Contacts of the helix formed by residues 545 - 563 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A LYS* 3.6 13.7 - - - -
528A HIS* 3.9 13.3 + - - -
542A GLU 3.5 13.5 - - - +
543A MET 2.8 15.0 + - - +
544A PHE* 1.3 75.2 - - - +
546A SER* 1.3 65.8 + - - +
547A LEU* 3.3 17.4 + - - +
548A SER* 3.4 9.0 + - - -
549A TYR* 3.1 22.5 + - - -
961A TYR* 4.9 2.2 - - - -
964A GLN* 4.1 15.0 - - - +
998A ARG* 2.6 27.9 + - - +
1137A 7O2 3.8 10.1 - - - -
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Residues in contact with SER 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A LYS* 5.1 1.0 + - - -
518A THR* 3.6 24.5 + - - +
521A LYS* 3.2 26.6 - - - +
545A ASP* 1.3 74.8 - - - +
547A LEU* 1.3 60.5 + - - +
549A TYR* 4.6 0.7 - - - -
550A PHE* 2.8 42.9 + - - +
961A TYR* 5.7 0.8 - - - -
1137A 7O2 4.2 14.3 - - - -
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Residues in contact with LEU 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A THR* 3.7 22.0 - - + +
521A LYS* 4.6 11.2 - - + -
522A ASP* 3.8 32.5 - - + +
527A SER* 3.5 18.6 - - - +
528A HIS* 3.4 40.8 - - + +
530A ILE* 4.1 10.6 - - + +
545A ASP* 3.2 14.4 - - - +
546A SER* 1.3 76.6 + - - +
548A SER* 1.3 65.1 + - - +
551A LYS* 3.0 35.2 + - + +
552A GLY 3.2 2.8 + - - -
699A TYR* 4.5 0.7 - - - +
998A ARG* 6.0 0.4 - - - +
1002A GLU* 5.8 1.8 - - - +
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Residues in contact with SER 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A LEU* 4.5 7.1 - - - +
484A TRP* 3.6 31.0 + - - +
487A GLU* 4.7 1.1 - - - -
488A GLY* 3.1 24.0 + - - -
528A HIS* 5.5 0.7 + - - -
530A ILE* 4.4 5.1 + - - +
543A MET* 2.8 47.5 + - - +
545A ASP* 3.4 6.3 + - - -
547A LEU* 1.3 77.7 - - - +
549A TYR* 1.3 65.4 + - - +
552A GLY* 4.0 1.7 - - - -
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Residues in contact with TYR 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A LEU* 5.2 0.2 - - + -
487A GLU* 3.0 43.2 + - + -
488A GLY* 3.7 1.2 - - - -
491A THR* 3.4 23.8 - - - +
544A PHE* 3.8 14.4 - + - -
545A ASP 3.1 30.3 + - - +
546A SER 3.4 1.9 + - - +
547A LEU 3.1 0.6 - - - -
548A SER* 1.3 81.2 - - - +
550A PHE* 1.3 66.8 + - + +
552A GLY 4.1 0.4 - - - -
553A SER* 3.2 26.5 + - - -
1136A ZN 3.7 2.0 - - - -
1137A 7O2 2.7 101.9 + + + +
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Residues in contact with PHE 550 (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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491A THR* 3.7 23.1 - - + -
495A TYR* 4.0 22.0 - + - -
511A PHE* 3.9 15.0 - + - -
514A ALA* 3.4 34.8 - - + +
515A ARG* 4.3 8.1 - - + +
518A THR* 3.2 29.6 - - - +
546A SER* 2.8 24.8 + - - +
549A TYR* 1.3 74.1 - - + +
551A LYS* 1.3 60.4 + - - +
552A GLY 3.3 0.4 - - - -
553A SER* 3.2 3.1 + - - -
554A SER* 3.0 27.2 + - - -
699A TYR* 5.4 0.4 - - - -
1137A 7O2 3.5 37.9 - + - -
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Residues in contact with LYS 551 (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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518A THR* 3.9 4.2 - - + +
522A ASP* 3.0 35.4 + - - +
528A HIS 5.3 1.0 + - - -
530A ILE* 4.3 23.0 - - + +
546A SER 3.6 1.8 + - - -
547A LEU* 3.0 25.7 + - + +
550A PHE* 1.3 75.5 - - - +
552A GLY* 1.3 59.1 + - - +
554A SER* 3.0 6.8 + - - -
555A LEU* 2.9 35.9 + - + +
610A TRP* 3.8 21.2 + - - -
613A GLN 3.9 15.2 + - - -
614A LYS* 4.7 0.8 - - - +
615A GLY 3.0 17.4 + - - +
652A TRP* 5.9 0.2 - - - +
699A TYR* 3.6 33.2 - - + +
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Residues in contact with GLY 552 (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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484A TRP* 3.8 14.5 - - - -
488A GLY* 3.9 6.5 - - - -
530A ILE* 3.5 20.1 - - - +
547A LEU 3.2 8.3 + - - -
548A SER 4.0 9.6 - - - -
549A TYR 3.9 1.2 + - - -
550A PHE 3.3 0.6 - - - -
551A LYS* 1.3 79.8 - - - +
553A SER* 1.3 60.5 + - - +
555A LEU* 3.4 4.9 - - - +
556A LEU* 3.3 24.4 + - - +
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Residues in contact with SER 553 (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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488A GLY* 3.3 22.7 - - - -
491A THR* 3.8 3.0 - - - +
492A PHE* 3.4 35.0 - - - -
511A PHE* 3.2 23.4 - - - -
549A TYR 3.2 15.2 + - - -
550A PHE* 3.2 13.3 + - - -
552A GLY* 1.3 75.8 - - - +
554A SER* 1.3 56.7 - - - +
555A LEU 3.4 0.2 - - - -
556A LEU* 3.7 2.2 - - - -
557A LEU* 3.1 20.8 + - - +
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Residues in contact with SER 554 (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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511A PHE* 4.7 0.4 - - - -
515A ARG* 3.4 29.6 - - - +
550A PHE 3.0 18.5 + - - -
551A LYS* 3.0 8.5 + - - -
553A SER* 1.3 76.2 - - - +
555A LEU* 1.3 66.3 + - - +
556A LEU 3.2 0.2 - - - -
557A LEU* 3.7 8.8 - - - +
558A MET* 3.0 24.9 + - - +
697A ASN 4.4 2.6 - - - +
698A GLY 5.8 0.6 - - - -
699A TYR* 3.1 32.3 - - - +
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Residues in contact with LEU 555 (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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484A TRP* 4.8 10.8 - - + -
530A ILE* 4.4 15.0 - - + -
551A LYS* 2.9 31.5 + - + +
552A GLY 3.4 9.4 - - - +
554A SER* 1.3 77.4 + - - +
556A LEU* 1.3 63.4 + - + +
558A MET* 3.3 28.0 + - + +
559A LEU* 3.1 21.9 + - - +
590A TRP* 5.5 0.7 - - + -
607A MET* 4.1 12.7 - - + +
610A TRP* 3.9 41.3 - - + +
611A THR* 4.0 21.3 - - + -
699A TYR* 4.8 5.2 - - + -
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Residues in contact with LEU 556 (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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484A TRP* 4.3 13.5 - - + -
488A GLY 4.0 0.9 - - - +
489A PHE* 3.3 67.3 - - + +
492A PHE* 3.9 24.0 - - + -
552A GLY 3.3 16.9 + - - +
553A SER 3.8 5.6 - - - +
554A SER 3.2 0.4 - - - -
555A LEU* 1.3 74.4 - - - +
557A LEU* 1.3 61.0 + - - +
559A LEU* 3.2 8.3 + - + +
560A LYS* 2.8 31.7 + - - +
568A PHE* 3.7 14.4 - - + -
589A LEU* 4.3 6.7 - - + -
590A TRP* 4.8 9.0 - - + -
593A PHE* 5.3 1.1 - - + -
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Residues in contact with LEU 557 (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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492A PHE* 3.7 14.4 - - + -
511A PHE* 4.1 10.1 - - + -
515A ARG* 3.9 36.1 - - - +
553A SER 3.1 18.3 + - - +
554A SER* 3.7 7.2 - - - +
555A LEU 3.2 0.4 - - - -
556A LEU* 1.3 73.1 - - - +
558A MET* 1.3 60.1 + - - +
560A LYS* 4.0 13.2 - - - +
561A THR* 2.7 43.1 + - - +
697A ASN* 3.7 29.8 - - - +
726A LYS* 5.9 2.0 - - - +
1140A BR 4.0 25.8 - - + -
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Residues in contact with MET 558 (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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554A SER 3.0 10.1 + - - +
555A LEU* 3.4 26.2 - - + +
557A LEU* 1.3 75.7 - - - +
559A LEU* 1.3 62.2 + - + +
561A THR* 3.9 3.4 - - - -
562A TYR* 3.1 26.3 + - - +
606A MET* 5.5 2.2 - - + -
607A MET* 4.6 4.7 - - + -
610A TRP* 3.4 51.6 - - + +
655A PRO* 3.8 29.7 - - + +
697A ASN 3.4 15.6 + - - +
698A GLY* 3.9 5.4 - - - -
699A TYR* 3.5 26.9 - - + -
700A TYR* 5.0 2.2 - - - -
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Residues in contact with LEU 559 (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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555A LEU 3.1 16.7 + - - +
556A LEU* 3.6 9.2 - - + +
557A LEU 3.2 0.2 - - - -
558A MET* 1.3 76.1 - - - +
560A LYS* 1.3 59.9 + - - +
562A TYR* 4.6 0.9 - - + -
563A LEU* 3.0 56.3 + - + +
568A PHE* 4.6 4.3 - - + -
590A TRP* 3.7 31.0 - - + -
593A PHE* 3.8 24.9 - - + -
603A VAL* 4.3 9.9 - - + -
606A MET* 3.9 22.0 - - + -
607A MET* 3.7 22.9 - - - -
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Residues in contact with LYS 560 (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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492A PHE* 3.6 20.9 - - + -
496A PHE* 3.5 23.1 - - + -
556A LEU 2.8 20.8 + - - +
557A LEU* 4.0 22.2 - - - +
559A LEU* 1.3 74.1 - - - +
561A THR* 1.3 67.0 + - - +
563A LEU* 3.1 17.2 - - - +
564A SER 3.7 6.7 - - - +
565A GLU* 3.5 34.1 + - + +
568A PHE* 3.4 35.8 - - + -
1140A BR 4.3 11.1 - - - +
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Residues in contact with THR 561 (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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557A LEU* 2.7 28.1 + - - +
558A MET* 3.9 3.8 - - - -
560A LYS* 1.3 80.6 + - - +
562A TYR* 1.3 59.1 + - - +
563A LEU 3.1 10.7 - - - +
697A ASN* 3.5 41.5 + - + +
1138A BR 3.4 23.6 - - + -
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Residues in contact with TYR 562 (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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558A MET 3.1 18.3 + - - +
559A LEU* 3.9 3.8 - - + +
561A THR* 1.3 75.0 - - - +
563A LEU* 1.3 79.6 + - + +
601A LEU* 3.5 27.4 - - + +
606A MET* 4.4 11.4 - - + -
655A PRO* 3.9 25.6 - - + -
671A VAL* 3.9 26.9 - - + -
672A SER* 5.0 1.3 - - - -
673A LEU* 3.1 38.2 - - + +
1138A BR 4.2 5.2 - - + -
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Residues in contact with LEU 563 (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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559A LEU* 3.0 31.1 + - + +
560A LYS* 3.1 4.4 - - - +
561A THR 3.1 11.3 - - - +
562A TYR* 1.3 101.5 - - + +
564A SER* 1.3 65.4 + - - +
567A VAL* 3.9 21.8 - - + -
568A PHE* 5.3 1.1 - - - +
593A PHE* 3.9 30.3 - - + -
597A THR* 4.6 11.7 - - + +
601A LEU* 3.8 20.6 - - + -
603A VAL* 4.6 4.3 - - + -
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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