Contacts of the helix formed by residues 549 - 563 (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 THR 549 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548B PHE* 1.3 75.7 - - - +
550B ASP* 1.3 66.1 + - - +
551B LEU* 3.6 9.0 + - - +
552B GLU* 3.0 44.0 + - - +
553B ARG* 2.9 22.8 + - - +
662B ARG* 4.5 8.3 - - - +
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Residues in contact with ASP 550 (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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498B CYS* 5.2 2.1 - - - +
549B THR* 1.3 71.8 - - - +
551B LEU* 1.3 63.9 + - + +
553B ARG* 2.8 36.9 + - - +
554B LYS* 3.1 41.0 + - - +
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Residues in contact with LEU 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B THR* 3.2 7.9 + - - +
550B ASP* 1.3 80.9 - - + +
552B GLU* 1.3 55.9 + - - +
554B LYS* 3.4 16.4 - - + +
555B GLY* 3.1 24.9 + - - -
614B LEU* 3.8 37.2 - - + -
618B GLU* 4.2 29.2 - - + +
621B GLN* 3.8 23.3 - - + +
622B VAL* 3.8 16.6 - - + +
625B ILE* 3.9 11.9 - - + +
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Residues in contact with GLU 552 (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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548B PHE* 3.5 14.7 - - + -
549B THR* 3.0 32.6 + - - +
551B LEU* 1.3 74.5 - - - +
553B ARG* 1.3 58.1 + - - +
556B LEU* 2.7 48.0 + - + +
625B ILE* 3.9 23.3 - - + +
659B GLN* 5.1 4.0 + - - -
662B ARG* 2.8 47.5 + - - +
666B ILE* 3.8 21.8 - - + +
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Residues in contact with ARG 553 (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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497B SER* 3.0 45.2 + - - +
498B CYS* 3.9 16.6 + - - +
541B LEU* 4.1 22.7 - - + +
545B HIS* 4.4 22.5 + - - +
548B PHE* 3.2 37.5 + - + -
549B THR 2.9 12.6 + - - +
550B ASP* 2.8 41.6 + - - +
552B GLU* 1.3 77.1 - - - +
554B LYS* 1.3 62.2 + - - +
556B LEU* 4.1 0.2 - - - -
557B LEU* 3.2 30.7 + - - +
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Residues in contact with LYS 554 (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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498B CYS* 3.6 18.9 - - - -
502B CYS* 3.6 29.4 + - - +
503B PHE* 3.7 20.0 - - + -
550B ASP* 3.1 36.5 + - - +
551B LEU* 3.4 22.0 - - + +
553B ARG* 1.3 77.1 - - - +
555B GLY* 1.3 64.6 + - - +
557B LEU* 4.1 1.7 - - - +
558B ILE* 3.2 30.1 + - - +
611B PHE* 4.3 20.4 - - + -
614B LEU* 4.3 19.0 - - + +
622B VAL* 4.6 1.3 - - + -
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Residues in contact with GLY 555 (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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551B LEU 3.1 17.4 + - - -
552B GLU 3.9 0.7 - - - -
554B LYS* 1.3 79.0 - - - +
556B LEU* 1.3 51.1 + - - +
558B ILE* 3.4 2.4 + - - -
559B ALA* 2.7 36.7 + - - +
611B PHE* 4.7 0.7 - - - -
622B VAL* 3.7 19.3 - - - -
625B ILE* 4.3 5.4 - - - -
626B ILE* 3.6 16.6 - - - +
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Residues in contact with LEU 556 (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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537B MET* 4.1 24.5 - - + -
541B LEU* 4.6 8.7 - - + -
548B PHE* 4.9 2.2 - - + -
552B GLU* 2.7 34.4 + - + +
553B ARG 4.2 2.0 - - - +
555B GLY* 1.3 74.5 - - - +
557B LEU* 1.3 56.0 + - - +
559B ALA* 3.5 2.3 - - - +
560B CYS* 3.0 34.0 + - - -
625B ILE* 4.0 13.4 - - + +
629B ALA* 3.7 20.6 - - + -
666B ILE* 3.6 39.0 - - + -
669B MET* 4.0 26.9 - - + -
670B MET* 4.5 0.4 - - - -
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Residues in contact with LEU 557 (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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490B PHE* 3.3 25.8 - - + -
493B MET* 4.1 13.9 - - + +
494B VAL* 4.1 13.5 - - + +
497B SER* 4.0 28.7 - - - +
498B CYS* 4.1 9.6 - - - -
534B ALA* 3.5 28.5 - - + +
537B MET* 4.0 7.6 - - + -
538B TYR* 3.8 21.3 - - + +
541B LEU* 4.0 6.3 - - + -
553B ARG 3.2 21.4 + - - +
554B LYS* 4.1 3.4 - - - +
556B LEU* 1.3 71.5 - - - +
558B ILE* 1.3 65.5 + - - +
560B CYS* 3.4 5.3 + - - +
561B LEU 3.1 16.6 + - - -
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Residues in contact with ILE 558 (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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490B PHE* 4.0 22.2 - - + -
494B VAL* 5.4 0.9 - - + -
503B PHE* 4.4 11.9 - - + -
508B LEU* 4.7 2.9 - - + -
511B PHE* 3.7 34.8 - - + -
554B LYS 3.2 17.7 + - - +
555B GLY 3.6 3.6 - - - +
557B LEU* 1.3 76.8 - - + +
559B ALA* 1.3 65.5 + - - +
560B CYS 3.2 0.2 + - - -
561B LEU* 3.2 3.1 + - + +
562B CYS* 3.0 26.5 + - - +
599B THR* 5.1 2.5 - - + -
603B LEU* 5.8 0.4 - - + -
610B ILE* 3.6 28.7 - - + -
611B PHE* 4.0 11.7 - - + -
626B ILE* 3.9 22.0 - - + -
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Residues in contact with ALA 559 (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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555B GLY 2.7 21.4 + - - +
556B LEU* 3.2 8.3 + - - +
558B ILE* 1.3 73.0 - - - +
560B CYS* 1.3 58.8 + - - +
562B CYS 3.2 2.3 + - - -
563B HIS* 2.9 32.7 + - - +
626B ILE* 4.1 26.7 - - + +
629B ALA* 3.8 28.9 - - + -
630B ILE* 3.8 5.3 - - + +
670B MET* 4.5 3.6 - - + -
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Residues in contact with CYS 560 (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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530B ALA* 3.8 7.9 - - - +
533B VAL* 3.8 15.2 - - + +
534B ALA* 3.7 23.8 - - - +
537B MET* 3.6 26.0 - - + -
556B LEU 3.0 22.7 + - - +
557B LEU 3.7 3.4 - - - +
558B ILE 3.1 0.2 - - - -
559B ALA* 1.3 74.9 - - - +
561B LEU* 1.3 62.7 + - - +
562B CYS 3.3 0.3 + - - -
563B HIS* 2.8 27.3 + - - -
670B MET* 3.6 31.4 - - - -
673B CYS* 4.7 1.8 - - - -
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Residues in contact with LEU 561 (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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490B PHE* 3.8 44.6 - - + -
511B PHE* 4.8 5.2 - - + -
512B ILE* 4.2 13.0 - - + -
515B VAL* 3.9 26.4 - - + +
519B TYR* 2.6 34.3 + - - -
527B TRP* 3.5 33.9 - - + -
530B ALA* 3.5 13.5 - - + +
531B VAL* 4.0 14.1 - - + -
534B ALA* 4.4 1.2 - - + +
557B LEU 3.1 13.9 + - - +
558B ILE 3.7 7.0 - - - +
560B CYS* 1.3 76.5 - - - +
562B CYS* 1.3 52.9 + - - +
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Residues in contact with CYS 562 (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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511B PHE* 3.7 31.9 - - - -
515B VAL* 3.8 17.3 - - - -
519B TYR* 3.4 3.4 - - - -
558B ILE* 3.0 20.8 + - - +
559B ALA* 3.9 2.9 - - - +
561B LEU* 1.3 78.9 - - - +
563B HIS* 1.3 61.8 + - - +
564B ASP 3.1 3.8 + - - -
565B LEU* 3.1 31.7 + - + +
595B HIS* 4.0 4.7 - - - +
599B THR* 3.4 28.8 + - + +
602B ILE* 6.5 0.2 - - - -
630B ILE* 4.2 4.2 - - + +
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Residues in contact with HIS 563 (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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519B TYR* 4.3 0.6 + - - -
529B HIS* 3.4 17.0 - + - -
530B ALA* 4.5 6.1 - - - -
533B VAL* 3.6 21.9 - - + +
559B ALA 2.9 15.9 + - - +
560B CYS* 2.8 25.2 + - - +
561B LEU 3.5 0.4 - - - -
562B CYS* 1.3 75.4 - - - +
564B ASP* 1.3 66.6 + - + +
565B LEU 3.6 0.4 - - - -
595B HIS* 2.9 25.2 - - - +
630B ILE* 3.9 20.2 - - + +
633B THR* 4.1 28.9 + - + +
670B MET* 4.4 1.8 - - + -
674B ASP* 3.1 4.3 + - - -
901B NI 2.2 43.9 - - + +
902B NI 4.2 1.8 - - + -
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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