8.7 + - - +
339T MET* 3.1 24.1 + - - +
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Residues in contact with ILE 336 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294T ILE* 5.9 0.9 - - - -
319T LEU* 5.0 16.3 - - + +
323T LEU* 4.8 18.4 - - + -
332T VAL 3.1 16.0 + - - +
333T GLN* 4.3 4.3 - - - +
335T MET* 1.3 73.6 - - - +
337T GLU* 1.3 65.6 + - - +
338T VAL 3.1 1.6 - - - -
339T MET* 3.0 17.5 + - - +
340T PHE* 3.0 14.0 + - - +
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Residues in contact with GLU 337 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A LEU 4.9 13.5 - - - +
356A ILE* 4.9 14.1 - - + +
333T GLN 3.4 16.2 + - - +
334T TYR* 3.4 7.7 + - - +
336T ILE* 1.3 77.8 - - - +
338T VAL* 1.3 62.5 + - - +
340T PHE* 3.5 6.7 + - - +
341T ALA* 3.0 23.2 + - - +
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Residues in contact with VAL 338 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334T TYR 3.0 14.6 + - - +
335T MET* 3.5 12.3 - - - +
336T ILE 3.1 0.2 - - - -
337T GLU* 1.3 77.6 - - - +
339T MET* 1.3 57.5 + - - +
341T ALA* 3.1 8.4 + - - +
342T VAL* 2.9 28.6 + - - +
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Residues in contact with MET 339 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294T ILE* 4.8 15.9 - - + +
297T LEU* 6.0 4.9 - - + -
335T MET 3.1 13.9 + - - +
336T ILE* 3.0 12.7 + - - +
338T VAL* 1.3 77.6 - - - +
340T PHE* 1.3 61.4 - - - +
342T VAL* 3.4 8.2 + - - +
343T ARG* 3.1 21.7 + - - +
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Residues in contact with PHE 340 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A PRO* 6.2 3.1 - - + -
355A LEU 5.2 11.2 - - - +
336T ILE 3.0 13.6 + - - +
337T GLU* 4.0 7.0 - - - +
339T MET* 1.3 76.7 - - - +
341T ALA* 1.3 58.7 + - - +
343T ARG* 3.4 7.6 + - - +
344T LYS* 3.0 28.4 + - - +
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Residues in contact with ALA 341 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337T GLU 3.0 15.5 + - - +
338T VAL* 3.3 12.1 - - - +
340T PHE* 1.3 78.0 - - - +
342T VAL* 1.3 62.3 + - - +
344T LYS* 3.3 8.1 + - - +
345T ASP* 3.1 23.0 + - - +
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Residues in contact with VAL 342 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298T LYS* 5.9 10.1 - - + -
338T VAL 2.9 13.5 + - - +
339T MET* 3.6 11.2 - - - +
341T ALA* 1.3 73.9 - - - +
343T ARG* 1.3 63.5 + - - +
345T ASP* 3.4 5.0 + - - +
346T GLY 3.3 3.6 + - - -
347T PHE* 2.9 34.0 + - + +
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Residues in contact with ARG 343 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339T MET 3.1 13.6 + - - +
340T PHE* 3.8 10.5 - - - +
342T VAL* 1.3 75.6 - - - +
344T LYS* 1.3 62.7 + - - +
346T GLY* 3.1 14.1 + - - -
347T PHE* 4.8 2.2 - - - +
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Residues in contact with LYS 344 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340T PHE 3.0 17.7 + - - +
341T ALA* 3.5 8.5 - - - +
342T VAL 3.2 0.2 - - - -
343T ARG* 1.3 77.9 - - - +
345T ASP* 1.3 56.8 + - - +
346T GLY* 3.1 3.7 + - - -
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Residues in contact with ASP 345 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341T ALA 3.1 14.9 + - - +
342T VAL* 3.4 4.2 + - - +
344T LYS* 1.3 75.7 - - - +
346T GLY* 1.3 61.9 + - - +
347T PHE 3.3 2.0 + - - +
348T LYS* 3.5 24.5 + - + +
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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