Contacts of the helix formed by residues 507 - 523 (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 SER 507 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A LYS* 4.5 2.2 - - - +
460A LYS* 4.7 4.9 - - - -
495A TYR* 3.4 23.0 + - - -
498A LEU* 3.4 46.4 + - - +
499A GLU* 4.5 4.3 + - - +
502A PHE 5.1 1.8 + - - -
505A LEU* 3.2 12.4 - - - +
506A SER* 1.3 76.3 - - - +
508A TYR* 1.3 63.4 + - - +
510A ASP* 3.1 24.4 + - - +
511A PHE 3.2 8.3 + - - -
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Residues in contact with TYR 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A TYR* 5.1 1.3 - - - -
499A GLU* 4.1 25.3 + - - +
503A LYS 5.8 0.4 - - - -
506A SER* 3.0 29.9 + - - -
507A SER* 1.3 79.9 + - - +
509A GLU* 1.3 79.6 + - + +
511A PHE* 3.7 11.3 - - + +
512A LEU* 3.1 24.8 + - + +
515A ARG* 5.0 0.5 + - - -
725A ASP* 2.5 32.8 + - - -
726A LYS* 3.7 47.9 - - + +
761A HIS* 4.9 3.3 - - - -
763A ALA* 5.4 2.7 - - + -
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Residues in contact with GLU 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LYS* 5.2 1.1 - - - +
506A SER* 3.1 25.6 - - - +
507A SER 3.1 0.2 - - - -
508A TYR* 1.3 99.7 + - + +
510A ASP* 1.3 61.1 + - - +
512A LEU* 3.2 6.8 + - - +
513A ASP* 2.9 29.9 + - - +
725A ASP* 4.5 2.3 - - - +
761A HIS* 6.2 0.2 - - - -
762A THR* 3.8 17.1 + - + +
763A ALA* 4.2 18.9 + - + -
815A SER* 3.0 27.4 + - - -
818A GLU* 3.0 28.0 - - - +
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Residues in contact with ASP 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LYS* 3.0 36.3 + - - -
460A LYS* 3.7 32.4 + - - +
495A TYR* 3.8 5.6 - - + +
507A SER* 3.1 10.8 + - - +
509A GLU* 1.3 73.9 - - - +
511A PHE* 1.3 67.6 + - - +
513A ASP* 3.2 6.1 + - - +
514A ALA* 2.9 26.2 + - - +
818A GLU* 4.5 4.7 - - - +
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Residues in contact with PHE 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A THR* 4.7 0.2 - - + -
492A PHE* 5.0 7.2 - + - -
495A TYR* 3.6 52.6 - + + -
507A SER 3.2 4.4 + - - +
508A TYR* 3.7 12.1 - - + +
509A GLU 3.3 0.2 - - - -
510A ASP* 1.3 79.1 - - - +
512A LEU* 1.3 61.8 + - - +
514A ALA* 3.3 2.3 + - - +
515A ARG* 3.1 52.4 + - - +
550A PHE* 3.9 15.5 - + - -
553A SER* 3.2 44.6 - - - -
554A SER* 4.7 0.4 - - - -
557A LEU* 4.1 21.8 - - + -
726A LYS* 6.2 0.9 - - - -
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Residues in contact with LEU 512 (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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508A TYR* 3.1 17.7 + - + +
509A GLU* 3.5 7.0 - - - +
511A PHE* 1.3 75.3 - - - +
513A ASP* 1.3 64.4 + - - +
515A ARG* 3.3 22.2 + - - +
516A PHE* 3.2 34.7 + - + -
695A ASN 4.5 4.9 - - - +
696A MET* 3.7 38.1 - - + -
726A LYS* 3.9 39.3 - - + +
729A ALA* 3.9 18.6 - - + -
763A ALA* 4.8 9.9 - - + -
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Residues in contact with ASP 513 (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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509A GLU 2.9 16.9 + - - +
510A ASP* 3.8 7.0 - - - +
512A LEU* 1.3 76.3 - - - +
514A ALA* 1.3 63.8 + - - +
515A ARG 3.3 0.2 + - - -
516A PHE* 3.4 13.1 + - - +
517A LYS* 2.9 48.7 + - - +
767A GLU* 4.3 13.9 - - - +
770A PHE* 5.3 4.5 - - - +
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Residues in contact with ALA 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A TYR* 5.4 0.4 - - - +
510A ASP 2.9 17.7 + - - +
511A PHE 3.7 1.3 - - - +
513A ASP* 1.3 79.1 - - - +
515A ARG* 1.3 58.4 + - - +
517A LYS* 3.4 9.4 + - - +
518A THR* 2.9 31.7 + - - -
550A PHE* 3.4 43.5 - - + -
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Residues in contact with ARG 515 (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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508A TYR 5.0 0.2 + - - -
511A PHE* 3.1 52.6 + - + +
512A LEU* 3.7 32.1 - - - +
513A ASP 3.2 0.4 - - - -
514A ALA* 1.3 75.2 - - - +
516A PHE* 1.3 66.2 + - - +
518A THR* 3.0 6.7 + - - +
519A MET* 2.8 33.1 + - + +
550A PHE* 4.3 9.4 - - + +
554A SER* 3.4 32.2 - - - +
557A LEU* 3.9 19.4 - - - +
695A ASN 4.8 1.0 + - - -
696A MET* 2.9 52.8 + - + +
698A GLY 5.4 0.6 + - - -
699A TYR* 5.4 4.9 - - + -
726A LYS* 4.7 12.7 - - - +
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Residues in contact with PHE 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A LEU* 3.2 33.2 + - + -
513A ASP* 3.4 16.2 - - - +
515A ARG* 1.3 76.0 - - - +
517A LYS* 1.3 61.5 + - + +
519A MET* 3.4 8.6 + - - +
520A LYS* 3.2 18.4 + - - +
696A MET* 3.4 35.9 - - + -
729A ALA* 3.7 22.9 - - + -
730A ASN* 3.8 11.0 - - - -
733A ASN* 3.4 32.8 - - + +
737A GLU* 3.7 7.8 - - - +
767A GLU* 3.3 39.9 - - + +
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Residues in contact with LYS 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A ASP* 2.9 42.3 + - - +
514A ALA* 3.6 10.8 - - - +
515A ARG 3.2 0.6 - - - -
516A PHE* 1.3 77.2 - - + +
518A THR* 1.3 66.4 + - - +
520A LYS* 3.5 10.3 + - + +
521A LYS* 3.2 20.4 + - - +
546A SER* 5.1 1.3 + - - -
770A PHE* 4.0 35.6 - - + -
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Residues in contact with THR 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ALA 2.9 18.0 + - - -
515A ARG* 3.0 6.0 + - - -
517A LYS* 1.3 76.1 - - - +
519A MET* 1.3 53.1 + - - +
521A LYS* 3.3 3.0 + - - +
522A ASP* 2.7 33.1 + - - +
546A SER* 3.6 38.7 - - - +
547A LEU* 3.7 20.0 - - + -
550A PHE* 3.2 19.5 - - - +
551A LYS* 3.9 13.2 - - - +
699A TYR* 3.9 9.9 - - + +
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Residues in contact with MET 519 (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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515A ARG 2.8 20.4 + - - +
516A PHE* 3.6 8.1 - - - +
518A THR* 1.3 74.3 - - - +
520A LYS* 1.3 66.3 + - - +
522A ASP 3.0 0.9 + - - -
523A SER* 2.8 22.7 + - - -
616A PHE* 3.5 47.4 - - + -
696A MET* 4.4 26.2 - - - +
699A TYR* 3.6 30.1 - - + -
700A TYR 3.6 23.3 - - - +
701A ILE* 3.6 18.2 - - + -
733A ASN* 5.6 2.9 - - - +
734A ASN* 5.9 0.2 - - - +
737A GLU* 4.4 7.2 - - - +
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Residues in contact with LYS 520 (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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516A PHE 3.2 10.9 + - - +
517A LYS* 3.8 12.3 - - - +
518A THR 3.4 0.2 - - - -
519A MET* 1.3 75.1 - - - +
521A LYS* 1.3 61.8 + - - +
523A SER* 2.8 24.7 + - - +
524A LEU* 3.8 9.2 - - - +
737A GLU* 3.9 25.5 + - + +
770A PHE* 5.5 11.4 - - + -
771A GLN* 5.4 2.8 + - - -
774A LEU* 3.9 20.2 - - + +
1006A VAL* 6.4 2.0 - - - -
1144A BR 3.7 26.2 - - - +
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Residues in contact with LYS 521 (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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517A LYS 3.2 11.1 + - - +
518A THR 3.4 7.9 - - - +
519A MET 3.2 0.4 - - - -
520A LYS* 1.3 77.6 - - - +
522A ASP* 1.3 63.3 + - - +
523A SER 3.1 0.9 + - - -
524A LEU* 3.1 27.2 + - + +
527A SER* 4.2 3.8 - - - -
545A ASP* 3.6 26.9 - - - +
546A SER* 3.2 24.0 - - - +
547A LEU* 4.6 12.6 - - + -
964A GLN* 3.8 31.5 + - - +
998A ARG* 4.3 7.7 - - - +
1002A GLU* 3.1 42.9 + - - +
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Residues in contact with ASP 522 (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 2.7 15.0 + - - +
519A MET 3.0 4.4 + - - +
521A LYS* 1.3 73.0 - - - +
523A SER* 1.3 61.1 + - - +
524A LEU 3.4 1.6 + - - +
527A SER* 2.9 30.6 + - - -
528A HIS 4.3 1.6 - - - +
547A LEU* 3.8 17.2 - - + +
551A LYS* 3.0 23.6 + - - +
614A LYS* 5.3 0.3 - - - +
615A GLY* 3.2 29.9 + - - +
616A PHE* 4.1 4.7 - - + -
699A TYR* 2.7 35.7 + - - +
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Residues in contact with SER 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A MET 2.8 13.5 + - - -
520A LYS* 2.8 20.4 + - - +
521A LYS 3.1 0.4 + - - -
522A ASP* 1.3 75.1 - - - +
524A LEU* 1.3 67.9 + - - +
525A ASN 3.8 0.2 + - - -
615A GLY* 5.3 0.4 - - - -
616A PHE* 4.0 6.0 - - - -
634A ARG* 5.0 1.8 + - - -
635A PHE* 3.7 41.5 - - - +
636A PHE* 3.8 24.0 - - - +
637A LEU 4.8 1.6 + - - -
737A GLU* 4.9 1.4 + - - -
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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