Contacts of the helix formed by residues 485 - 499 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462B PHE* 3.9 24.9 - - + -
464B LEU* 5.0 0.9 - - - -
465B PRO* 3.8 37.7 - - + -
467B ARG* 4.1 12.6 - - - +
468B LEU* 4.0 10.8 - - + -
482B PHE* 2.8 44.8 + - + +
484B ASN* 1.3 79.3 - - + +
486B TRP* 1.3 58.1 + - - +
487B PRO* 3.4 3.1 - - - -
488B GLY* 3.0 3.8 + - - +
489B ILE* 2.8 39.5 + - + +
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Residues in contact with TRP 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479B ILE* 2.9 49.8 + - + +
480B GLY* 3.9 14.8 - - - -
482B PHE 3.1 17.3 + - - -
483B GLU* 3.0 51.5 + - + +
485B MET* 1.3 76.5 - - - +
487B PRO* 1.4 70.4 - - + +
489B ILE* 3.3 11.5 + - + +
490B PHE* 3.2 17.5 + - - +
527B TRP* 3.7 26.7 - + - +
528B LYS* 3.5 48.9 - - + -
531B VAL* 3.7 23.3 - - + +
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Residues in contact with PRO 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B LEU* 3.6 17.0 - - + -
483B GLU 4.1 4.0 - - - +
484B ASN* 3.9 12.3 - - - +
485B MET 3.5 4.3 - - - -
486B TRP* 1.4 92.6 - - + +
488B GLY* 1.3 56.0 + - - +
490B PHE* 3.2 6.9 + - + +
491B VAL* 3.1 28.4 + - - +
512B ILE* 3.9 13.5 - - + +
513B MET* 3.9 28.5 - - + -
516B LYS* 5.0 6.7 - - + -
527B TRP* 4.1 20.4 - - + +
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Residues in contact with GLY 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B LEU* 3.5 12.8 - - - +
462B PHE* 3.4 37.1 - - - -
485B MET* 3.0 6.4 + - - +
487B PRO* 1.3 77.7 - - - +
489B ILE* 1.3 59.1 + - - +
491B VAL* 3.5 5.7 + - - +
492B TYR* 3.0 28.9 + - - +
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Residues in contact with ILE 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B LEU* 3.6 24.9 - - + -
468B LEU* 5.4 0.9 - - + -
472B ILE* 3.9 19.5 - - + +
477B PHE* 5.0 6.7 - - + -
479B ILE* 4.6 17.9 - - + -
482B PHE* 4.3 14.6 - - + -
485B MET* 2.8 39.1 + - + +
486B TRP* 3.5 18.6 - - + +
488B GLY* 1.3 74.4 - - - +
490B PHE* 1.3 64.1 + - - +
492B TYR* 3.4 6.6 + - - +
493B MET* 3.0 38.6 + - + +
531B VAL* 4.4 9.9 - - + -
535B HIS* 5.4 0.7 - - + -
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Residues in contact with PHE 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B TRP 3.2 12.4 + - - +
487B PRO* 3.2 10.7 + - + +
489B ILE* 1.3 75.6 - - - +
491B VAL* 1.3 64.7 + - - +
493B MET* 3.3 13.1 + - + +
494B VAL* 3.0 46.6 + - + +
508B LEU* 4.5 1.6 - - + -
512B ILE* 3.4 33.7 - - + -
531B VAL* 4.9 4.3 - - + -
534B ALA* 3.8 18.6 - - + -
557B LEU* 3.3 40.2 - - + -
558B ILE* 4.0 19.1 - - + -
561B LEU* 3.8 35.7 - - + -
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Residues in contact with VAL 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B LEU* 3.8 24.2 - - + +
462B PHE* 6.1 1.1 - - + +
487B PRO 3.1 10.9 + - - +
488B GLY* 3.7 8.1 - - - +
489B ILE 3.4 0.2 - - - -
490B PHE* 1.3 74.7 - - - +
492B TYR* 1.3 53.1 + - - +
494B VAL* 3.2 7.6 + - - +
495B HIS* 2.8 64.2 + - + +
505B LEU* 4.6 7.9 - - + -
508B LEU* 4.6 5.6 - - + -
509B CYS* 4.4 7.9 - - - -
512B ILE* 3.4 27.8 - - + -
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Residues in contact with TYR 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B PHE* 5.8 0.2 - - + -
464B LEU* 4.2 31.9 - - + -
469B CYS* 3.8 28.3 + - - +
472B ILE* 3.8 37.0 - - + -
473B GLU* 4.4 2.0 + - - -
488B GLY 3.0 18.4 + - - +
489B ILE* 3.7 7.0 - - - +
490B PHE 3.3 0.2 - - - -
491B VAL* 1.3 76.1 - - - +
493B MET* 1.3 61.4 + - - +
495B HIS* 3.0 9.6 + - + +
496B ARG* 2.9 77.6 + - + +
538B TYR* 4.2 6.3 - - - -
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Residues in contact with MET 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B ILE* 3.9 12.8 - - + -
489B ILE* 3.0 34.8 + - + +
490B PHE* 3.8 24.0 - - + +
492B TYR* 1.3 75.0 - - + +
494B VAL* 1.3 58.4 + - + +
497B SER* 2.9 34.1 + - - -
531B VAL* 4.8 3.1 - - + +
534B ALA* 4.1 7.6 - - + +
535B HIS* 3.5 40.6 - - + +
538B TYR* 3.4 54.4 - - + -
557B LEU* 4.3 6.3 - - + -
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Residues in contact with VAL 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B PHE* 3.0 52.6 + - + +
491B VAL* 3.5 8.7 - - - +
493B MET* 1.3 76.1 - - - +
495B HIS* 1.3 61.7 + - + +
498B CYS* 2.8 44.0 + - + +
499B GLY 3.4 3.2 + - - +
503B PHE* 3.6 35.9 - - + -
508B LEU* 4.4 11.9 - - + -
557B LEU* 4.1 18.2 - - + -
558B ILE* 5.4 0.4 - - + -
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Residues in contact with HIS 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B VAL* 2.8 44.3 + - + +
492B TYR* 3.0 11.7 + - + +
494B VAL* 1.3 74.4 - - + +
496B ARG* 1.3 63.1 + - - +
499B GLY* 2.9 33.4 + - - -
500B THR* 3.7 45.8 + - + +
503B PHE 5.4 2.7 + - - -
505B LEU* 3.8 23.2 - - + +
508B LEU* 4.2 13.6 - - + +
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Residues in contact with ARG 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B GLU* 4.8 6.2 + - - -
492B TYR* 2.9 68.8 + - + +
495B HIS* 1.3 77.5 - - - +
497B SER* 1.3 62.3 + - - +
499B GLY 4.7 0.5 + - - -
538B TYR* 3.3 20.6 - - + +
542B GLN* 4.3 11.1 + - - +
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Residues in contact with SER 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B MET 2.9 18.2 + - - -
496B ARG* 1.3 78.8 - - - +
498B CYS* 1.3 59.7 + - - +
538B TYR* 3.9 17.3 - - - -
541B LEU* 4.3 9.2 - - - +
542B GLN* 4.0 13.1 + - - -
553B ARG* 3.0 52.0 + - - +
557B LEU* 4.0 14.4 - - - +
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Residues in contact with CYS 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B VAL* 2.8 24.7 + - + +
497B SER* 1.3 84.1 - - - +
499B GLY* 1.3 56.3 + - - +
502B CYS* 3.9 30.2 - - + +
550B ASP* 5.2 2.2 - - - +
553B ARG* 3.9 17.8 + - - +
554B LYS* 3.6 37.5 - - - -
557B LEU* 4.1 15.0 - - - -
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Residues in contact with GLY 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B VAL* 3.4 3.7 + - - +
495B HIS* 2.9 27.3 + - - +
496B ARG 4.7 0.4 + - - -
497B SER 3.7 0.6 - - - -
498B CYS* 1.3 78.5 - - - +
500B THR* 1.3 60.3 + - - -
501B SER* 3.1 11.1 + - - -
502B CYS* 3.4 16.6 + - - +
503B PHE 4.6 1.0 + - - -
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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
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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