Contacts of the helix formed by residues 538 - 553 (chain A) in PDB entry 4REC
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 CYS 538 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A GLY* 3.7 12.1 - - - +
455A PHE 3.0 21.3 + - - +
456A LEU 3.3 31.4 - - - -
457A GLN* 3.4 24.2 - - - +
536A ARG 3.4 0.4 + - - -
537A ILE* 1.3 71.8 - - - +
539A LYS* 1.3 64.8 + - - +
540A GLY 3.4 0.8 + - - +
541A PRO* 3.6 17.2 - - + +
542A ARG* 3.2 23.4 + - - +
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Residues in contact with LYS 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A LEU* 3.9 30.5 - - + -
457A GLN* 5.2 1.2 + - - +
467A GLU* 4.1 7.7 + - - -
536A ARG* 3.6 38.1 - - - +
537A ILE 4.5 4.0 - - - +
538A CYS* 1.3 72.6 - - - +
540A GLY* 1.3 68.9 + - - +
542A ARG* 3.8 7.3 + - - +
543A ALA* 3.0 23.2 + - - +
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Residues in contact with GLY 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ILE* 5.0 2.7 - - - -
538A CYS* 4.6 0.4 - - - +
539A LYS* 1.3 80.3 - - - +
541A PRO* 1.3 70.5 - - - +
543A ALA* 3.0 11.3 + - - +
544A VAL* 3.3 14.9 + - - +
547A ARG* 5.5 0.2 + - - -
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Residues in contact with PRO 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ILE* 4.0 30.7 - - + -
418A TYR* 4.0 5.2 - - - +
454A GLY 3.4 23.3 - - - +
455A PHE* 3.8 30.5 - - + -
538A CYS* 3.6 19.7 - - + +
540A GLY* 1.3 88.2 - - - +
542A ARG* 1.3 61.9 + - - +
544A VAL* 2.9 15.2 + - + +
545A PHE* 3.2 16.6 + - + -
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Residues in contact with ARG 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A TYR* 3.7 9.1 + - - -
422A PHE* 3.7 34.4 + - + +
424A ARG 5.2 4.2 + - - -
426A LEU* 3.8 48.4 - - - +
537A ILE* 3.6 22.0 - - + -
538A CYS 3.2 18.4 + - - +
539A LYS* 3.8 5.7 + - - +
540A GLY 3.2 0.6 - - - -
541A PRO* 1.3 78.3 - - - +
543A ALA* 1.3 61.0 + - - +
545A PHE* 3.3 1.4 + - - -
546A SER* 2.9 39.3 + - - +
610A HIS* 6.0 3.2 - - - -
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Residues in contact with ALA 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A LYS 3.0 16.8 + - - +
540A GLY* 3.0 5.3 + - - +
542A ARG* 1.3 78.0 - - - +
544A VAL* 1.3 64.6 - - - +
546A SER* 3.4 9.2 - - - -
547A ARG* 3.1 38.5 + - - +
610A HIS* 6.5 1.1 - - + -
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Residues in contact with VAL 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A PHE* 3.9 13.7 - - + -
399A GLN* 6.0 0.2 - - - +
400A GLU* 3.8 45.3 - - + +
403A ILE* 4.6 12.1 - - + -
404A VAL* 4.3 8.5 - - + -
540A GLY 3.3 13.4 + - - +
541A PRO* 2.9 13.4 + - + +
543A ALA* 1.3 75.1 - - - +
545A PHE* 1.3 68.0 + - + +
547A ARG* 3.2 17.6 + - - +
548A ILE* 3.0 37.5 + - + +
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Residues in contact with PHE 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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379A PHE* 3.9 20.9 - + + -
383A LEU* 4.0 20.0 - - + -
403A ILE* 4.2 15.7 - - + -
404A VAL* 4.0 23.1 - - + -
407A PHE* 3.8 27.4 - + + -
418A TYR* 3.4 41.1 - + - -
422A PHE* 3.8 21.5 - + + -
455A PHE* 4.0 11.7 - + - -
541A PRO 3.2 18.9 + - - -
542A ARG* 3.8 1.1 - - - +
544A VAL* 1.3 76.0 - - + +
546A SER* 1.3 57.7 + - - +
548A ILE* 3.1 8.9 + - + +
549A LEU* 2.8 34.8 + - + +
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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
----------------------------------------------------------
422A PHE* 4.2 11.6 - - - -
542A ARG* 2.9 31.9 + - - -
543A ALA* 3.4 13.0 - - - -
544A VAL 3.1 0.2 - - - -
545A PHE* 1.3 77.5 - - - +
547A ARG* 1.3 57.4 + - - +
549A LEU* 3.5 6.7 + - - +
550A LEU* 3.1 29.0 + - - +
610A HIS* 4.2 21.9 + - - -
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Residues in contact with ARG 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A LEU 4.1 13.5 + - - -
396A PHE* 3.9 19.4 - - + -
400A GLU* 2.5 40.7 + - - -
540A GLY 5.5 0.2 + - - -
543A ALA* 3.1 26.8 + - + +
544A VAL* 3.2 23.5 + - - +
546A SER* 1.3 74.3 - - - +
548A ILE* 1.3 66.0 + - - +
550A LEU* 3.3 8.5 + - - +
551A LEU* 3.0 27.0 + - - +
599A ARG* 4.2 2.2 + - - +
602A LEU* 4.0 23.0 - - + +
603A ILE* 3.5 41.2 - - - +
606A ALA* 4.2 18.2 - - + -
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Residues in contact with ILE 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A VAL* 3.9 15.3 - - + +
383A LEU* 3.9 25.1 - - + -
386A VAL* 3.5 31.4 - - + +
387A LEU* 4.7 6.5 - - + -
393A MET* 5.0 1.1 - - + -
396A PHE* 3.8 19.7 - - + -
404A VAL* 3.8 29.4 - - + -
544A VAL* 3.0 24.6 + - + +
545A PHE* 3.1 11.6 + - + +
547A ARG* 1.3 76.1 - - - +
549A LEU* 1.3 65.0 + - + +
551A LEU* 3.0 18.0 + - - +
552A PHE* 3.1 9.7 + - - +
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Residues in contact with LEU 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A PHE* 4.7 14.6 - - + -
382A VAL* 4.1 27.1 - - + -
383A LEU* 6.4 0.7 - - + -
422A PHE* 4.1 30.5 - - + -
423A GLN* 5.5 3.6 - - - +
545A PHE* 2.8 20.2 + - + +
546A SER* 3.5 10.3 - - - +
548A ILE* 1.3 75.0 - - + +
550A LEU* 1.3 63.3 + - + +
552A PHE* 3.2 12.3 + - + +
553A SER* 3.3 13.0 + - - +
575A LEU* 5.7 7.6 - - + -
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Residues in contact with LEU 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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546A SER 3.1 16.2 + - - +
547A ARG* 3.4 11.2 - - - +
548A ILE 3.2 0.4 - - - -
549A LEU* 1.3 78.0 - - + +
551A LEU* 1.3 63.2 + - - +
552A PHE 3.2 0.7 + - - -
553A SER 3.3 3.4 - - - +
554A LEU* 3.1 31.8 + - + +
557A SER* 3.7 28.7 - - - +
602A LEU* 4.8 8.1 - - + -
605A TYR* 4.1 24.5 - - + -
606A ALA* 3.7 36.8 - - + -
609A THR* 4.6 13.7 - - + +
610A HIS* 5.3 4.3 - - - +
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Residues in contact with LEU 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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386A VAL* 4.1 19.7 - - + -
392A ASP* 4.2 31.9 - - + +
395A LEU* 4.2 9.0 - - + -
396A PHE* 3.5 38.1 - - + -
547A ARG 3.0 14.3 + - - +
548A ILE 3.0 7.2 + - - +
550A LEU* 1.3 76.4 - - - +
552A PHE* 1.3 61.4 + - - +
554A LEU* 4.4 14.2 - - + +
591A ARG* 5.4 2.6 + - - -
596A PHE* 3.8 32.8 - - + -
602A LEU* 4.0 15.0 - - + -
861A ASN* 4.5 4.5 + - - -
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Residues in contact with PHE 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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381A VAL* 4.7 2.0 - - + -
382A VAL* 3.7 38.8 - - + -
385A THR* 3.6 39.9 - - + -
386A VAL* 3.9 7.6 - - + +
548A ILE 3.1 5.2 + - - +
549A LEU* 3.6 9.0 - - + +
550A LEU 3.1 0.2 - - - -
551A LEU* 1.3 78.3 - - - +
553A SER* 1.3 70.6 + - - +
554A LEU 4.0 0.6 + - - -
575A LEU* 5.6 8.3 - - + -
579A LEU* 3.8 32.8 - - + -
861A ASN* 2.9 26.6 + - - +
863A CYS* 3.7 36.3 - - + +
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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
----------------------------------------------------------
549A LEU 3.3 8.9 + - - +
550A LEU* 3.3 7.7 - - - +
552A PHE* 1.3 96.6 - - - +
554A LEU* 1.3 62.9 + - - +
555A THR* 3.3 7.5 + - - +
556A ASP* 2.8 43.2 + - - +
557A SER* 3.9 3.8 + - - -
575A LEU* 4.9 9.5 + - - -
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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
------------------------------------------------------------
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