Contacts of the helix formed by residues 534 - 554 (chain A) in PDB entry 5VR6
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 534 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491A TRP* 3.5 3.9 + - - +
493A LYS* 4.7 9.6 - - - +
532A SER 3.6 2.4 + - - -
533A GLU* 1.3 78.3 - - - +
535A TYR* 1.3 63.8 + - - +
536A ASP* 3.6 9.4 + - - +
537A THR* 2.9 32.5 + - - -
538A TYR 3.0 18.4 + - - -
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Residues in contact with TYR 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A TRP* 3.6 41.9 - + + +
534A SER* 1.3 72.7 - - - +
536A ASP* 1.3 73.6 + - - +
538A TYR* 3.1 6.3 + + - +
539A ILE* 2.9 56.3 + - + +
570A GLU* 5.2 0.2 + - - -
581A PRO* 4.1 5.8 - - + +
582A GLN 2.7 33.8 + - - -
583A ASN* 4.0 1.1 - - - -
584A SER* 3.7 27.1 - - - -
587A PHE* 3.5 48.5 - + + +
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Residues in contact with ASP 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A SER* 3.3 7.9 + - - +
535A TYR* 1.3 93.3 - - - +
537A THR* 1.3 55.5 + - - +
539A ILE* 3.4 5.1 + - - +
540A SER* 2.7 40.1 + - - +
581A PRO* 6.1 0.5 - - - +
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Residues in contact with THR 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A VAL* 4.9 10.3 - - + -
533A GLU* 3.7 20.4 - - + +
534A SER* 2.9 33.1 + - - -
536A ASP* 1.3 77.9 - - - +
538A TYR* 1.3 57.4 + - - +
540A SER* 3.8 4.6 - - - -
541A ARG* 2.9 36.2 + - + +
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Residues in contact with TYR 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A GLY 5.4 0.2 - - - -
488A LEU 5.2 0.8 + - - -
489A PHE 3.5 15.6 + - - -
490A GLU* 3.9 4.0 - - - -
491A TRP* 3.4 58.8 - + + -
533A GLU* 3.7 8.3 + - - +
534A SER 3.0 5.7 + - - -
535A TYR* 3.1 8.9 + + - +
537A THR* 1.3 77.9 - - - +
539A ILE* 1.3 71.3 + - + +
541A ARG* 3.5 16.8 - - - +
542A SER* 2.8 45.6 + - - -
567A SER* 2.9 41.4 + - - -
568A SER* 3.7 7.8 + - - -
571A ALA* 3.7 17.8 - - + +
572A CYS* 5.9 0.2 - - - -
587A PHE* 4.1 10.1 - + - -
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Residues in contact with ILE 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A TYR* 2.9 59.3 + - + +
536A ASP* 3.9 5.8 - - - +
538A TYR* 1.3 81.1 - - + +
540A SER* 1.3 61.0 + - - +
542A SER* 3.3 5.8 + - - -
543A PHE* 3.1 18.0 + - - +
570A GLU* 6.0 0.9 - - + -
571A ALA* 3.8 32.9 - - + +
574A CYS* 5.4 4.9 - - + -
575A GLN* 3.3 21.7 - - + +
581A PRO* 3.8 25.4 - - + -
587A PHE* 4.1 9.4 - - + -
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Residues in contact with SER 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A ASP* 2.7 25.5 + - - +
537A THR* 3.8 5.3 - - - -
539A ILE* 1.3 78.0 - - - +
541A ARG* 1.3 58.6 + - - +
543A PHE* 3.3 6.0 + - - +
544A GLN* 2.9 29.4 + - - +
575A GLN* 4.1 13.3 + - - -
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Residues in contact with ARG 541 (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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486A PRO 3.7 6.3 + - - -
487A GLY 2.8 35.4 + - - +
489A PHE* 2.9 16.1 + - - -
490A GLU 2.9 21.2 + - - -
492A THR* 4.0 6.9 - - - +
524A ILE* 4.0 18.8 - - + +
529A LEU* 3.7 22.5 - - - +
533A GLU* 2.7 43.4 + - - -
537A THR* 2.9 26.1 + - + +
538A TYR* 3.5 12.8 - - - +
540A SER* 1.3 73.2 - - - +
542A SER* 1.3 59.5 + - - +
544A GLN* 3.6 13.0 - - - +
545A VAL* 2.8 33.5 + - - +
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Residues in contact with SER 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A GLY 4.8 4.0 + - - -
538A TYR* 2.8 43.8 + - - -
539A ILE 3.4 5.4 - - - -
541A ARG* 1.3 76.1 - - - +
543A PHE* 1.3 60.6 - - - +
545A VAL* 3.4 8.2 - - - +
546A THR* 2.7 33.9 + - - -
571A ALA* 3.5 30.7 - - - +
572A CYS* 4.2 7.1 - - - -
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Residues in contact with PHE 543 (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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539A ILE 3.1 5.8 + - - +
540A SER* 3.5 8.7 - - - +
542A SER* 1.3 73.8 - - - +
544A GLN* 1.3 65.4 + - - +
546A THR* 3.3 4.5 + - - -
547A LYS* 3.1 65.6 + - + +
571A ALA 4.1 5.7 + - - +
572A CYS 5.2 1.3 - - - -
575A GLN* 3.3 70.2 - - + +
576A LEU* 3.6 16.4 - - + -
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Residues in contact with GLN 544 (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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523A HIS 4.9 2.8 + - - -
524A ILE* 4.0 22.3 - - - +
540A SER 2.9 15.6 + - - +
541A ARG* 3.6 13.6 - - - +
543A PHE* 1.3 79.0 - - - +
545A VAL* 1.3 62.8 + - - +
547A LYS* 3.3 14.1 + - - +
548A GLU* 3.1 51.4 + - + +
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Residues in contact with VAL 545 (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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485A GLU* 3.5 41.1 - - + +
487A GLY* 3.8 20.2 - - - +
488A LEU* 4.0 17.5 - - + -
523A HIS* 4.4 10.1 - - + -
524A ILE* 4.1 9.4 - - + -
541A ARG 2.8 23.5 + - - +
542A SER* 3.4 10.3 - - - +
544A GLN* 1.3 73.7 - - - +
546A THR* 1.3 60.8 + - - +
548A GLU* 3.3 9.4 + - - +
549A ILE* 2.9 38.6 + - + +
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Residues in contact with THR 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU* 3.6 30.5 - - + -
542A SER 2.7 22.1 + - - -
543A PHE* 3.8 3.6 - - - -
544A GLN 3.3 0.2 - - - -
545A VAL* 1.3 80.2 - - - +
547A LYS* 1.3 56.6 + - - +
549A ILE* 3.3 8.2 + - - +
550A ILE* 2.9 39.6 + - + +
562A ILE* 4.7 4.8 - - + +
572A CYS* 3.3 42.4 - - + +
576A LEU* 4.2 5.4 - - + -
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Residues in contact with LYS 547 (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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543A PHE* 3.1 66.3 + - + +
544A GLN* 3.6 13.5 - - - +
546A THR* 1.3 76.8 - - - +
548A GLU* 1.3 58.0 + - + +
550A ILE* 3.3 8.4 + - - +
551A SER* 2.8 31.1 + - - -
576A LEU* 4.7 10.3 - - + -
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Residues in contact with GLU 548 (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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523A HIS* 3.2 46.0 + - + +
524A ILE* 4.8 0.2 - - - +
544A GLN* 3.1 44.5 + - + +
545A VAL* 3.7 7.1 - - - +
546A THR 3.3 0.2 - - - -
547A LYS* 1.3 73.9 - - + +
549A ILE* 1.3 63.9 + - - +
551A SER* 3.8 6.8 - - - -
552A GLU* 3.2 25.5 + - - +
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Residues in contact with ILE 549 (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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375A LEU* 5.0 0.7 - - + -
456A TYR* 3.6 48.0 - - + -
485A GLU* 4.5 1.6 - - + -
488A LEU* 4.1 21.3 - - + -
520A TYR* 4.8 0.2 - - - +
523A HIS* 4.3 9.6 - - + -
545A VAL* 2.9 29.5 + - + +
546A THR* 3.5 6.1 - - - +
548A GLU* 1.3 73.4 - - - +
550A ILE* 1.3 67.4 + - + +
552A GLU* 3.3 10.1 + - - +
553A CYS* 3.2 24.4 + - - -
560A ILE* 3.9 18.8 - - + -
562A ILE* 4.1 24.0 - - + -
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Residues in contact with ILE 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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373A ARG* 3.4 26.5 + - - +
375A LEU* 4.6 9.4 - - + -
546A THR* 2.9 28.4 + - + +
547A LYS* 3.7 6.1 - - - +
549A ILE* 1.3 75.3 - - - +
551A SER* 1.3 63.8 + - - +
553A CYS* 3.2 3.8 + - - +
554A LYS 3.1 17.8 + - - -
560A ILE* 4.0 20.6 - - + +
576A LEU* 3.7 41.1 - - + -
611A TRP* 3.7 28.5 - - + +
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Residues in contact with SER 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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373A ARG* 5.3 0.2 - - - +
547A LYS 2.8 22.1 + - - -
548A GLU* 3.8 8.7 - - - -
549A ILE 3.3 0.2 - - - -
550A ILE* 1.3 75.1 - - - +
552A GLU* 1.3 60.2 + - - +
554A LYS* 3.4 20.6 + - - +
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Residues in contact with GLU 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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454A HIS* 5.4 0.7 + - - -
456A TYR* 2.5 37.3 + - - +
483A ARG* 4.6 6.6 + - - +
520A TYR* 3.5 11.0 - - - -
521A ARG 5.3 0.5 - - - +
523A HIS* 2.8 38.5 + - + -
548A GLU 3.2 11.3 + - - +
549A ILE* 3.3 5.5 + - - +
550A ILE 3.3 0.2 - - - -
551A SER* 1.3 76.3 - - - +
553A CYS* 1.3 59.1 + - - +
554A LYS 3.4 2.1 - - - +
556A LYS* 5.0 4.9 - - - +
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Residues in contact with CYS 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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373A ARG* 5.0 2.0 - - - -
454A HIS* 3.3 40.6 - - - +
456A TYR* 3.3 34.3 - - - -
483A ARG* 3.8 3.8 - - - -
549A ILE 3.2 8.9 + - - +
550A ILE 3.2 3.6 + - - +
552A GLU* 1.3 76.3 - - - +
554A LYS* 1.3 66.0 + - - +
555A SER 3.4 0.7 + - - -
556A LYS* 3.2 16.4 + - - +
557A GLY 3.5 12.7 - - - +
560A ILE* 3.7 25.6 - - + -
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Residues in contact with LYS 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ARG* 3.5 30.5 - - - +
550A ILE 3.1 4.5 + - - +
551A SER* 3.4 18.7 + - - +
552A GLU 4.8 1.9 - - - +
553A CYS* 1.3 76.7 - - - +
555A SER* 1.3 70.6 + - - +
556A LYS* 3.2 4.0 + - - +
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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