Contacts of the helix formed by residues 545 - 563 (chain B) in PDB entry 5MJ6
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 545 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B LYS* 3.2 26.6 + - - +
528B HIS* 4.0 14.9 + - - -
542B GLU 3.5 15.2 - - - +
543B MET 3.0 17.6 + - - +
544B PHE* 1.3 76.6 - - - +
546B SER* 1.3 64.7 + - - +
547B LEU* 3.1 18.9 + - - +
548B SER* 3.4 9.9 + - - -
549B TYR* 3.2 19.5 - - - -
961B TYR* 4.7 1.8 - - - -
964B GLN* 3.8 22.4 - - - +
1127B 7O2 3.8 11.9 - - - -
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Residues in contact with SER 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B LYS* 5.7 2.3 - - - +
518B THR* 3.8 23.5 + - - -
521B LYS* 3.8 27.2 + - - +
545B ASP* 1.3 74.5 - - - +
547B LEU* 1.3 57.3 + - - +
549B TYR* 3.3 1.3 + - - -
550B PHE* 2.9 45.3 + - - +
551B LYS 3.7 0.5 + - - -
961B TYR* 5.5 3.5 - - - -
1127B 7O2 4.2 9.7 - - - -
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Residues in contact with LEU 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B THR* 3.9 14.6 - - + +
521B LYS* 4.9 10.1 - - + -
522B ASP* 3.5 38.4 - - + +
527B SER* 3.3 25.6 - - - +
528B HIS* 3.3 36.6 - - + +
529B PRO 5.4 0.7 - - - -
530B ILE* 3.4 8.2 - - + +
545B ASP* 3.1 16.2 + - - +
546B SER* 1.3 77.7 - - - +
548B SER* 1.3 64.7 + - - +
551B LYS* 3.0 39.4 + - + +
552B GLY 3.1 3.6 + - - -
1002B GLU* 5.9 0.4 - - - +
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Residues in contact with SER 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B LEU* 4.4 8.0 - - - +
484B TRP* 3.5 34.9 + - - +
487B GLU* 4.4 1.8 - - - -
488B GLY* 3.4 20.2 + - - -
528B HIS* 5.1 1.6 + - - -
530B ILE* 4.2 6.0 + - - -
543B MET* 2.9 42.2 + - - +
545B ASP* 3.4 6.7 + - - -
546B SER 3.4 0.4 - - - -
547B LEU* 1.3 80.0 - - - +
549B TYR* 1.3 66.2 + - - +
552B GLY* 3.7 2.6 - - - -
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Residues in contact with TYR 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B HIS* 4.1 1.1 - - - -
483B LEU* 5.2 0.2 - - + -
487B GLU* 3.2 37.9 + - + -
488B GLY* 3.7 1.4 - - - -
491B THR* 3.5 23.1 - - - +
544B PHE* 3.6 20.8 - + - -
545B ASP 3.2 22.4 - - - +
546B SER 3.3 3.7 + - - +
547B LEU 3.2 0.6 - - - -
548B SER* 1.3 79.7 - - - +
550B PHE* 1.3 66.9 + - + +
551B LYS 3.6 0.2 - - - -
552B GLY 4.0 0.2 - - - -
553B SER* 3.0 26.9 + - - -
1126B ZN 3.7 2.0 - - - -
1127B 7O2 2.6 101.4 + + + +
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Residues in contact with PHE 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B THR* 3.8 23.8 - - + -
495B TYR* 4.4 17.3 - + - -
511B PHE* 4.4 10.1 - + - -
514B ALA* 3.5 33.9 - - + +
515B ARG* 4.4 4.3 - - + +
518B THR* 3.2 30.7 - - - +
546B SER* 2.9 20.3 + - - +
549B TYR* 1.3 74.3 - - + +
551B LYS* 1.3 61.9 + - - +
552B GLY 3.3 0.9 - - - -
553B SER* 3.3 4.2 + - - -
554B SER* 2.7 31.6 + - - -
1127B 7O2 3.4 40.8 - + - -
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Residues in contact with LYS 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B THR* 3.8 6.7 - - + +
522B ASP* 2.9 22.3 + - - +
528B HIS 5.5 1.2 + - - +
530B ILE* 4.0 21.6 - - + +
546B SER 3.7 1.8 + - - -
547B LEU* 3.0 29.7 + - + +
550B PHE* 1.3 75.0 - - - +
552B GLY* 1.3 64.6 + - - +
554B SER* 3.2 6.0 + - - -
555B LEU* 3.1 29.9 + - + +
610B TRP* 4.0 20.8 + - - +
613B GLN 4.0 10.7 + - - -
614B LYS* 4.7 1.0 - - - +
615B GLY 2.8 34.1 + - - +
699B TYR* 3.6 31.4 - - + +
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Residues in contact with GLY 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B TRP* 3.7 14.7 - - - -
488B GLY* 3.8 7.2 - - - -
530B ILE* 3.3 17.6 - - - +
547B LEU 3.1 9.7 + - - -
548B SER 3.7 12.7 + - - -
550B PHE 3.3 0.4 - - - -
551B LYS* 1.3 79.2 - - - +
553B SER* 1.3 59.3 + - - +
555B LEU* 3.4 10.8 + - - +
556B LEU* 3.5 16.6 + - - +
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Residues in contact with SER 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B GLY* 3.3 21.5 - - - -
491B THR* 3.5 3.8 - - - +
492B PHE* 3.6 27.1 - - - -
511B PHE* 3.5 19.0 - - - -
549B TYR 3.0 17.2 + - - -
550B PHE* 3.3 12.8 + - - -
552B GLY* 1.3 73.5 - - - +
554B SER* 1.3 58.4 + - - +
556B LEU* 3.4 4.0 + - - +
557B LEU* 2.9 29.7 + - - +
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Residues in contact with SER 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B ARG* 3.0 32.0 - - - +
550B PHE 2.7 24.0 + - - -
551B LYS 3.2 6.0 + - - -
553B SER* 1.3 74.4 + - - +
555B LEU* 1.3 60.9 + - - +
557B LEU* 3.4 8.2 + - - +
558B MET* 3.0 28.8 + - - +
697B ASN 4.4 3.3 - - - +
699B TYR* 3.6 35.1 - - - +
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Residues in contact with LEU 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B TRP* 4.1 21.1 - - + -
530B ILE* 4.5 12.8 - - + -
551B LYS* 3.1 24.8 + - + +
552B GLY 3.6 4.9 - - - +
554B SER* 1.3 74.5 - - - +
556B LEU* 1.3 61.1 + - + +
558B MET* 3.1 12.0 + - + +
559B LEU* 2.9 30.8 + - - +
590B TRP* 5.2 0.7 - - + -
607B MET* 3.9 17.9 - - + +
610B TRP* 3.8 44.9 - - + +
611B THR* 4.0 26.2 - - + -
699B TYR* 5.1 5.2 - - + -
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Residues in contact with LEU 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B TRP* 4.5 11.4 - - + -
488B GLY 4.1 5.8 - - - -
489B PHE* 3.5 72.5 - - + +
492B PHE* 4.0 18.8 - - + -
552B GLY 3.5 10.3 + - - +
553B SER 3.4 6.7 + - - +
554B SER 3.3 0.2 - - - -
555B LEU* 1.3 77.8 - - - +
557B LEU* 1.3 51.2 + - - +
559B LEU* 3.3 7.2 + - + +
560B LYS* 2.8 36.6 + - - +
568B PHE* 3.7 14.9 - - + -
589B LEU* 4.5 11.4 - - + -
590B TRP* 4.9 9.0 - - + -
593B PHE* 5.2 1.8 - - + -
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Residues in contact with LEU 557 (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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492B PHE* 3.6 19.0 - - + -
511B PHE* 3.7 17.7 - - + -
515B ARG* 3.6 38.8 - - - +
553B SER 2.9 18.5 + - - +
554B SER* 3.6 5.4 - - - +
556B LEU* 1.3 76.0 - - - +
558B MET* 1.3 57.1 + - - +
560B LYS* 4.0 17.4 - - - +
561B THR* 2.9 42.4 + - - +
697B ASN* 4.1 22.4 - - - +
1129B BR 4.3 12.8 - - + -
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Residues in contact with MET 558 (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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554B SER 3.0 15.0 + - - +
555B LEU* 3.4 13.7 - - + +
557B LEU* 1.3 75.5 - - - +
559B LEU* 1.3 65.4 + - - +
561B THR* 3.5 4.5 + - - -
562B TYR* 3.1 25.5 + - - +
606B MET* 5.1 2.5 - - + -
607B MET* 4.5 8.5 - - + -
610B TRP* 3.4 54.7 - - + +
655B PRO* 3.9 28.7 - - + +
697B ASN 3.7 16.6 - - - +
698B GLY* 4.0 6.5 - - - -
699B TYR* 3.6 23.3 - - + -
700B TYR* 4.9 2.7 - - - -
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Residues in contact with LEU 559 (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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555B LEU 2.9 11.1 + - - +
556B LEU* 3.5 12.1 - - + +
558B MET* 1.3 74.4 - - - +
560B LYS* 1.3 60.3 + - - +
562B TYR* 3.1 4.2 + - + +
563B LEU* 2.9 47.5 + - + +
568B PHE* 4.7 3.6 - - + -
590B TRP* 3.5 35.2 - - + -
593B PHE* 3.9 30.5 - - + -
603B VAL* 4.2 14.4 - - + -
606B MET* 4.0 27.6 - - + +
607B MET* 4.1 12.8 - - + -
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Residues in contact with LYS 560 (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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407B TYR* 5.9 0.2 - - - +
492B PHE* 3.4 24.0 - - + -
496B PHE* 3.8 18.4 - - + -
556B LEU 2.8 21.1 + - - +
557B LEU* 4.0 20.1 - - - +
559B LEU* 1.3 72.3 - - - +
561B THR* 1.3 60.9 + - - +
563B LEU* 2.5 28.0 - - - +
564B SER 3.3 8.5 - - - +
565B GLU* 3.1 35.8 + - + -
568B PHE* 3.5 36.0 - - + -
1129B BR 4.3 9.0 - - - +
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Residues in contact with THR 561 (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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557B LEU* 2.9 28.9 + - - +
558B MET* 3.8 4.7 - - - -
560B LYS* 1.3 83.1 + - - +
562B TYR* 1.3 58.7 + - - +
563B LEU 3.2 8.3 - - - +
657B SER* 5.9 0.4 - - - -
697B ASN* 3.5 41.7 + - + +
1128B BR 3.5 22.6 - - + +
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Residues in contact with TYR 562 (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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558B MET 3.1 18.2 + - - +
559B LEU* 3.1 3.5 + - + +
561B THR* 1.3 73.4 - - - +
563B LEU* 1.3 82.1 + - + +
601B LEU* 4.3 22.7 - - + +
606B MET* 4.4 24.5 - - + -
655B PRO* 3.8 22.7 - - + -
671B VAL* 3.7 32.3 - - + -
673B LEU* 3.8 32.5 - - + +
1125B NAG 5.5 2.1 + - - -
1128B BR 3.9 7.6 - - + -
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Residues in contact with LEU 563 (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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559B LEU* 2.9 29.5 + - + +
560B LYS* 2.5 16.8 - - - +
561B THR 3.2 6.8 - - - +
562B TYR* 1.3 95.4 - - + +
564B SER* 1.3 65.9 + - - +
567B VAL* 4.0 20.4 - - + -
568B PHE* 5.0 0.9 - - + +
593B PHE* 3.7 33.7 - - + -
597B THR* 4.3 10.3 - - + -
601B LEU* 3.7 30.3 - - + -
603B VAL* 4.7 6.1 - - + -
1125B NAG 5.0 8.1 - - - +
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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
------------------------------------------------------------
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