Contacts of the helix formed by residues 366 - 382 (chain A) in PDB entry 3TT9
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 366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A HIS* 3.1 40.6 + - + +
365A MET* 1.3 76.3 - - - +
367A PRO* 1.4 72.1 - - + +
368A SER* 3.3 2.0 - - - +
369A ARG* 3.1 21.4 + - + +
370A ILE* 3.1 24.0 + - - +
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Residues in contact with PRO 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A MET 3.1 12.3 - - - +
366A LEU* 1.4 85.3 - - + +
368A SER* 1.3 59.1 + - - +
370A ILE 3.8 0.2 - - - -
371A SER* 2.8 36.0 + - - +
406A VAL* 5.5 1.8 - - + -
408A ASN* 3.6 34.3 - - + +
410A ASP* 5.7 1.6 - - + -
411A VAL* 3.6 18.5 - - + +
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Residues in contact with SER 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A LEU* 3.3 1.6 - - - +
367A PRO* 1.3 80.9 - - - +
369A ARG* 1.3 59.1 + - - +
371A SER* 4.5 4.0 - - - -
372A ALA* 2.9 30.8 + - - +
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Residues in contact with ARG 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A MET* 5.8 2.6 - - - -
355A ARG* 4.7 8.9 - - - +
358A SER* 4.3 2.6 + - - -
359A MET* 3.7 51.4 + - + +
361A GLU* 2.9 37.8 + - - -
364A HIS* 3.3 23.4 + - + -
366A LEU* 3.1 27.3 + - + +
368A SER* 1.3 76.7 - - - +
370A ILE* 1.3 67.5 + - - +
373A ALA* 3.1 24.9 + - - +
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Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A MET 4.8 2.5 - - - +
360A LEU* 4.3 8.7 - - + +
364A HIS* 3.6 15.9 - - + -
365A MET* 4.1 22.4 - - - -
366A LEU 3.1 18.3 + - - +
367A PRO 3.9 2.9 - - - +
369A ARG* 1.3 76.8 - - - +
371A SER* 1.3 58.6 + - - +
373A ALA* 3.3 1.4 + - - +
374A ALA* 2.8 28.2 + - - +
403A LEU* 3.9 43.3 - - + -
406A VAL* 4.2 12.3 - - + -
411A VAL* 3.7 29.8 - - + +
415A VAL* 4.1 11.7 - - + -
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Residues in contact with SER 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A PRO 2.8 23.9 + - - -
368A SER* 4.1 4.3 - - - -
370A ILE* 1.3 73.4 - - - +
372A ALA* 1.3 58.2 + - - +
375A THR* 2.7 38.9 + - - +
410A ASP* 3.6 25.9 + - - +
411A VAL* 3.7 11.6 + - - -
414A ALA* 3.9 13.9 - - - -
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Residues in contact with ALA 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A MET* 6.2 1.1 - - + -
351A MET* 3.8 10.1 - - + +
359A MET* 4.4 12.6 - - + -
368A SER 2.9 19.7 + - - +
369A ARG* 4.0 3.4 - - - +
371A SER* 1.3 75.8 - - - +
373A ALA* 1.3 58.1 + - - +
375A THR* 3.5 6.9 + - - -
376A PHE* 3.1 27.7 + - - +
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Residues in contact with ALA 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A MET* 4.2 4.0 - - - +
356A ALA* 3.3 35.4 - - - +
359A MET* 3.8 12.8 - - + +
360A LEU* 3.7 14.6 - - + -
369A ARG 3.1 17.9 + - - +
372A ALA* 1.3 75.6 - - - +
374A ALA* 1.3 65.0 + - - +
376A PHE* 3.3 4.0 + - - +
377A ILE* 3.1 27.8 + - - +
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Residues in contact with ALA 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A LEU* 4.3 1.7 - - + +
370A ILE* 2.8 21.7 + - + +
373A ALA* 1.3 70.0 - - - +
375A THR* 1.3 61.0 + - - +
377A ILE* 3.3 6.6 + - - +
378A GLN* 2.9 24.4 + - - +
400A LEU* 3.9 25.6 - - + -
414A ALA* 3.6 30.3 - - + +
415A VAL* 4.0 6.5 - - + +
418A ALA* 3.4 9.0 - - - +
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Residues in contact with THR 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A SER* 2.7 30.7 + - - +
372A ALA* 3.5 6.9 + - - -
374A ALA* 1.3 72.8 - - - +
376A PHE* 1.3 67.6 + - - +
378A GLN* 3.7 19.5 - - - +
379A HIS* 2.8 48.2 + - + -
414A ALA* 3.6 19.5 - - + -
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Residues in contact with PHE 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A MET* 3.5 44.9 - - + -
352A THR* 3.4 21.5 - - - -
353A LEU* 3.4 36.3 - - + -
356A ALA* 4.0 7.0 - - + -
372A ALA 3.1 21.2 + - - +
373A ALA 3.5 5.6 - - - +
374A ALA 3.3 0.2 - - - -
375A THR* 1.3 76.4 + - - +
377A ILE* 1.3 59.1 + - - +
379A HIS* 3.3 9.3 + - + +
380A GLU* 2.9 46.6 + - + +
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Residues in contact with ILE 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A LEU* 4.1 15.3 - - + -
356A ALA* 4.0 13.9 - - + -
357A VAL* 4.1 17.0 - - + -
360A LEU* 4.0 26.7 - - + -
373A ALA 3.1 17.0 + - - +
374A ALA* 3.6 9.2 - - - +
375A THR 3.2 0.4 - - - -
376A PHE* 1.3 75.3 - - - +
378A GLN* 1.3 65.3 + - - +
380A GLU 3.3 0.3 + - - -
381A CYS* 2.9 28.9 + - - +
391A VAL* 4.0 22.0 - - + -
400A LEU* 4.5 8.7 - - + -
418A ALA* 4.1 6.7 - - + -
422A LEU* 4.0 24.5 - - + -
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Residues in contact with GLN 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A ALA 2.9 18.2 + - - +
375A THR* 3.5 21.1 - - - +
377A ILE* 1.3 73.4 - - - +
379A HIS* 1.3 86.9 + - - +
381A CYS 3.4 0.7 + - - -
382A PHE* 3.2 9.5 + - - +
413A ARG 5.0 0.4 + - - -
414A ALA* 4.8 4.8 + - - +
417A GLY* 3.6 26.8 - - - +
418A ALA* 3.7 18.1 - - - +
421A ASN* 2.9 39.0 + - - +
457A GLN* 4.0 9.2 + - - -
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Residues in contact with HIS 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A THR* 2.8 41.2 + - + +
376A PHE* 3.8 7.4 - + + +
378A GLN* 1.3 95.2 + - - +
380A GLU* 1.3 66.1 + - - +
382A PHE* 3.4 19.8 + - - +
383A GLN 4.7 0.7 + - - -
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Residues in contact with GLU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A LEU* 4.0 24.8 - - + +
376A PHE* 2.9 41.5 + - + +
377A ILE 4.0 2.5 - - - +
379A HIS* 1.3 76.3 - - - +
381A CYS* 1.3 60.4 + - - +
382A PHE 3.4 0.9 + - - -
383A GLN 4.2 0.3 + - - -
384A LYS* 2.9 56.5 + - + +
387A ALA* 3.6 17.9 - - + +
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Residues in contact with CYS 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A LEU* 5.4 0.2 - - - -
377A ILE* 2.9 26.0 + - - +
378A GLN 3.8 0.7 - - - -
380A GLU* 1.3 74.9 - - - +
382A PHE* 1.3 65.1 + - - +
383A GLN 3.3 1.3 - - - -
384A LYS 4.1 7.9 - - - -
387A ALA* 3.7 26.7 - - - -
388A ARG* 2.9 26.3 + - + -
391A VAL* 4.3 1.6 - - - -
421A ASN* 3.5 28.0 - - + +
422A LEU* 3.6 32.5 - - + +
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Residues in contact with PHE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A GLN 3.2 10.0 + - - +
379A HIS* 3.5 16.8 - - - +
380A GLU 3.3 1.4 - - - -
381A CYS* 1.3 75.8 - - - +
383A GLN* 1.3 95.5 + - + +
388A ARG* 3.1 12.3 + - - -
421A ASN* 3.7 20.9 - - - +
424A PHE* 5.0 4.7 - - - +
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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