Contacts of the helix formed by residues 485 - 499 (chain A) in PDB entry 4MS0
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 MET 485 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462A PHE* 3.8 22.4 - - + -
464A LEU* 4.8 1.1 - - - -
465A PRO* 4.0 27.6 - - + -
468A LEU* 3.5 27.6 - - + -
482A PHE* 2.9 25.2 + - + +
484A ASN* 1.3 99.8 - - - +
486A TRP* 1.3 58.5 + - - +
487A PRO* 3.4 1.8 - - - -
488A GLY* 3.0 4.8 + - - -
489A ILE* 2.8 36.4 + - + +
756B ARG* 3.6 35.2 - - - +
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Residues in contact with TRP 486 (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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479A ILE* 2.7 48.2 + - + -
480A GLY 4.0 13.2 - - - -
482A PHE 3.2 13.9 + - - -
483A GLU* 3.1 54.0 + - + +
485A MET* 1.3 75.9 - - - +
487A PRO* 1.4 70.5 - - + +
489A ILE* 3.3 13.3 + - + +
490A PHE* 3.2 19.9 + - - +
527A TRP* 3.5 33.9 - + - +
528A LYS* 3.4 52.5 - - + -
531A VAL* 4.1 15.6 - - + +
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Residues in contact with PRO 487 (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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459A LEU* 3.6 15.4 - - + +
483A GLU 4.3 2.9 - - - +
484A ASN 3.6 11.4 - - - +
485A MET 3.5 3.4 - - - -
486A TRP* 1.4 92.4 - - + +
488A GLY* 1.3 55.0 + - - +
490A PHE* 3.1 18.0 + - + +
491A VAL* 3.1 17.3 + - - +
512A ILE* 4.1 9.7 - - + +
513A MET* 3.6 37.7 - - + -
516A LYS* 4.7 5.2 - - + -
527A TRP* 3.9 22.4 - - + +
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Residues in contact with GLY 488 (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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459A LEU* 3.5 16.4 - - - +
462A PHE* 3.7 27.4 - - - -
464A LEU* 4.8 1.2 - - - +
484A ASN 5.3 0.2 + - - -
485A MET* 3.0 7.4 + - - +
487A PRO* 1.3 77.3 - - - +
489A ILE* 1.3 63.9 + - - +
490A PHE 3.1 1.6 - - - -
491A VAL* 3.3 6.0 + - - +
492A TYR* 2.9 24.0 + - - +
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Residues in contact with ILE 489 (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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464A LEU* 3.7 21.7 - - + +
468A LEU* 5.3 1.8 - - + -
472A ILE* 4.1 15.5 - - + -
477A PHE* 4.4 24.5 - - + -
479A ILE* 4.6 8.7 - - + -
482A PHE* 4.6 8.5 - - + -
485A MET* 2.8 33.1 + - + +
486A TRP* 3.3 22.4 + - + +
488A GLY* 1.3 71.9 - - - +
490A PHE* 1.3 63.3 + - - +
492A TYR* 3.4 7.2 + - - +
493A MET* 3.0 47.6 + - + +
531A VAL* 4.6 9.2 - - + -
535A HIS* 5.5 0.7 - - + -
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Residues in contact with PHE 490 (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 TRP 3.2 10.6 + - - +
487A PRO* 3.1 12.7 + - + +
489A ILE* 1.3 76.4 - - - +
491A VAL* 1.3 65.5 + - - +
493A MET* 3.3 13.3 + - + +
494A VAL* 3.0 44.7 + - + +
508A LEU* 4.9 0.7 - - + -
512A ILE* 3.5 28.0 - - + -
531A VAL* 5.3 4.5 - - + -
534A ALA* 3.6 25.8 - - + -
557A LEU* 3.4 40.2 - - + -
558A ILE* 3.9 16.6 - - + -
561A LEU* 3.8 34.3 - - + -
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Residues in contact with VAL 491 (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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459A LEU* 3.8 25.8 - - + +
487A PRO 3.1 13.8 + - - +
488A GLY* 3.4 8.7 - - - +
490A PHE* 1.3 73.8 - - - +
492A TYR* 1.3 56.2 + - - +
494A VAL* 3.0 8.5 + - - +
495A HIS* 2.8 62.3 + - + +
505A LEU* 4.5 6.7 - - + -
508A LEU* 4.8 5.6 - - + -
509A CYS* 4.8 6.7 - - - -
512A ILE* 3.7 20.9 - - + -
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Residues in contact with TYR 492 (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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464A LEU* 3.9 20.4 - - + -
469A CYS* 3.7 41.1 + - - +
472A ILE* 4.0 31.2 - - + -
473A GLU* 4.0 7.9 + - - -
488A GLY 2.9 17.1 + - - +
489A ILE* 3.6 6.5 - - - +
491A VAL* 1.3 78.6 - - - +
493A MET* 1.3 62.5 + - + +
495A HIS* 3.4 6.0 + - + +
496A ARG* 2.8 63.5 + - + +
538A TYR* 3.9 9.9 - - - -
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Residues in contact with MET 493 (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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472A ILE* 3.9 14.8 - - + -
489A ILE* 3.0 35.1 + - + +
490A PHE* 3.8 21.5 - - + +
492A TYR* 1.3 74.9 - - + +
494A VAL* 1.3 61.4 + - + +
497A SER* 2.9 29.0 + - - -
531A VAL* 4.7 4.0 - - + +
534A ALA* 4.2 5.2 - - + +
535A HIS* 3.6 40.2 - - + +
538A TYR* 3.3 59.6 - - + -
557A LEU* 4.6 5.4 - - + -
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Residues in contact with VAL 494 (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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490A PHE* 3.0 50.5 + - + +
491A VAL* 3.6 6.5 - - - +
493A MET* 1.3 75.1 - - - +
495A HIS* 1.3 62.2 + - + +
498A CYS* 2.8 37.8 + - + +
499A GLY 3.5 0.7 + - - +
502A CYS* 5.0 1.6 - - + -
503A PHE* 3.5 39.5 - - + -
508A LEU* 4.4 15.0 - - + -
557A LEU* 4.2 19.1 - - + -
558A ILE* 5.2 1.8 - - + -
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Residues in contact with HIS 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A VAL* 2.8 34.3 + - + +
492A TYR* 3.8 6.9 - - + +
494A VAL* 1.3 76.8 - - + +
496A ARG* 1.3 61.4 + - + +
499A GLY* 3.0 33.3 + - - -
500A THR* 3.7 47.9 + - + +
503A PHE* 5.3 4.2 + + - -
505A LEU* 3.6 35.7 - - + +
508A LEU* 4.0 16.0 - - + +
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Residues in contact with ARG 496 (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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473A GLU* 5.0 2.5 - - - -
492A TYR* 2.8 57.5 + - + +
495A HIS* 1.3 83.0 + - + +
497A SER* 1.3 61.3 + - - +
499A GLY* 4.5 1.0 + - - -
538A TYR* 3.1 24.2 - - + +
542A GLN* 4.3 11.6 + - - +
545A HIS* 5.4 1.2 - - - -
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Residues in contact with SER 497 (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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493A MET 2.9 17.7 + - - -
496A ARG* 1.3 80.4 - - - +
498A CYS* 1.3 60.6 + - - +
538A TYR* 4.1 11.8 - - - -
541A LEU* 4.4 8.7 - - - +
542A GLN* 4.0 12.1 + - - -
545A HIS* 3.3 12.6 - - - -
553A ARG* 3.3 41.1 + - - +
557A LEU* 3.9 19.0 - - - +
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Residues in contact with CYS 498 (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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494A VAL* 2.8 22.9 + - + +
497A SER* 1.3 86.2 - - - +
499A GLY* 1.3 61.7 + - - +
502A CYS* 3.6 32.4 + - + +
550A ASP* 4.9 3.2 - - + +
553A ARG* 4.0 18.1 + - - +
554A LYS* 3.7 35.0 - - + -
557A LEU* 4.1 7.6 - - - -
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Residues in contact with GLY 499 (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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494A VAL 3.5 0.9 + - - +
495A HIS* 3.0 27.7 + - - -
496A ARG 4.4 1.2 + - - -
497A SER 3.7 1.0 - - - -
498A CYS* 1.3 79.5 - - - +
500A THR* 1.3 62.5 + - - -
501A SER* 3.1 7.4 + - - -
502A CYS* 3.2 15.7 + - - +
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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