Contacts of the helix formed by residues 537 - 553 (chain C) in PDB entry 3QHE
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 537 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C ILE* 3.7 27.5 - - - +
535C SER* 3.0 13.6 + - - -
536C GLU* 1.3 76.7 - - - +
538C GLU* 1.3 57.5 + - - +
539C ASP* 3.6 7.6 + - - +
540C LEU* 3.1 23.8 + - - +
541C GLN* 2.9 29.3 + - - +
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Residues in contact with GLU 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C GLU 3.5 7.4 + - - +
537C SER* 1.3 72.0 - - - +
539C ASP* 1.3 53.6 + - - +
541C GLN* 3.1 20.5 + - - +
542C GLN* 2.7 35.3 + - - +
578C GLU 4.2 1.7 - - - +
579C VAL* 3.7 8.1 - - - -
580C LYS* 2.7 39.5 + - - +
581C LYS* 2.8 39.2 + - + +
584C THR* 3.1 23.3 + - + +
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Residues in contact with ASP 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499C ARG* 3.7 29.0 + - - +
537C SER* 3.2 5.7 + - - +
538C GLU* 1.3 75.3 - - - +
540C LEU* 1.3 62.9 + - - +
542C GLN* 3.1 9.7 + - - +
543C VAL* 3.1 26.7 + - - +
581C LYS* 3.0 31.7 + - - +
583C SER* 5.3 1.6 + - - -
584C THR* 5.3 0.9 + - - -
389D GLN* 5.0 12.7 + - - +
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Residues in contact with LEU 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C ILE* 4.1 15.9 - - + +
498C ARG* 3.8 35.7 - - + +
499C ARG* 3.7 26.8 - - + +
532C GLN* 3.7 25.8 - - + +
535C SER* 3.7 20.6 - - - +
537C SER* 3.1 22.1 + - - +
539C ASP* 1.3 75.4 - - - +
541C GLN* 1.3 64.1 + - - +
543C VAL* 3.2 4.5 + - + +
544C ILE* 3.0 46.4 + - + +
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Residues in contact with GLN 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C GLN 4.1 4.7 - - - +
533C LEU* 3.2 34.9 + - + +
534C LYS 4.4 0.6 - - - -
535C SER 2.4 33.1 + - - +
536C GLU 4.6 1.2 - - - -
537C SER 2.9 18.2 + - - +
538C GLU* 3.1 19.6 + - - +
540C LEU* 1.3 76.0 - - - +
542C GLN* 1.3 58.0 + - - +
544C ILE* 3.5 7.3 + - - +
545C ALA* 3.0 30.7 + - - +
575C CYS* 3.6 20.9 - - - +
579C VAL* 4.1 6.8 - - - +
584C THR* 3.9 16.3 - - + +
588C VAL* 4.7 0.5 - - - +
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Residues in contact with GLN 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C GLU 2.7 18.8 + - - +
539C ASP* 3.1 9.1 + - - +
541C GLN* 1.3 73.3 - - - +
543C VAL* 1.3 56.9 + - - +
545C ALA* 3.5 0.7 + - - -
546C SER* 2.8 41.4 + - - -
583C SER* 3.4 30.8 + - - +
584C THR* 3.9 15.7 - - - +
587C SER* 3.3 22.8 + - - +
387D TYR* 2.6 30.0 + - - -
388D SER 2.8 26.5 + - - -
389D GLN* 3.7 14.8 + - - +
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Residues in contact with VAL 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C ARG 4.6 1.1 - - - +
499C ARG* 3.4 48.5 - - + +
502C GLY* 3.4 26.7 - - - -
503C MET* 3.6 5.2 - - + +
539C ASP 3.1 14.1 + - - +
540C LEU* 3.2 8.7 + - + +
542C GLN* 1.3 75.4 - - - +
544C ILE* 1.3 68.4 + - + +
546C SER* 3.1 16.8 + - - -
547C VAL* 3.1 13.0 + - - +
387D TYR* 3.7 27.6 - - + +
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Residues in contact with ILE 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C LEU* 5.1 6.1 - - + -
498C ARG* 5.4 2.7 - - + +
502C GLY* 5.7 0.7 - - - -
529C LEU* 3.1 57.0 - - + +
532C GLN* 3.7 32.3 - - + -
533C LEU* 3.9 15.3 - - + -
540C LEU* 3.0 29.8 + - + +
541C GLN* 3.9 4.7 - - - +
543C VAL* 1.3 76.9 - - + +
545C ALA* 1.3 65.0 + - - +
547C VAL* 3.0 10.1 + - + +
548C LEU* 3.0 27.7 + - + +
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Residues in contact with ALA 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C LEU* 4.4 0.8 - - + +
541C GLN 3.0 18.3 + - - +
544C ILE* 1.3 76.1 - - - +
546C SER* 1.3 56.2 + - - +
548C LEU* 3.7 1.7 - - - -
549C ARG* 2.8 31.4 + - - +
572C LEU* 4.1 15.9 - - + -
587C SER* 3.5 33.7 - - - +
588C VAL* 3.6 19.3 - - + +
591C ALA* 3.8 3.6 - - - +
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Residues in contact with SER 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506C THR* 3.7 20.9 - - - -
542C GLN* 2.8 30.7 + - - -
543C VAL 3.1 10.1 + - - -
545C ALA* 1.3 74.7 - - - +
547C VAL* 1.3 60.6 + - - +
549C ARG* 3.4 25.1 + - - +
550C ASN* 3.2 23.0 + - - +
587C SER* 3.5 13.1 + - - -
387D TYR* 3.9 10.9 - - - -
388D SER 4.8 0.7 + - - -
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Residues in contact with VAL 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C GLY* 3.4 23.8 - - - +
505C LEU* 4.4 8.3 - - + +
506C THR* 3.3 23.6 - - - +
509C THR* 5.3 1.6 - - - +
519C LEU* 3.7 29.6 - - + -
529C LEU* 4.1 22.2 - - + -
543C VAL 3.1 12.5 + - - +
544C ILE* 3.0 9.8 + - - +
546C SER* 1.3 75.9 - - - +
548C LEU* 1.3 58.5 + - - +
550C ASN* 3.2 6.8 + - - +
551C LEU* 3.0 35.0 + - + +
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Residues in contact with LEU 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C MET* 4.0 25.6 - - + -
529C LEU* 4.7 14.8 - - + -
530C VAL* 4.7 9.4 - - + -
533C LEU* 4.1 21.3 - - + -
544C ILE* 3.0 35.6 + - + +
545C ALA* 3.9 4.0 - - - +
547C VAL* 1.3 72.5 - - + +
549C ARG* 1.3 58.4 + - - +
551C LEU* 3.8 7.7 - - + +
552C SER* 2.7 36.5 + - - -
563C LEU* 4.3 11.1 - - + +
568C SER* 4.4 10.3 - - - +
572C LEU* 4.1 18.4 - - + -
591C ALA* 4.1 10.1 - - + -
595C LEU* 5.3 2.2 - - + +
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Residues in contact with ARG 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506C THR* 3.6 13.3 - - - +
545C ALA 2.8 18.6 + - - +
546C SER* 3.4 21.0 + - - +
548C LEU* 1.3 76.1 - - - +
550C ASN* 1.3 72.0 + - - +
552C SER* 3.0 12.1 + - - -
553C TRP* 3.1 4.5 + - - +
586C LYS* 6.3 0.6 - - - +
587C SER* 4.6 8.6 + - - +
590C SER* 3.8 25.1 + - - -
591C ALA* 3.7 13.1 - - + +
594C ASN* 2.8 25.1 + - - +
383D TYR* 3.3 41.1 + - - +
384D GLU 4.4 0.2 - - - -
385D GLY* 2.9 36.3 + - - +
386D TYR 3.3 15.8 + - - -
387D TYR* 4.8 0.4 - - - +
388D SER* 5.5 7.1 - - - +
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Residues in contact with ASN 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C THR* 2.8 31.1 + - - +
509C THR* 3.2 18.8 + - - +
510C PHE* 3.3 12.2 - - - +
516C LYS* 3.2 26.0 + - - -
546C SER 3.2 9.6 + - - +
547C VAL* 3.2 6.5 + - - +
549C ARG* 1.3 92.2 + - - +
551C LEU* 1.3 62.3 + - - +
552C SER 3.2 0.7 + - - -
553C TRP* 3.3 8.7 + - - +
384D GLU* 3.5 10.6 - - + -
385D GLY 2.9 39.3 + - - +
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Residues in contact with LEU 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509C THR* 4.0 8.5 - - + -
516C LYS* 3.7 43.2 - - + +
519C LEU* 3.9 30.1 - - + -
520C CYS* 4.0 12.7 - - - -
526C MET* 3.7 37.2 - - + -
547C VAL* 3.0 28.6 + - + +
548C LEU* 3.9 8.3 - - + +
550C ASN* 1.3 76.9 - - - +
552C SER* 1.3 57.9 + - - +
553C TRP 3.4 1.3 - - - +
555C ALA* 3.3 22.7 - - - +
559C SER* 4.8 0.7 - - - -
563C LEU* 3.6 10.9 - - + +
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Residues in contact with SER 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548C LEU 2.7 20.9 + - - -
549C ARG* 3.0 13.0 + - - -
550C ASN 3.1 0.2 - - - -
551C LEU* 1.3 76.4 - - - +
553C TRP* 1.3 62.6 + - - +
554C ARG 3.6 0.2 + - - -
555C ALA 4.1 1.2 + - - -
563C LEU* 3.8 8.7 - - - -
591C ALA 3.6 5.2 + - - -
594C ASN* 3.1 23.8 + - - +
595C LEU* 3.7 29.6 - - - -
598C HIS* 2.8 26.8 + - - -
381D GLU* 3.4 6.1 - - - +
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Residues in contact with TRP 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709A ASN* 3.4 34.5 - - + -
516C LYS* 3.0 44.8 + - - +
549C ARG 3.1 5.6 + - - +
550C ASN 3.3 10.2 + - - +
551C LEU 4.2 0.2 - - - +
552C SER* 1.3 76.1 - - - +
554C ARG* 1.3 104.5 + - + +
555C ALA* 3.2 0.9 + - - -
594C ASN* 3.7 13.2 - - - +
381D GLU* 3.6 30.7 - - + -
382D GLY 3.3 24.5 - - - -
383D TYR* 3.5 20.6 - - + +
384D GLU* 3.3 36.5 + - + -
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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