Contacts of the helix formed by residues 374 - 391 (chain B) in PDB entry 7ATU
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 374 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373B PHE* 1.3 74.7 - - - +
375B GLU* 1.3 56.5 + - - +
376B GLU* 3.4 13.0 + - - +
377B THR* 2.6 59.4 + - - +
378B GLN* 2.8 10.2 + - - -
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Residues in contact with GLU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B PHE 4.2 0.8 + - - -
374B ASP* 1.3 71.4 - - - +
376B GLU* 1.3 56.8 + - - +
378B GLN* 3.5 16.0 + - - +
379B ARG* 2.8 32.1 + - - +
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Residues in contact with GLU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ASP* 2.8 15.3 + - - +
375B GLU* 1.3 78.1 - - - +
377B THR* 1.3 55.2 + - - +
379B ARG* 3.8 5.7 + - - +
380B THR* 3.2 26.7 + - - +
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Residues in contact with THR 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B PHE* 3.6 22.8 - - + -
374B ASP* 2.6 52.2 + - - +
376B GLU* 1.3 74.6 - - - +
378B GLN* 1.3 56.6 + - - -
380B THR* 3.7 15.0 + - - -
381B PHE* 3.1 26.0 - - - -
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Residues in contact with GLN 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B LEU* 3.4 51.0 + - + +
373B PHE* 4.2 13.6 + - + +
374B ASP 2.8 12.7 + - - +
375B GLU* 3.2 15.3 + - - +
377B THR* 1.3 78.2 - - - +
379B ARG* 1.3 59.0 + - - +
380B THR 3.4 0.4 - - - -
381B PHE* 3.7 9.0 - - - +
382B LEU* 3.3 23.7 + - - +
404B TYR* 5.6 1.0 + - - -
408B ARG* 5.6 2.0 - - - +
409B LEU* 4.0 32.7 - - + +
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Residues in contact with ARG 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B GLU 2.8 16.1 + - - +
376B GLU* 4.1 7.6 - - - +
377B THR 3.5 0.2 - - - -
378B GLN* 1.3 78.4 - - - +
380B THR* 1.3 60.6 + - + +
381B PHE 3.3 0.2 - - - -
382B LEU* 3.2 9.2 + - - +
383B LYS* 2.9 26.7 + - - +
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Residues in contact with THR 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B GLU 3.2 18.2 - - - +
377B THR* 3.7 15.8 + - - -
379B ARG* 1.3 76.3 - - + +
381B PHE* 1.3 69.8 + - - +
383B LYS* 3.5 8.8 + - - +
384B GLU* 3.2 32.9 + - - +
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Residues in contact with PHE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B LEU* 4.3 14.4 - - + -
373B PHE* 3.4 40.4 - + - -
377B THR* 3.1 25.6 - - - -
378B GLN* 3.7 13.8 + - - +
379B ARG 3.3 0.4 - - - -
380B THR* 1.3 82.5 + - - +
382B LEU* 1.3 54.9 + - - +
384B GLU* 2.7 31.1 + - - +
385B VAL* 3.1 14.1 + - - +
388B MET* 4.8 1.6 - - - +
411B PHE* 4.3 15.3 - + + -
481B LEU* 3.8 32.8 - - + -
483B ARG* 3.7 34.5 + - - +
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B GLN 3.3 10.3 + - - +
379B ARG* 3.2 13.3 + - - +
381B PHE* 1.3 78.3 - - - +
383B LYS* 1.3 60.6 + - - +
384B GLU 3.4 0.2 + - - -
385B VAL* 3.6 20.6 + - + +
386B LYS 5.1 0.2 + - - -
402B VAL* 3.7 29.8 - - + -
404B TYR* 3.8 23.3 - - + +
409B LEU* 3.7 24.2 - - + -
411B PHE* 4.5 1.1 - - + -
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Residues in contact with LYS 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B ARG 2.9 16.2 + - - +
380B THR* 3.8 10.1 - - - +
381B PHE 3.1 0.2 - - - -
382B LEU* 1.3 76.8 - - - +
384B GLU* 1.3 61.4 + - + +
385B VAL 3.7 0.3 + - - -
386B LYS* 4.2 21.0 + - - +
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Residues in contact with GLU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B THR* 3.2 19.3 + - - +
381B PHE* 2.7 22.8 + - - +
383B LYS* 1.3 72.1 - - + +
385B VAL* 1.3 60.9 + - - -
386B LYS 3.0 4.9 + - - -
387B VAL* 3.1 19.3 + - + +
388B MET* 3.2 14.6 + - - +
483B ARG* 3.2 31.4 + - - +
484B LEU* 5.8 1.6 - - - +
485B MET* 3.9 37.6 + - - +
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Residues in contact with VAL 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B PHE 3.1 13.7 + - - +
382B LEU* 3.6 33.4 - - + +
383B LYS 3.4 1.0 - - - -
384B GLU* 1.3 77.1 - - - +
386B LYS* 1.3 62.7 + - - +
388B MET* 3.7 21.7 - - + -
389B ARG* 3.0 46.1 + - - +
399B PHE* 3.5 20.4 - - + -
402B VAL* 4.0 14.4 - - + -
411B PHE* 4.3 3.4 - - + -
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Residues in contact with LYS 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A GLY* 4.5 10.9 - - - +
614A HIS* 5.7 4.9 - - + +
615A LEU* 3.8 17.6 - - + +
616A PRO* 6.5 0.7 - - + -
331B HIS* 5.6 11.2 - - + -
382B LEU 5.1 0.2 + - - -
383B LYS 4.2 15.8 + - - +
384B GLU 3.0 0.6 + - - -
385B VAL* 1.3 79.7 - - - +
387B VAL* 1.3 67.1 + - + +
389B ARG* 3.4 14.9 + - - +
390B CYS* 3.6 19.2 + - - -
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Residues in contact with VAL 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A MET* 5.8 1.8 - - - -
615A LEU* 3.7 32.8 - - + -
616A PRO* 6.0 1.6 - - + -
384B GLU* 3.1 12.3 + - + +
386B LYS* 1.3 75.8 - - + +
388B MET* 1.3 66.6 + - - +
390B CYS* 3.3 9.4 + - - +
391B LEU* 3.4 28.2 + - + +
454B MET* 5.8 3.4 - - + +
456B ILE* 4.8 6.5 - - + -
485B MET* 4.5 26.7 - - + -
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Residues in contact with MET 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B PHE 4.8 1.6 - - - +
384B GLU 3.2 15.1 + - - +
385B VAL* 3.9 15.3 - - + +
386B LYS 3.3 0.2 - - - -
387B VAL* 1.3 77.0 - - - +
389B ARG* 1.3 62.3 + - - +
390B CYS 3.3 0.7 + - - -
391B LEU* 3.7 13.1 + - + +
399B PHE* 3.6 45.9 + - + +
411B PHE* 3.7 26.0 - - + -
481B LEU* 4.9 1.3 - - - -
483B ARG* 3.2 34.5 - - - +
485B MET* 4.5 10.1 - - + -
701B RXN 3.2 41.8 + - + +
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Residues in contact with ARG 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B MET* 4.0 16.0 - - - +
330B PRO 3.5 17.7 + - - -
331B HIS* 2.8 51.5 + - - +
332B ARG* 4.1 4.7 - - - +
385B VAL* 3.0 40.7 + - - +
386B LYS* 3.9 8.8 + - - +
387B VAL 3.3 0.4 - - - -
388B MET* 1.3 77.5 - - - +
390B CYS* 1.3 62.1 + - - +
391B LEU 3.6 4.3 - - - +
399B PHE* 4.0 23.7 - - + +
400B ILE 4.1 18.4 + - - +
401B GLY* 4.4 8.9 - - - -
402B VAL 5.5 0.6 - - - +
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Residues in contact with CYS 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608A ARG* 2.6 36.9 + - - +
609A MET* 4.1 27.7 - - + +
612A ALA* 4.0 9.6 - - - -
613A GLY* 3.4 37.9 - - - -
615A LEU* 4.2 5.8 - - + -
329B MET 6.1 0.4 - - - -
386B LYS 3.6 13.9 + - - +
387B VAL 3.3 4.9 + - - +
388B MET 3.2 0.8 - - - -
389B ARG* 1.3 81.0 - - - +
391B LEU* 1.3 62.2 + - - +
392B GLU* 3.9 0.7 - - - +
450B TYR* 4.0 0.2 + - - -
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A MET* 5.1 3.6 - - - -
387B VAL* 3.4 24.6 + - + +
388B MET* 4.1 8.4 - - + +
389B ARG 3.6 5.4 - - - +
390B CYS* 1.3 76.7 - - - +
392B GLU* 1.3 60.1 + - - +
393B HIS 4.2 0.9 - - - -
396B VAL* 4.6 6.7 - - + -
397B LEU 5.6 0.8 - - - +
398B LYS* 5.6 8.1 - - - +
450B TYR* 3.1 25.1 - - + +
451B LEU* 3.9 13.0 - - + -
454B MET* 4.1 18.8 - - + -
456B ILE* 4.4 11.9 - - + -
485B MET* 6.0 1.3 - - + -
701B RXN 3.6 49.1 + - + +
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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