Contacts of the helix formed by residues 616 - 634 (chain O) in PDB entry 5A31
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 616 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390O PHE* 5.6 4.7 - - + +
431O LEU* 3.5 38.4 - - + +
432O TYR* 4.9 2.5 - - + -
577O THR* 4.1 15.7 - - + -
578O GLU* 3.9 35.9 - - + +
581O ILE* 4.4 9.2 - - + -
611O SER* 2.9 13.5 + - - +
614O TYR* 3.2 30.3 - - + +
615O ARG* 1.3 71.4 - - - +
617O GLN* 1.3 59.5 + - - +
618O TYR* 3.3 3.1 - - + -
619O LEU* 3.1 21.0 + - + -
620O ALA* 2.9 25.8 + - - +
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Residues in contact with GLN 617 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432O TYR 3.6 18.9 + - - +
433O GLY* 5.0 2.3 + - - -
434O ARG* 3.9 37.6 + - - +
615O ARG 3.3 7.5 + - - +
616O LEU* 1.3 71.3 - - - +
618O TYR* 1.3 60.7 + - - +
620O ALA* 3.8 11.7 - - + -
621O SER* 2.8 38.2 + - - +
650O PRO* 3.5 38.6 + - - +
654O ASP* 4.8 4.4 + - - -
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Residues in contact with TYR 618 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430O ARG* 4.2 19.0 + - - +
431O LEU 5.1 4.7 - - - +
433O GLY* 3.4 34.8 - - - +
435O SER* 4.7 8.3 - - - -
479O GLU* 2.4 46.3 + - - -
480O GLN* 5.7 0.5 + - - -
616O LEU 3.3 0.9 - - - -
617O GLN* 1.3 78.0 - - - +
619O LEU* 1.3 68.7 + - + +
621O SER* 4.2 3.4 - - - -
622O GLU* 3.5 20.1 + - - +
654O ASP 3.5 22.8 + - - -
655O GLY* 3.9 15.5 - - - -
656O ALA* 5.0 2.0 - - + -
659O ASP* 4.5 17.9 - - - +
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Residues in contact with LEU 619 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578O GLU* 4.0 22.0 - - - +
581O ILE* 3.4 35.4 - - + +
582O SER* 3.9 28.0 - - - +
585O LEU* 4.2 7.9 - - + +
611O SER* 4.6 0.2 - - - -
616O LEU* 3.1 26.1 + - + +
617O GLN 3.1 0.2 - - - -
618O TYR* 1.3 87.1 - - + +
620O ALA* 1.3 64.0 + - - +
621O SER 3.3 0.3 + - - -
622O GLU* 3.4 13.9 + - - +
623O THR* 3.0 25.6 + - - +
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Residues in contact with ALA 620 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608O LEU* 5.3 0.4 - - + -
611O SER* 3.2 29.2 + - - +
612O LYS* 5.0 10.5 - - + -
615O ARG 6.1 0.2 - - - -
616O LEU 2.9 15.2 + - - +
617O GLN* 3.6 16.2 - - + +
619O LEU* 1.3 76.1 - - - +
621O SER* 1.3 58.3 + - - +
623O THR* 2.9 5.1 - - - +
624O VAL* 2.7 41.8 + - + +
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Residues in contact with SER 621 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617O GLN* 2.8 27.8 + - - +
618O TYR* 4.2 4.7 - - - -
619O LEU 3.2 0.4 - - - -
620O ALA* 1.3 72.4 - - - +
622O GLU* 1.3 63.5 + - - +
624O VAL* 3.9 5.9 - - - +
625O LEU* 3.0 26.9 + - - +
647O ALA* 4.0 9.2 + - - +
650O PRO* 4.1 12.9 - - - +
651O ILE* 3.4 37.4 + - - +
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Residues in contact with GLU 622 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585O LEU* 4.1 16.2 - - + +
589O GLU* 4.7 9.7 - - - +
618O TYR 3.5 11.6 + - - +
619O LEU* 3.4 17.3 + - + +
621O SER* 1.3 77.9 - - - +
623O THR* 1.3 56.1 + - - +
625O LEU* 3.5 12.5 - - + +
626O ASN* 3.0 32.5 + - - +
659O ASP* 4.2 13.8 - - - +
662O ARG* 3.5 35.8 + - - +
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Residues in contact with THR 623 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581O ILE* 4.4 6.1 - - + -
585O LEU* 3.6 26.7 - - - +
604O LEU* 3.7 10.2 + - - +
608O LEU* 3.4 38.6 - - + +
611O SER* 4.0 2.7 - - - +
619O LEU 3.0 16.3 + - - +
620O ALA* 2.9 29.4 - - - +
622O GLU* 1.3 72.8 - - - +
624O VAL* 1.3 59.5 + - - +
626O ASN* 2.9 8.8 + - - +
627O LEU* 2.8 29.1 + - - +
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Residues in contact with VAL 624 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1753A TYR* 5.0 5.6 - - + +
608O LEU* 3.4 24.9 - - + -
612O LYS* 5.5 3.4 - - + -
620O ALA* 2.7 35.1 + - + +
621O SER* 3.9 4.3 - - - +
623O THR* 1.3 69.3 - - - +
625O LEU* 1.3 66.7 + - - +
627O LEU* 3.2 10.9 + - - +
628O ALA 3.1 16.6 + - - -
643O LEU* 3.6 27.6 - - + +
646O MET* 6.2 0.4 - - + -
647O ALA* 3.4 28.5 - - + +
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Residues in contact with LEU 625 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621O SER 3.0 13.8 + - - +
622O GLU* 3.5 15.5 - - + +
624O VAL* 1.3 78.6 - - - +
626O ASN* 1.3 70.4 + - + +
628O ALA* 3.0 19.0 + - - +
629O PHE* 3.0 10.6 + - - +
644O LEU* 4.4 7.9 - - + -
647O ALA* 4.8 0.4 - - - +
651O ILE* 4.0 28.3 - - + -
659O ASP* 4.7 7.9 - - + +
662O ARG* 4.9 16.4 - - + +
663O ALA* 4.6 18.8 - - + +
666O LEU* 3.7 24.1 - - + +
755O LEU* 3.9 27.1 - - + -
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Residues in contact with ASN 626 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585O LEU* 4.8 13.5 + - - +
588O ALA* 5.8 0.4 - - - -
589O GLU* 5.3 11.3 + - - +
592O TRP* 3.3 32.4 + - - -
604O LEU* 3.9 21.5 - - + +
622O GLU* 3.0 25.0 + - - +
623O THR* 2.9 14.0 + - - +
625O LEU* 1.3 81.3 - - - +
627O LEU* 1.3 59.5 + - - +
629O PHE* 3.2 7.6 + - - +
630O ALA* 3.1 18.9 + - - +
662O ARG* 5.1 5.5 - - - +
755O LEU* 4.0 17.9 - - - +
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Residues in contact with LEU 627 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1753A TYR* 3.9 23.1 - - + -
1754A PHE* 4.2 20.4 - - + -
601O LEU* 4.9 2.7 - - - +
604O LEU* 3.8 30.9 - - + +
605O LEU* 4.3 17.7 - - + -
608O LEU* 3.7 34.3 - - + -
623O THR* 2.8 17.1 + - - +
624O VAL* 3.2 9.8 + - - +
626O ASN* 1.3 72.0 - - - +
628O ALA* 1.3 58.2 + - - +
630O ALA* 2.9 22.1 + - + +
631O GLN* 2.9 25.2 + - - +
643O LEU* 4.7 1.6 - - + -
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Residues in contact with ALA 628 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624O VAL 3.1 3.9 + - - +
625O LEU 3.0 10.9 + - - +
627O LEU* 1.3 78.9 - - - +
629O PHE* 1.3 61.7 + - - +
631O GLN* 3.1 4.8 + - - +
632O LEU* 3.0 19.8 + - - +
640O ALA* 3.2 24.8 - - + +
643O LEU* 3.7 25.9 - - + +
644O LEU* 3.8 22.4 - - + -
666O LEU* 4.0 7.2 - - + -
670O CYS* 4.8 0.6 - - - -
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Residues in contact with PHE 629 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592O TRP* 4.0 26.2 - + - -
625O LEU 3.0 8.7 + - - +
626O ASN 3.2 7.8 + - - +
628O ALA* 1.3 76.4 - - - +
630O ALA* 1.3 63.4 + - - +
632O LEU* 3.3 27.1 + - + +
633O ILE* 3.1 37.0 + - + +
666O LEU* 3.9 18.5 - - + +
669O LYS* 3.8 10.8 - - - -
752O ILE* 3.1 44.0 - - + -
755O LEU* 3.1 45.8 - - + -
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Residues in contact with ALA 630 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1754A PHE* 4.6 6.7 - - + -
592O TRP* 3.5 30.7 - - + -
601O LEU* 3.9 22.4 - - + -
604O LEU* 4.8 2.7 - - + -
626O ASN 3.1 8.5 + - - +
627O LEU* 2.9 17.5 + - + +
629O PHE* 1.3 76.9 - - - +
631O GLN* 1.3 60.2 + - - +
633O ILE* 3.0 5.7 + - - +
634O LEU* 2.9 25.5 + - + +
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Residues in contact with GLN 631 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1753A TYR* 3.4 29.1 + - - +
1754A PHE* 3.5 29.1 - - + -
627O LEU* 2.9 24.2 + - - +
628O ALA* 3.1 2.0 + - - +
630O ALA* 1.3 74.9 - - - +
632O LEU* 1.3 61.6 + - - +
634O LEU* 3.3 2.5 + - - +
635O GLY 3.2 4.7 + - - -
636O ILE* 3.0 40.4 + - + +
639O GLN* 3.4 8.2 - - + +
640O ALA* 3.0 38.5 + - + -
643O LEU* 3.4 27.3 - - - +
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Residues in contact with LEU 632 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628O ALA 3.0 8.2 + - - +
629O PHE* 3.5 36.3 - - + +
630O ALA 3.2 0.2 - - - -
631O GLN* 1.3 76.1 - - - +
633O ILE* 1.3 75.5 + - + +
635O GLY* 3.2 12.5 + - - -
637O PRO* 4.2 19.8 - - + +
640O ALA* 3.9 0.6 - - - +
666O LEU* 4.1 9.2 - - + -
669O LYS* 4.6 17.5 - - + +
670O CYS* 3.9 34.5 - - - +
673O ALA* 5.2 9.3 - - + +
752O ILE* 6.2 1.8 - - + -
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Residues in contact with ILE 633 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1795A GLN* 4.4 6.8 + - - -
1799A ARG* 5.9 0.9 + - - -
592O TRP* 3.6 38.6 - - + -
597O PRO* 5.0 11.0 - - + -
629O PHE* 3.1 24.5 + - + +
630O ALA 3.0 12.0 + - - +
632O LEU* 1.3 88.5 - - + +
634O LEU* 1.3 74.5 + - + +
635O GLY 3.2 1.1 + - - -
752O ILE* 4.3 18.2 - - + +
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Residues in contact with LEU 634 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1754A PHE* 3.6 28.9 - - + -
1767A ILE* 4.2 12.6 - - - +
1771A PHE* 3.9 19.5 - - + -
1791A ILE* 4.5 7.2 - - + -
1795A GLN* 3.3 42.1 + - + +
592O TRP* 5.7 0.7 - - + -
597O PRO* 5.8 1.8 - - + -
598O THR* 5.3 9.9 - - - +
601O LEU* 4.1 27.8 - - + -
630O ALA 2.9 18.2 + - - +
631O GLN 3.3 4.7 + - - +
633O ILE* 1.3 92.8 - - + +
635O GLY* 1.3 59.3 + - - +
636O ILE* 3.4 8.0 + - + +
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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