Contacts of the helix formed by residues 615 - 633 (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 SER 615 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613B THR 4.0 1.0 + - - -
614B LEU* 1.3 76.7 - - - +
616B SER* 1.3 59.5 + - - +
617B SER* 3.3 11.1 + - - -
618B GLU* 2.9 41.2 + - - +
619B TYR* 2.7 27.4 + - - +
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Residues in contact with SER 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B LEU 3.9 0.2 + - - -
615B SER* 1.3 73.6 - - - +
617B SER* 1.3 61.9 + - - +
619B TYR* 3.9 8.6 - - - +
620B GLU* 3.3 22.3 + - - +
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Residues in contact with SER 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B SER* 3.1 9.1 - - - -
616B SER* 1.3 82.2 + - - +
618B GLU* 1.3 62.5 + - - +
620B GLU* 3.4 6.1 + - - +
621B GLN* 3.1 38.2 + - - +
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Residues in contact with GLU 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B LEU* 4.2 23.1 - - + +
613B THR 4.8 0.7 - - - +
614B LEU* 3.5 29.9 - - + +
615B SER* 2.9 39.1 + - - +
617B SER* 1.3 73.3 - - - +
619B TYR* 1.3 60.6 + - - +
621B GLN* 3.2 14.5 + - - +
622B VAL* 3.0 30.5 + - - +
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Residues in contact with TYR 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B LEU* 4.4 8.0 - - - +
604B GLN* 5.5 4.7 + - - +
609B ASN* 2.9 42.2 + - - -
611B PHE* 3.8 27.4 - + + -
612B SER* 5.3 2.2 - - - -
614B LEU* 4.0 11.1 - - + +
615B SER 2.7 20.0 + - - +
616B SER* 4.0 9.9 - - - +
618B GLU* 1.3 74.2 - - - +
620B GLU* 1.3 64.1 + - - +
622B VAL* 3.5 4.7 - - - +
623B LEU* 3.2 47.7 + - + +
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Residues in contact with GLU 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616B SER 3.3 17.4 + - - +
617B SER* 3.8 5.6 - - - +
618B GLU 3.3 0.4 - - - -
619B TYR* 1.3 81.0 - - - +
621B GLN* 1.3 63.2 + - + +
623B LEU* 3.6 4.1 + - - +
624B GLU* 3.1 32.1 + - + +
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Residues in contact with GLN 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B LEU* 3.8 21.9 - - + +
617B SER* 3.1 33.1 + - - +
618B GLU* 3.2 15.9 + - - +
620B GLU* 1.3 77.9 - - + +
622B VAL* 1.3 58.9 + - - +
624B GLU* 3.3 8.1 - - - +
625B ILE* 3.0 36.8 + - + +
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Residues in contact with VAL 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B LEU* 3.8 26.0 - - + +
554B LYS* 4.6 0.7 - - + -
555B GLY* 3.7 27.6 - - - +
611B PHE* 3.9 35.9 - - + -
614B LEU* 4.0 6.5 - - + -
618B GLU 3.0 13.6 + - - +
619B TYR* 3.5 12.3 - - - +
621B GLN* 1.3 75.3 - - - +
623B LEU* 1.3 74.6 + - + +
625B ILE* 3.4 6.2 + - + +
626B ILE* 2.9 35.0 + - + +
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Residues in contact with LEU 623 (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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596B PHE* 3.6 34.7 - - + -
599B THR* 5.5 0.4 - - + -
600B VAL* 4.2 11.7 - - + +
603B LEU* 4.2 25.4 - - + -
611B PHE* 4.5 3.4 - - + -
619B TYR* 3.2 54.4 + - + +
620B GLU* 4.2 4.3 - - - +
622B VAL* 1.3 85.8 - - + +
624B GLU* 1.3 62.7 + - - +
626B ILE* 3.7 7.6 - - + +
627B ARG* 2.8 33.6 + - - +
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Residues in contact with GLU 624 (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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620B GLU* 3.1 25.1 + - + +
621B GLN* 3.3 12.6 - - - +
623B LEU* 1.3 77.3 - - - +
625B ILE* 1.3 62.7 + - + +
627B ARG* 2.5 38.3 + - - +
628B LYS* 2.9 48.5 + - - +
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Residues in contact with ILE 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B LEU* 3.9 21.8 - - + +
552B GLU* 3.9 29.4 - - + +
555B GLY* 4.3 4.5 - - - -
556B LEU* 4.0 37.2 - - + +
621B GLN* 3.0 24.4 + - + +
622B VAL* 3.5 13.7 - - - +
624B GLU* 1.3 74.0 - - + +
626B ILE* 1.3 59.1 + - - +
628B LYS* 3.5 7.6 + - - +
629B ALA* 3.0 27.4 + - - +
659B GLN* 6.3 0.7 - - - +
666B ILE* 5.4 8.8 - - + +
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Residues in contact with ILE 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B GLY* 3.6 22.0 - - - +
558B ILE* 3.9 13.9 - - + -
559B ALA* 4.1 17.0 - - + -
596B PHE* 4.2 11.2 - - + -
599B THR* 4.3 11.0 - - + -
603B LEU* 5.2 3.1 - - + -
611B PHE* 3.8 34.8 - - + -
622B VAL 2.9 27.8 + - - +
623B LEU* 3.7 12.8 - - + +
625B ILE* 1.3 71.9 - - - +
627B ARG* 1.3 60.5 - - - +
629B ALA* 3.3 1.0 + - - +
630B ILE* 2.9 48.5 + - + +
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Residues in contact with ARG 627 (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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596B PHE* 3.5 45.4 - - + +
623B LEU 2.8 16.8 + - - +
624B GLU* 2.5 40.9 + - - +
626B ILE* 1.3 79.2 - - - +
628B LYS* 1.3 81.1 + - - +
630B ILE* 3.8 1.7 - - - +
631B ILE* 2.9 51.0 + - + +
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Residues in contact with LYS 628 (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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624B GLU* 2.9 44.8 + - - +
625B ILE* 3.9 6.0 - - - +
627B ARG* 1.3 93.7 - - - +
629B ALA* 1.3 58.8 + - - +
631B ILE* 3.4 5.9 + - - +
632B ALA* 2.9 30.5 + - - +
659B GLN* 4.4 12.3 - - - +
663B ASP* 3.1 43.9 + - + +
666B ILE* 6.2 2.2 - - + -
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Residues in contact with ALA 629 (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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556B LEU* 3.7 25.6 - - + -
559B ALA* 3.8 13.7 - - + -
625B ILE 3.0 19.5 + - - +
626B ILE 3.7 4.3 - - - +
627B ARG 3.2 0.2 - - - -
628B LYS* 1.3 78.4 - - - +
630B ILE* 1.3 61.8 + - - +
632B ALA* 3.3 17.4 + - - +
633B THR* 3.5 7.1 + - - +
666B ILE* 4.4 6.5 - - + +
670B MET* 3.5 25.3 - - + +
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Residues in contact with ILE 630 (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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559B ALA* 3.8 23.3 - - + +
562B CYS* 4.2 4.0 - - + +
563B HIS* 3.9 21.3 - - + +
592B GLU* 3.5 29.7 - - - +
595B HIS* 4.0 13.9 - - + -
596B PHE* 4.1 14.8 - - + +
599B THR* 3.7 23.3 - - - +
626B ILE* 2.9 34.9 + - + +
627B ARG* 3.9 3.6 - - - +
629B ALA* 1.3 72.8 - - - +
631B ILE* 1.3 64.5 + - + +
633B THR* 2.5 30.6 + - - -
670B MET* 4.9 0.2 - - - -
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Residues in contact with ILE 631 (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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589B SER* 4.4 9.6 - - - +
592B GLU* 3.9 10.0 - - + +
593B GLN* 3.9 40.8 - - + +
596B PHE* 5.4 1.8 - - + -
627B ARG* 2.9 43.1 + - + +
628B LYS* 3.8 5.6 - - - +
630B ILE* 1.3 77.5 - - + +
632B ALA* 1.3 55.0 + - - +
634B ASP* 3.0 28.6 + - - +
637B LEU* 3.6 23.2 - - + +
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Residues in contact with ALA 632 (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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628B LYS 2.9 17.6 + - - +
629B ALA* 3.5 8.5 - - - +
630B ILE 3.2 0.4 - - - -
631B ILE* 1.3 75.1 - - - +
633B THR* 1.3 60.3 + - - +
634B ASP 3.1 10.1 + - - +
637B LEU* 4.9 9.6 - - - +
638B TYR* 5.0 4.0 + - - +
667B GLY* 3.6 34.7 - - - +
670B MET* 4.4 2.5 - - + -
671B THR* 3.9 15.4 + - - -
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Residues in contact with THR 633 (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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563B HIS* 4.1 30.1 + - + -
564B ASP* 5.4 1.0 + - - -
592B GLU* 3.7 12.1 - - - +
595B HIS* 5.5 0.2 - - - -
629B ALA 3.6 14.8 - - - +
630B ILE* 2.5 19.6 + - - +
632B ALA* 1.3 74.2 - - - +
634B ASP* 1.3 59.4 + - - +
635B LEU* 3.1 10.5 + - - +
670B MET* 3.7 35.0 - - + +
671B THR* 5.3 4.0 - - - +
674B ASP* 3.9 22.8 - - - +
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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
------------------------------------------------------------
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