Contacts of the helix formed by residues 504 - 518 (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 GLU 504 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503A PHE* 1.3 70.8 - - - +
505A LEU* 1.3 65.0 + - - +
506A GLU* 3.3 10.3 - - + +
507A LYS* 3.2 17.6 + - + +
508A LEU* 3.1 18.4 + - - +
609A ASN 5.7 1.2 - - - +
610A ILE* 5.7 0.6 + - - +
612A SER* 5.6 2.9 - - - -
613A THR* 3.5 29.0 - - + +
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Residues in contact with LEU 505 (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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460A MET* 3.5 39.9 - - + +
491A VAL* 4.5 6.7 - - + -
495A HIS* 3.6 33.9 - - + +
500A THR 5.9 1.6 - - - +
503A PHE 3.3 6.8 + - - +
504A GLU* 1.3 71.5 - - - +
506A GLU* 1.3 58.7 + - - +
508A LEU* 3.2 13.4 + - + +
509A CYS* 2.8 49.9 + - - -
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Residues in contact with GLU 506 (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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456A TRP* 4.5 10.4 - - + -
460A MET* 3.7 37.6 - - + +
504A GLU* 4.0 9.1 - - + +
505A LEU* 1.3 81.7 + - - +
507A LYS* 1.3 57.3 + - - +
509A CYS* 3.3 2.9 + - - +
510A ARG* 3.0 51.3 + - - +
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Residues in contact with LYS 507 (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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503A PHE* 6.3 0.2 - - + -
504A GLU* 3.2 21.3 + - + +
506A GLU* 1.3 75.5 - - - +
508A LEU* 1.3 61.6 + - - +
510A ARG* 3.3 5.0 + - - +
511A PHE* 2.8 30.5 + - - +
607A GLY 3.4 27.2 - - - +
608A HIS 4.4 4.0 - - - +
609A ASN 4.9 2.9 - - - +
610A ILE* 3.7 18.2 - - + +
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Residues in contact with LEU 508 (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* 4.9 2.5 - - + -
491A VAL* 4.8 7.2 - - + -
494A VAL* 4.4 15.0 - - + -
495A HIS* 4.0 29.2 - - + +
503A PHE* 3.8 33.7 - - + +
504A GLU 3.1 13.0 + - - +
505A LEU* 3.4 16.4 - - + +
507A LYS* 1.3 75.9 - - - +
509A CYS* 1.3 56.9 - - - +
511A PHE* 3.2 2.9 + - + +
512A ILE* 2.9 56.6 + - + +
558A ILE* 4.7 8.1 - - + -
610A ILE* 3.8 18.9 - - + +
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Residues in contact with CYS 509 (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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456A TRP* 3.6 21.6 - - + +
459A LEU* 3.8 22.5 - - + +
460A MET* 3.3 42.0 - - + -
491A VAL* 4.8 5.2 - - - -
505A LEU* 2.8 33.5 + - - +
506A GLU* 3.8 3.8 - - - +
508A LEU* 1.3 71.9 - - - +
510A ARG* 1.3 65.5 + - - +
512A ILE 3.6 0.2 + - - -
513A MET* 3.2 30.0 + - - +
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Residues in contact with ARG 510 (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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451A CYS* 3.7 4.1 - - - -
456A TRP* 3.6 62.0 - - + +
506A GLU* 3.0 36.9 + - - +
507A LYS* 3.7 7.2 - - - +
509A CYS* 1.3 73.1 - - - +
511A PHE* 1.3 65.7 + - - +
514A SER* 3.0 29.8 + - - -
606A GLU 4.4 3.6 - - - -
607A GLY* 3.1 34.8 + - - +
608A HIS* 3.6 24.5 - - + +
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Residues in contact with PHE 511 (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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507A LYS 2.8 18.1 + - - +
508A LEU* 3.5 4.7 - - + +
510A ARG* 1.3 79.2 - - - +
512A ILE* 1.3 59.4 + - + +
514A SER* 3.7 1.7 - - - -
515A VAL* 2.8 50.6 + - + +
558A ILE* 3.7 36.6 - - + -
561A LEU* 4.9 3.8 - - + -
562A CYS* 3.6 24.0 - - - -
599A THR* 4.6 2.7 - - + -
602A ILE* 3.6 27.3 - - + +
603A LEU* 3.7 26.0 - - + -
608A HIS* 3.7 24.0 - - + +
610A ILE* 3.8 20.9 - - + -
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Residues in contact with ILE 512 (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* 4.0 18.6 - - + -
487A PRO* 4.1 14.4 - - + +
490A PHE* 3.5 34.1 - - + -
491A VAL* 3.7 28.9 - - + +
508A LEU* 2.9 37.8 + - + +
510A ARG 3.4 0.2 - - - -
511A PHE* 1.3 78.8 - - + +
513A MET* 1.3 58.3 + - - +
515A VAL* 3.3 8.5 + - - +
516A LYS* 3.0 24.1 + - - +
527A TRP* 3.9 22.2 - - + -
561A LEU* 4.4 7.9 - - + -
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Residues in contact with MET 513 (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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451A CYS* 3.6 23.1 - - + +
455A GLU* 4.1 31.7 - - + +
456A TRP* 4.1 14.8 - - - -
459A LEU* 3.9 15.0 - - + -
487A PRO* 3.6 35.2 - - + -
509A CYS 3.2 17.8 + - - +
512A ILE* 1.3 73.8 - - - +
514A SER* 1.3 65.3 + - - +
516A LYS* 3.3 30.5 + - + +
517A LYS* 3.1 22.3 + - - +
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Residues in contact with SER 514 (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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449A SER 4.0 10.5 - - - -
450A ILE* 3.8 1.4 - - - -
451A CYS* 3.0 28.4 + - - +
510A ARG 3.0 12.9 + - - -
511A PHE 3.8 1.1 - - - -
513A MET* 1.3 75.8 - - - +
515A VAL* 1.3 66.3 + - - +
517A LYS* 3.3 2.3 + - - +
518A ASN* 2.9 29.7 + - - -
602A ILE* 4.3 7.4 - - - -
605A LEU* 4.4 1.3 - - - -
608A HIS* 2.6 34.2 + - - -
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Residues in contact with VAL 515 (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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511A PHE* 2.8 55.4 + - + +
512A ILE 3.5 5.8 - - - +
513A MET 3.3 0.2 - - - -
514A SER* 1.3 75.2 - - - +
516A LYS* 1.3 64.0 + - - +
518A ASN* 2.9 13.9 + - - -
519A TYR* 3.4 32.2 + - + -
527A TRP* 4.2 2.9 - - + -
561A LEU* 3.9 28.9 - - + +
562A CYS* 4.1 6.3 - - - -
565A LEU* 3.6 6.1 - - + +
602A ILE* 3.9 19.3 - - + -
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Residues in contact with LYS 516 (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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455A GLU* 5.4 6.2 + - - +
487A PRO* 4.7 4.5 - - + -
512A ILE 3.0 13.5 + - - +
513A MET* 3.3 35.6 - - + +
514A SER 3.2 0.2 - - - -
515A VAL* 1.3 75.5 - - - +
517A LYS* 1.3 61.3 + - - +
518A ASN 3.2 1.2 + - - -
519A TYR* 3.3 21.0 + - - +
527A TRP* 3.7 58.8 - - + +
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Residues in contact with LYS 517 (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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449A SER* 3.8 27.8 + - - +
450A ILE 2.9 32.1 + - - +
451A CYS* 4.2 7.1 - - - +
452A THR* 4.7 11.5 - - - +
455A GLU* 4.4 15.3 + - - +
513A MET 3.1 15.2 + - - +
514A SER* 3.8 8.1 - - - +
515A VAL 3.3 0.4 - - - -
516A LYS* 1.3 76.6 - - + +
518A ASN* 1.3 59.2 + - - +
519A TYR 3.5 6.4 + - - +
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Residues in contact with ASN 518 (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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447A GLY 4.6 1.9 - - - +
448A THR* 3.6 14.7 - - - +
449A SER* 2.7 51.4 + - - +
514A SER 2.9 16.9 + - - +
515A VAL 2.9 5.4 + - - +
517A LYS* 1.3 76.2 - - - +
519A TYR* 1.3 55.3 + - - +
520A ARG* 4.9 0.6 - - - +
565A LEU* 3.6 21.5 - - + -
566A ASP* 2.8 38.0 + - - +
598A GLN* 4.2 12.0 - - - +
602A ILE* 3.6 14.2 - - + +
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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