Contacts of the helix formed by residues 658 - 675 (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 ASN 658 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653B SER 4.7 1.0 + - - -
655B ASN* 3.0 18.9 + - - +
657B ASN* 1.3 78.3 - - - +
659B GLN* 1.3 67.2 + - - +
660B SER* 4.4 3.8 - - - +
661B HIS* 3.0 50.7 + - + +
662B ARG* 2.9 22.4 + - - +
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Residues in contact with GLN 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B GLU* 5.1 4.8 + - - -
625B ILE* 6.3 1.0 - - - +
628B LYS* 4.4 11.0 - - - +
657B ASN 3.6 4.4 + - - -
658B ASN* 1.3 71.7 - - - +
660B SER* 1.3 58.4 + - - +
662B ARG* 3.1 22.5 + - - +
663B ASP* 2.6 60.7 + - - +
666B ILE* 5.6 1.2 - - - +
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Residues in contact with SER 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658B ASN* 3.2 3.3 - - - +
659B GLN* 1.3 78.3 - - - +
661B HIS* 1.3 72.5 + - - +
663B ASP* 3.7 12.5 - - - +
664B ARG* 3.2 33.2 + - - +
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Residues in contact with HIS 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B LEU* 4.7 0.3 - - - +
648B MET* 3.2 38.9 - - + +
653B SER* 3.4 14.3 + - - -
654B LEU* 3.5 3.6 - - + -
655B ASN 2.8 47.6 - - - +
656B LEU* 4.8 1.1 - - - -
658B ASN* 3.0 32.6 + - + +
660B SER* 1.3 83.0 + - - +
662B ARG* 1.3 65.5 + - - +
664B ARG* 3.1 15.4 + - - +
665B VAL* 3.1 18.7 + - - +
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Residues in contact with ARG 662 (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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547B LEU 2.7 30.1 + - - -
548B PHE* 3.9 8.8 - - - +
549B THR* 4.2 9.0 - - - +
552B GLU* 2.8 40.9 + - - +
656B LEU* 2.8 68.2 + - + +
657B ASN* 5.3 1.3 + - - +
658B ASN 2.9 11.6 + - - +
659B GLN* 3.4 25.8 - - - +
661B HIS* 1.3 75.0 - - - +
663B ASP* 1.3 56.4 + - - +
665B VAL* 3.2 4.5 + - - +
666B ILE* 2.9 37.6 + - + +
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Residues in contact with ASP 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B LYS* 3.1 43.6 + - + +
659B GLN* 2.6 49.7 + - - +
660B SER* 3.7 12.6 - - - +
662B ARG* 1.3 72.6 - - - +
664B ARG* 1.3 52.9 + - + +
666B ILE* 3.5 11.8 + - - +
667B GLY* 2.8 30.0 + - - -
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Residues in contact with ARG 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B GLY 4.6 0.4 - - - -
641B ASN* 2.9 71.6 + - - +
644B GLN* 3.6 33.1 - - - +
645B LEU* 3.5 17.0 - - + +
648B MET* 4.4 17.7 - - - -
660B SER* 3.2 17.5 + - - +
661B HIS* 3.1 11.4 + - - +
663B ASP* 1.3 78.3 - - + +
665B VAL* 1.3 59.1 + - - +
667B GLY 3.2 0.3 + - - -
668B LEU 2.9 13.2 + - - -
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Residues in contact with VAL 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B PHE* 4.9 6.1 - - + -
645B LEU* 3.8 21.8 - - + -
654B LEU* 4.1 4.0 - - + -
656B LEU* 3.9 25.1 - - + -
661B HIS 3.1 16.0 + - - +
662B ARG* 3.8 7.0 - - - +
664B ARG* 1.3 71.4 - - - +
666B ILE* 1.3 61.8 + - - +
668B LEU* 3.1 6.4 + - + +
669B MET* 2.9 43.6 + - + +
741B LEU* 5.0 2.6 - - + +
744B ILE* 3.9 27.6 - - + -
745B LEU* 4.6 13.2 - - + -
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Residues in contact with ILE 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B PHE* 4.3 14.8 - - + -
552B GLU* 3.8 30.5 - - + +
556B LEU* 3.6 44.0 - - + -
625B ILE* 5.4 8.1 - - + +
628B LYS* 5.9 2.0 - - + -
629B ALA* 4.4 13.9 - - + +
659B GLN* 5.6 1.1 - - - +
662B ARG* 2.9 26.5 + - + +
663B ASP* 3.6 12.6 - - - +
665B VAL* 1.3 75.5 - - + +
667B GLY* 1.3 56.9 + - - +
669B MET* 3.3 10.0 + - - +
670B MET* 2.8 29.9 + - + +
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Residues in contact with GLY 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B ALA* 6.0 0.2 - - - -
632B ALA* 3.6 27.5 - - - +
641B ASN* 3.9 9.2 - - - -
663B ASP 2.8 19.8 + - - -
664B ARG* 3.2 6.0 + - - -
666B ILE* 1.3 74.3 - - - +
668B LEU* 1.3 61.1 + - - +
670B MET* 3.2 6.2 + - - +
671B THR* 3.1 23.5 + - - -
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Residues in contact with LEU 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B TYR* 3.8 33.2 - - + -
641B ASN* 3.5 4.1 - - - +
642B ARG* 4.3 11.0 - - + -
645B LEU* 3.8 16.6 - - + -
664B ARG 2.9 12.6 + - - +
665B VAL* 3.1 8.3 + - + +
667B GLY* 1.3 71.4 - - - +
669B MET* 1.3 56.0 + - - +
671B THR* 3.1 7.1 + - - -
672B ALA* 2.8 33.1 + - - +
737B CYS* 3.9 15.0 - - - +
740B THR* 3.8 19.1 - - + -
741B LEU* 3.6 38.4 - - + +
744B ILE* 4.4 6.1 - - + -
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Residues in contact with MET 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B MET* 3.8 29.2 - - + -
540B ILE* 4.1 22.4 - - + -
541B LEU* 4.3 2.9 - - + -
548B PHE* 3.3 46.2 - - + -
556B LEU* 4.0 13.5 - - + -
665B VAL* 2.9 25.6 + - - +
666B ILE* 3.3 11.7 - - - +
668B LEU* 1.3 72.3 - - - +
670B MET* 1.3 58.7 + - - +
672B ALA* 3.4 3.5 + - - +
673B CYS* 2.8 37.5 + - - -
741B LEU* 3.8 22.8 - - + +
745B LEU* 4.1 4.0 - - + -
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Residues in contact with MET 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B VAL* 5.0 2.5 - - + +
537B MET* 3.5 25.4 - - + -
556B LEU* 4.5 3.4 - - - +
559B ALA 4.5 1.3 - - - -
560B CYS* 3.6 32.8 - - - +
563B HIS* 4.4 7.9 - - + -
629B ALA* 3.5 53.2 - - + +
632B ALA* 4.4 3.1 - - + -
633B THR* 3.7 24.3 - - + +
666B ILE* 2.8 23.8 + - + +
667B GLY 3.2 9.4 + - - +
669B MET* 1.3 73.1 - - - +
671B THR* 1.3 58.6 + - - +
673B CYS* 3.4 3.4 + - - +
674B ASP* 2.8 29.7 + - - +
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Residues in contact with THR 671 (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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632B ALA 3.9 11.1 + - - -
633B THR* 5.3 2.8 - - - +
635B LEU* 3.8 15.4 - - + -
638B TYR* 3.7 41.4 - - + +
667B GLY 3.1 12.7 + - - -
668B LEU 3.1 8.8 + - - -
670B MET* 1.3 76.3 - - - +
672B ALA* 1.3 62.2 + - - +
674B ASP* 3.1 7.1 + - + +
675B LEU* 2.9 50.7 + - + +
737B CYS* 4.0 5.2 - - - -
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Residues in contact with ALA 672 (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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536B CYS* 4.3 2.4 - - - -
540B ILE* 4.7 3.6 - - + -
668B LEU 2.8 20.2 + - - +
669B MET 3.7 5.2 - - - +
671B THR* 1.3 73.5 - - - +
673B CYS* 1.3 60.6 + - - +
676B CYS* 3.4 7.6 + - - +
737B CYS* 3.6 12.4 - - - -
738B TYR* 2.7 49.0 + - + -
741B LEU* 3.7 24.0 - - + -
751B LEU* 4.9 0.4 - - + -
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Residues in contact with CYS 673 (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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533B VAL* 3.5 31.7 - - + +
536B CYS* 3.6 12.3 - - + -
537B MET* 3.3 45.5 - - - -
540B ILE* 3.6 13.0 - - - -
560B CYS* 4.7 1.6 - - - -
669B MET 2.8 24.9 + - - +
670B MET* 3.7 4.5 - - - +
672B ALA* 1.3 67.3 - - - +
674B ASP* 1.3 67.1 + - - +
675B LEU 3.1 2.3 + - - -
676B CYS* 3.2 21.7 + - - -
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Residues in contact with ASP 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B TYR* 3.6 8.3 + - - -
529B HIS* 2.9 25.5 + - - -
533B VAL* 3.7 8.2 - - + +
563B HIS* 3.1 7.5 + - - -
633B THR* 3.9 22.1 - - + +
670B MET 2.8 18.6 + - - +
671B THR* 3.1 13.4 + - + +
673B CYS* 1.3 74.4 - - - +
675B LEU* 1.3 69.0 + - + +
676B CYS* 3.5 0.7 + - - -
677B SER* 5.1 0.3 + - - -
901B NI 2.3 43.5 - - - +
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Residues in contact with LEU 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B TYR* 5.1 6.5 - - - +
635B LEU* 4.6 9.9 - - + -
671B THR* 2.9 36.0 + - + +
672B ALA 3.5 0.2 + - - -
673B CYS 3.1 0.2 - - - -
674B ASP* 1.3 89.8 - - + +
676B CYS* 1.3 52.0 + - - +
677B SER* 2.8 18.2 + - - -
678B VAL* 3.1 24.5 + - + +
729B PHE* 3.9 26.0 - - + -
733B VAL* 3.9 24.0 - - + -
734B ALA* 4.7 9.6 - - - -
737B CYS* 4.9 6.3 - - + -
738B TYR* 3.3 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
------------------------------------------------------------
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