Contacts of the helix formed by residues 542 - 556 (chain N) in PDB entry 5GJQ
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 GLU 542 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541N HIS* 1.3 75.2 - - - +
543N LYS* 1.3 58.5 + - + +
545N LEU* 3.6 1.0 - - - +
546N ARG* 2.7 54.5 + - - +
577N ILE* 4.7 3.3 - - - +
30V GLN* 5.6 0.4 - - - +
32V TYR* 3.4 28.3 + - + +
208V ARG* 5.8 2.6 - - - +
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Residues in contact with LYS 543 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506N ALA* 4.8 17.3 - - + +
510N GLU* 2.6 29.2 - - + +
541N HIS* 4.3 0.8 - - - +
542N GLU* 1.3 80.4 - - + +
544N ILE* 1.3 58.7 + - - +
546N ARG* 2.6 42.0 + - - +
547N GLY 2.8 8.7 + - - -
772N TRP* 5.9 10.5 - - + -
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Residues in contact with ILE 544 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501N LEU* 4.1 26.9 - - + +
504N ASP* 3.4 21.1 - - - +
505N ASP 3.3 11.7 - - - +
506N ALA* 3.3 37.0 - - - +
509N GLY* 4.1 2.0 - - - +
510N GLU* 3.4 19.1 - - - +
513N GLY* 5.5 1.2 - - - -
539N THR* 4.1 18.6 - - + +
541N HIS* 3.4 32.1 - - + +
543N LYS* 1.3 78.0 - - - +
545N LEU* 1.3 61.8 + - - +
547N GLY 3.8 0.2 + - - -
548N LEU* 3.0 24.6 + - - +
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Residues in contact with LEU 545 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536N ALA* 3.1 36.7 - - + +
539N THR* 4.0 8.1 - - - +
541N HIS* 2.9 25.4 + - - +
542N GLU* 3.5 2.4 + - - +
543N LYS 3.1 0.4 - - - -
544N ILE* 1.3 80.8 - - - +
546N ARG* 1.3 64.8 + - - +
548N LEU* 3.2 23.9 - - - +
549N ALA* 4.2 1.2 + - - +
575N ASP* 6.0 6.1 - - + -
577N ILE* 4.6 16.6 - - + +
578N LEU* 5.4 1.4 - - + +
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Residues in contact with ARG 546 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510N GLU* 4.9 2.7 - - - +
542N GLU* 2.7 30.8 + - - +
543N LYS* 2.6 57.4 + - - +
545N LEU* 1.3 72.8 - - - +
547N GLY* 1.3 57.9 + - - +
548N LEU 2.8 11.7 + - - -
549N ALA* 3.1 18.0 + - - +
550N VAL* 3.9 5.8 + - + +
577N ILE* 4.0 26.8 - - + +
580N ARG* 6.0 2.5 - - + -
768N GLN* 2.9 44.8 - - - +
771N PHE* 5.2 10.2 - - - +
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Residues in contact with GLY 547 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510N GLU* 3.3 21.9 + - - -
513N GLY* 3.0 14.9 - - - +
514N LEU* 4.6 5.2 - - - -
543N LYS 2.8 13.5 + - - -
544N ILE 4.6 0.4 - - - -
546N ARG* 1.3 73.9 - - - +
548N LEU* 1.3 62.1 + - - +
549N ALA 3.4 0.2 - - - -
550N VAL* 3.0 18.6 + - - +
551N GLY 2.9 18.9 + - - -
768N GLN* 5.5 0.4 - - - -
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Residues in contact with LEU 548 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501N LEU* 3.9 23.8 - - + -
513N GLY* 4.2 8.0 - - - -
532N MET* 3.6 42.3 - - + +
535N TYR* 3.6 8.5 - - + -
536N ALA* 3.3 39.5 - - + +
539N THR* 3.7 5.6 - - - +
544N ILE* 3.0 21.5 + - + +
545N LEU* 3.2 13.5 - - - +
546N ARG 2.8 0.8 + - - -
547N GLY* 1.3 75.3 - - - +
549N ALA* 1.3 50.3 + - - +
551N GLY* 2.7 7.8 + - - -
552N ILE* 2.6 37.8 + - + +
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Residues in contact with ALA 549 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545N LEU 4.2 0.8 + - - +
546N ARG 3.1 8.9 + - - +
548N LEU* 1.3 77.7 - - - +
550N VAL* 1.3 50.9 + - - +
552N ILE* 3.0 15.4 + - + +
553N ALA 2.3 32.7 + - - -
570N LEU* 5.1 2.2 - - + -
577N ILE* 3.4 20.4 - - + +
578N LEU* 4.1 15.5 - - + +
581N SER* 2.4 43.2 - - - -
585N THR* 3.8 0.2 + - - -
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Residues in contact with VAL 550 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514N LEU* 3.6 22.7 - - + -
546N ARG* 4.2 5.4 - - + +
547N GLY* 3.1 22.0 - - - +
548N LEU 3.0 0.4 - - - -
549N ALA* 1.3 76.3 - - - +
551N GLY* 1.3 51.0 + - - +
553N ALA* 2.7 11.3 + - + +
554N LEU* 2.6 45.2 + - + +
580N ARG* 6.4 2.0 - - + -
581N SER* 4.2 7.0 - - - -
584N TYR* 5.6 4.9 - - + -
764N LEU* 4.4 25.6 - - + +
767N THR* 6.1 1.1 - - - +
768N GLN* 4.8 15.0 - - - +
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Residues in contact with GLY 551 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513N GLY 3.2 17.5 + - - -
517N GLY* 3.7 20.7 - - - -
532N MET* 5.5 6.1 - - - -
547N GLY 2.9 7.5 + - - -
548N LEU 2.7 11.7 + - - -
550N VAL* 1.3 73.1 - - - +
552N ILE* 1.3 61.0 + - - -
554N LEU* 3.0 5.3 + - - +
555N VAL* 2.9 28.0 + - - +
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Residues in contact with ILE 552 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529N ILE* 4.8 4.7 - - - +
532N MET* 3.8 25.5 - - + +
533N VAL* 4.5 8.5 - - - +
548N LEU* 2.6 22.0 + - + +
549N ALA* 3.1 20.0 - - + +
551N GLY* 1.3 71.2 - - - -
553N ALA* 1.3 61.5 + - - +
555N VAL* 4.4 6.7 - - - -
556N MET* 3.1 30.4 + - - +
566N LEU* 3.7 28.3 - - + -
570N LEU* 5.5 2.9 - - + -
578N LEU* 6.0 2.2 - - + -
585N THR* 3.8 5.6 + - - +
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Residues in contact with ALA 553 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549N ALA 2.3 26.6 + - - +
550N VAL* 2.7 18.1 + - + +
552N ILE* 1.3 67.5 - - - +
554N LEU* 1.3 53.3 + - + +
556N MET 2.5 28.9 - - - +
581N SER 3.7 0.4 - - - +
584N TYR* 3.5 20.6 - - + +
585N THR* 3.1 34.5 + - - +
588N MET* 3.3 13.5 - - + +
764N LEU* 5.7 1.8 - - + -
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Residues in contact with LEU 554 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514N LEU* 3.3 31.4 - - + +
517N GLY* 3.4 22.0 - - - +
518N LEU* 3.4 22.7 - - + +
521N LEU* 3.1 35.2 - - + +
550N VAL* 2.6 27.3 + - + +
551N GLY* 3.0 14.5 + - - +
553N ALA* 1.3 76.4 - - - +
555N VAL* 1.3 58.6 + - - +
556N MET 2.9 6.9 + - - -
557N TYR* 3.2 9.0 - - - +
588N MET* 4.8 8.1 - - + -
761N VAL* 5.7 7.2 - - + -
764N LEU* 5.2 10.5 - - + -
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Residues in contact with VAL 555 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517N GLY* 4.4 4.9 - - - +
520N MET* 3.5 20.9 - - + +
521N LEU* 4.0 1.1 - - - +
522N GLY 2.6 18.6 - - - +
523N SER 2.9 22.7 - - - +
524N LYS* 2.5 34.2 - - + +
525N ASN 4.7 1.1 - - - +
528N ALA* 5.7 4.3 - - + -
529N ILE* 4.0 26.7 - - + +
532N MET* 6.2 2.2 - - + -
551N GLY 2.9 19.4 + - - +
552N ILE* 4.0 4.5 - - - +
554N LEU* 1.3 72.2 - - - +
556N MET* 1.3 56.6 + - - +
559N ARG* 3.4 1.4 + - - -
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Residues in contact with MET 556 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529N ILE* 3.9 13.5 - - + -
552N ILE 3.1 17.9 + - - +
553N ALA 2.5 19.8 - - - +
554N LEU 2.9 3.0 - - - -
555N VAL* 1.3 77.3 - - - +
557N TYR* 1.3 56.8 + - - +
558N GLY 4.3 0.2 - - - -
559N ARG* 3.5 27.1 - - + +
563N ALA* 3.4 28.3 - - + -
566N LEU* 4.6 5.2 - - + -
585N THR* 3.5 19.8 - - + +
588N MET* 3.2 7.8 - - - +
589N ALA* 3.6 7.2 + - + -
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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