Contacts of the helix formed by residues 395 - 411 (chain A) in PDB entry 6EJ9
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 395 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A GLY* 1.3 71.9 - - - -
396A SER* 1.3 62.3 + - - +
397A LEU 3.2 1.2 + - - -
398A LEU* 3.2 15.9 + - - +
399A SER* 3.5 11.1 + - - +
470A GLU* 2.8 19.7 + - + +
475A MET* 3.6 10.9 - - + +
521A TYR 4.6 3.9 - - - +
522A SER* 3.6 27.6 - - - +
523A TYR* 5.3 0.2 - - - -
524A THR 4.1 11.4 - - - +
527A PRO* 3.8 10.5 - - - +
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Residues in contact with SER 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A MET* 3.7 25.0 - - - +
389A ALA 3.7 12.4 + - - -
390A THR* 3.8 12.5 - - - -
391A ILE 4.3 1.7 + - - -
394A GLY* 4.2 2.4 - - - -
395A ALA* 1.3 78.2 - - - +
397A LEU* 1.3 57.2 + - - +
399A SER* 3.2 11.2 + - - -
400A THR* 2.8 32.4 + - - -
470A GLU* 2.8 30.2 + - - -
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Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A VAL* 4.3 20.4 - - + -
390A THR* 4.3 17.6 - - + +
391A ILE 5.5 2.5 - - - +
393A GLY 6.3 0.9 - - - +
394A GLY 3.4 13.9 + - - +
395A ALA 3.2 1.2 - - - -
396A SER* 1.3 80.9 + - - +
398A LEU* 1.3 61.4 + - - +
400A THR* 3.4 6.8 + - - -
401A TYR* 3.2 57.5 + - + +
494A ASP* 4.1 20.0 - - - +
495A TRP* 6.3 2.2 - - + -
527A PRO* 5.2 3.4 - - + -
528A ALA* 4.3 7.6 - - + -
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Residues in contact with LEU 398 (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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395A ALA 3.2 6.1 + - - +
397A LEU* 1.3 75.7 - - - +
399A SER* 1.3 67.0 + - - +
401A TYR* 3.2 5.3 + - + +
402A LEU* 2.9 47.6 + - + +
518A LYS* 5.8 1.8 - - - +
521A TYR* 3.7 34.5 - - + +
522A SER* 6.0 0.2 - - - -
527A PRO* 3.7 24.4 - - + +
528A ALA* 4.7 5.3 - - - +
531A PHE* 3.8 26.9 - - + -
532A PHE* 3.8 30.5 - - + -
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Residues in contact with SER 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A MET* 4.0 19.2 - - - +
395A ALA* 3.5 10.4 + - - +
396A SER* 3.2 12.5 + - - -
398A LEU* 1.3 78.4 - - - +
400A THR* 1.3 62.2 + - - +
402A LEU* 3.9 7.2 - - - +
403A GLN* 3.0 28.1 + - - +
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Residues in contact with THR 400 (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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331A VAL* 6.0 0.9 - - + -
333A VAL* 4.2 17.9 - - + -
359A HIS* 4.0 22.1 + - + +
386A TRP* 3.3 26.1 - - + -
388A MET* 3.5 17.8 - - - +
390A THR* 3.5 15.1 - - + +
396A SER 2.8 16.9 + - - -
397A LEU* 3.5 13.0 - - + +
399A SER* 1.3 76.3 - - - +
401A TYR* 1.3 65.8 + - + +
404A SER* 3.0 24.0 + - - -
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Residues in contact with TYR 401 (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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331A VAL* 4.7 3.8 - - + -
333A VAL* 3.9 25.3 - - + +
397A LEU* 3.2 46.8 + - + +
398A LEU* 3.2 5.8 + - - +
400A THR* 1.3 79.1 - - + +
402A LEU* 1.3 59.1 + - - +
404A SER* 2.8 21.4 + - - -
405A MET* 2.9 25.8 + - + +
419A PHE* 4.4 14.1 - + - -
421A ASN* 3.2 40.9 + - + +
494A ASP* 4.4 3.8 + - - -
495A TRP* 3.8 18.2 - - - -
496A PHE* 4.4 11.2 - + - -
528A ALA* 4.1 20.0 - - + -
532A PHE* 4.4 16.4 - + + -
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Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LEU* 2.9 46.1 + - + +
399A SER* 4.0 6.1 - - - +
401A TYR* 1.3 76.6 - - - +
403A GLN* 1.3 63.3 + - - +
405A MET* 3.2 15.5 + - + +
406A ARG* 3.1 23.0 + - - +
506A VAL* 3.7 31.4 - - + +
507A THR* 4.9 5.2 + - - +
518A LYS* 4.5 26.9 - - + +
531A PHE* 4.2 11.0 - - + -
532A PHE* 4.5 1.8 - - + -
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Residues in contact with GLN 403 (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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386A TRP* 3.4 39.0 - - + +
388A MET* 6.5 0.2 - - - -
399A SER 3.0 19.0 + - - +
402A LEU* 1.3 76.9 - - - +
404A SER* 1.3 57.8 + - - +
406A ARG* 3.3 22.6 + - - +
407A ASP* 3.0 57.1 + - - +
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Residues in contact with SER 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A VAL* 4.2 15.5 - - - +
357A TYR* 4.3 20.4 - - - -
359A HIS* 6.4 0.7 - - - -
384A THR* 5.3 1.8 - - - -
386A TRP* 3.7 13.6 - - - -
400A THR* 3.0 18.8 + - - -
401A TYR* 2.8 22.7 + - - -
403A GLN* 1.3 77.0 - - - +
405A MET* 1.3 56.7 + - - +
407A ASP* 3.5 1.6 + - - +
408A LEU* 3.0 34.0 + - - +
419A PHE* 4.0 14.2 - - - -
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Residues in contact with MET 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A TYR* 2.9 26.7 + - + +
402A LEU* 3.6 13.9 - - - +
404A SER* 1.3 75.0 - - - +
406A ARG* 1.3 66.7 + - - +
408A LEU* 3.3 6.0 + - - +
409A LEU* 3.0 30.8 + - - +
416A TRP* 5.8 0.2 - - - -
419A PHE* 3.7 40.8 - - + -
496A PHE* 4.6 1.3 - - + -
498A LEU* 4.1 14.6 - - + -
503A VAL* 3.6 31.1 - - + +
506A VAL* 4.9 6.5 - - - -
507A THR* 3.9 5.8 - - - +
532A PHE* 3.7 36.1 - - + -
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Residues in contact with ARG 406 (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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402A LEU 3.1 13.2 + - - +
403A GLN* 3.6 27.6 + - - +
405A MET* 1.3 76.1 - - - +
407A ASP* 1.3 63.5 + - - +
409A LEU* 3.3 5.0 + - - +
410A GLU* 3.2 43.9 + - + +
507A THR* 3.1 43.4 + - + +
508A PHE* 3.7 26.3 - - + -
518A LYS* 4.6 7.5 - - - +
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Residues in contact with ASP 407 (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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357A TYR* 2.9 28.4 + - + +
385A PRO* 5.0 0.7 - - - +
386A TRP* 2.9 31.0 + - - -
403A GLN* 3.0 40.4 + - - +
404A SER 3.6 5.2 - - - +
406A ARG* 1.3 76.1 - - - +
408A LEU* 1.3 62.8 + - - +
410A GLU* 3.1 20.6 + - - +
411A MET* 3.2 22.5 + - + +
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Residues in contact with LEU 408 (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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329A ALA* 4.1 19.7 - - + -
331A VAL* 3.7 28.0 - - + -
357A TYR* 3.9 22.7 - - + -
404A SER 3.0 22.1 + - - +
405A MET* 3.8 4.5 - - - +
407A ASP* 1.3 77.1 - - - +
409A LEU* 1.3 62.2 + - - +
411A MET* 3.3 26.8 + - - +
414A TRP* 4.0 30.1 - - + -
416A TRP* 3.3 28.6 + - + +
419A PHE* 4.1 16.6 - - + -
500A ARG* 5.0 0.7 + - - -
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Residues in contact with LEU 409 (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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405A MET 3.0 20.1 + - - +
406A ARG* 3.8 4.3 - - - +
407A ASP 3.3 0.2 - - - -
408A LEU* 1.3 77.5 - - - +
410A GLU* 1.3 61.4 + - - +
411A MET 3.6 2.9 + - - -
412A THR* 4.9 2.3 + - - -
416A TRP* 3.8 21.8 - - + -
500A ARG* 3.9 34.5 + - + +
503A VAL* 4.0 5.2 - - + +
504A GLU* 3.6 34.8 - - + +
507A THR* 3.7 31.0 - - + +
508A PHE* 3.9 22.9 - - + -
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Residues in contact with GLU 410 (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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406A ARG* 3.2 39.5 + - + +
407A ASP* 3.1 11.4 + - - +
409A LEU* 1.3 75.7 - - - +
411A MET* 1.3 59.4 + - - +
412A THR* 2.9 14.7 + - - -
508A PHE* 5.0 14.1 - - + -
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Residues in contact with MET 411 (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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357A TYR* 3.7 40.2 - - + +
382A ARG* 3.4 30.5 - - - +
407A ASP* 3.2 18.1 + - + +
408A LEU* 3.3 20.2 + - - +
409A LEU 4.5 2.4 - - - +
410A GLU* 1.3 72.3 - - - +
412A THR* 1.3 64.7 + - - +
413A ASP* 3.2 12.6 - - - +
414A TRP* 3.2 45.4 + - + +
500A ARG* 5.5 2.6 + - - -
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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
------------------------------------------------------------
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