Contacts of the helix formed by residues 658 - 675 (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 ASN 658 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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655A ASN* 3.0 28.1 + - - +
657A ASN* 1.3 75.0 - - - +
659A GLN* 1.3 56.2 + - - +
660A SER* 2.7 25.5 + - - -
661A HIS* 2.7 54.5 + - + +
662A ARG* 2.9 12.3 + - - +
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Residues in contact with GLN 659 (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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552A GLU* 5.0 4.9 + - - +
625A ILE* 6.2 1.6 - - - +
628A LYS* 4.7 6.6 - - - +
657A ASN 3.8 4.4 + - - -
658A ASN* 1.3 71.2 + - - +
660A SER* 1.3 57.4 + - - +
662A ARG* 3.2 25.4 + - - +
663A ASP* 2.8 60.9 + - - +
666A ILE* 5.8 1.2 - - - +
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Residues in contact with SER 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A MET* 5.7 0.6 - - - +
658A ASN* 2.7 20.4 + - - -
659A GLN* 1.3 78.9 - - - +
661A HIS* 1.3 70.9 + - - +
663A ASP* 3.7 9.2 + - - +
664A ARG* 3.4 29.0 + - - +
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Residues in contact with HIS 661 (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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645A LEU* 4.5 0.5 - - - +
648A MET* 3.5 33.5 - - + +
653A SER* 3.3 26.0 - - - -
654A LEU* 3.6 19.3 - - + +
655A ASN* 2.9 40.3 + - + +
656A LEU* 4.9 0.7 - - - -
658A ASN* 2.7 33.7 + - + +
660A SER* 1.3 80.0 + - - +
662A ARG* 1.3 58.4 + - - +
664A ARG* 3.2 7.6 + - - +
665A VAL* 3.0 34.1 + - - +
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Residues in contact with ARG 662 (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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547A LEU* 2.8 27.9 + - - +
548A PHE* 3.9 7.7 - - - +
549A THR* 4.4 7.9 - - - +
552A GLU* 2.5 45.3 + - - +
655A ASN 4.8 0.2 + - - -
656A LEU* 2.8 64.7 + - + +
657A ASN* 5.0 7.7 + - - +
658A ASN 2.9 8.3 + - - +
659A GLN* 3.4 31.0 - - - +
661A HIS* 1.3 73.1 - - - +
663A ASP* 1.3 60.0 + - - +
665A VAL* 3.3 7.2 + - - +
666A ILE* 2.9 39.6 + - + +
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Residues in contact with ASP 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A LYS* 2.9 46.3 + - + +
659A GLN* 2.8 47.9 + - - +
660A SER* 3.9 8.8 - - - +
662A ARG* 1.3 77.5 - - - +
664A ARG* 1.3 57.9 + - + +
666A ILE* 3.4 11.3 + - - +
667A GLY* 2.9 24.4 + - - -
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Residues in contact with ARG 664 (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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640A GLY 4.2 1.4 + - - -
641A ASN* 3.0 59.5 + - - +
644A GLN* 3.7 37.9 + - - +
645A LEU* 3.3 16.4 - - + +
648A MET* 4.3 22.4 - - - +
660A SER* 3.4 16.0 + - - +
661A HIS 3.2 9.2 + - - +
663A ASP* 1.3 75.5 - - + +
665A VAL* 1.3 59.6 + - - +
667A GLY* 3.2 1.5 + - - +
668A LEU 3.0 23.9 + - - -
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Residues in contact with VAL 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A PHE* 4.9 7.0 - - + -
645A LEU* 3.9 20.9 - - + -
654A LEU* 4.3 3.1 - - + -
656A LEU* 4.3 22.0 - - + -
661A HIS 3.0 17.2 + - - +
662A ARG* 3.7 8.5 - - - +
664A ARG* 1.3 71.3 - - - +
666A ILE* 1.3 68.0 + - + +
668A LEU* 3.3 4.7 + - - +
669A MET* 3.0 38.3 + - + +
741A LEU* 4.9 2.1 - - + +
744A ILE* 4.3 30.5 - - + -
745A LEU* 4.7 8.5 - - + -
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Residues in contact with ILE 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A PHE* 4.3 20.2 - - + -
552A GLU* 3.8 33.7 - - + +
556A LEU* 3.8 35.9 - - + -
625A ILE* 5.4 8.7 - - + +
628A LYS* 5.9 2.2 - - + -
629A ALA* 4.4 14.4 - - + +
659A GLN* 5.8 0.7 - - - +
662A ARG* 2.9 27.3 + - + +
663A ASP* 3.6 12.1 - - - +
665A VAL* 1.3 77.3 - - + +
667A GLY* 1.3 56.8 + - - +
669A MET* 3.1 9.9 + - - +
670A MET* 2.9 27.4 + - + +
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Residues in contact with GLY 667 (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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629A ALA* 5.8 0.7 - - - -
632A ALA* 3.6 27.6 - - - +
641A ASN* 3.9 9.0 - - - -
663A ASP 2.9 14.3 + - - -
664A ARG* 3.2 4.7 + - - -
666A ILE* 1.3 77.7 - - - +
668A LEU* 1.4 60.0 + - - +
670A MET* 3.1 6.1 + - - +
671A THR* 3.1 23.7 + - - -
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Residues in contact with LEU 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A TYR* 3.8 33.4 - - + -
641A ASN* 3.4 5.4 - - - +
642A ARG* 4.3 11.9 - - + -
645A LEU* 3.8 22.7 - - + -
664A ARG 3.0 6.1 + - - -
665A VAL* 3.9 5.2 - - - +
667A GLY* 1.4 72.0 - - - +
669A MET* 1.3 65.9 + - - +
671A THR* 3.3 3.8 + - - -
672A ALA* 2.9 23.2 + - - +
737A CYS* 3.8 22.0 - - - +
740A THR* 3.9 18.6 - - + -
741A LEU* 3.7 40.4 - - + +
744A ILE* 4.7 3.4 - - + -
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Residues in contact with MET 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A MET* 3.8 30.3 - - + -
540A ILE* 3.9 19.3 - - + -
541A LEU* 4.2 3.4 - - + -
548A PHE* 3.4 43.7 - - + -
556A LEU* 4.0 12.6 - - + -
665A VAL* 3.0 26.8 + - + +
666A ILE* 3.3 13.5 - - - +
668A LEU* 1.3 75.4 - - - +
670A MET* 1.3 58.8 + - - +
672A ALA* 3.2 4.4 + - - +
673A CYS* 2.9 35.4 + - - -
741A LEU* 3.8 21.5 - - + -
745A LEU* 4.1 7.6 - - + -
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Residues in contact with MET 670 (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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533A VAL* 5.1 1.5 - - + +
537A MET* 3.6 12.3 - - + -
556A LEU* 4.4 4.3 - - - +
559A ALA* 4.2 4.3 - - + -
560A CYS* 3.6 46.4 - - - +
563A HIS* 4.4 6.3 - - + -
629A ALA* 3.6 53.6 - - + +
630A ILE 4.4 0.2 - - - +
632A ALA* 4.5 2.2 - - + -
633A THR* 3.8 23.1 - - + +
666A ILE* 2.9 19.0 + - + +
667A GLY* 3.1 9.6 + - - +
669A MET* 1.3 77.6 - - - +
671A THR* 1.3 55.7 + - - +
673A CYS* 3.3 3.9 + - - +
674A ASP* 2.9 31.0 + - - +
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Residues in contact with THR 671 (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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632A ALA 4.1 9.9 + - - -
633A THR* 5.0 2.4 - - - +
635A LEU* 4.2 9.4 - - + +
638A TYR* 3.7 42.6 - - + +
641A ASN* 5.6 0.7 + - - -
667A GLY 3.1 13.1 + - - -
668A LEU* 3.5 11.0 - - - -
670A MET* 1.3 77.2 - - - +
672A ALA* 1.3 61.6 + - - +
674A ASP* 3.4 5.0 + - - +
675A LEU* 3.1 40.8 + - + +
737A CYS* 3.7 14.4 - - - -
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Residues in contact with ALA 672 (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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536A CYS* 4.3 1.9 - - - -
540A ILE* 4.5 6.3 - - + -
668A LEU 2.9 13.6 + - - +
669A MET 3.5 8.5 - - - +
671A THR* 1.3 73.0 - - - +
673A CYS* 1.3 62.6 + - - +
676A CYS* 3.2 10.6 + - - +
737A CYS* 3.7 8.8 - - - -
738A TYR* 2.7 43.3 + - + -
741A LEU* 3.5 31.2 - - + -
751A LEU* 4.7 0.9 - - + -
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Residues in contact with CYS 673 (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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533A VAL* 3.6 30.3 - - + +
536A CYS* 3.7 8.7 - - - -
537A MET* 3.3 41.1 - - - -
540A ILE* 3.4 22.0 - - - -
560A CYS* 4.4 4.9 - - - -
669A MET 2.9 20.2 + - - +
670A MET* 3.7 4.0 - - - +
672A ALA* 1.3 77.6 - - - +
674A ASP* 1.3 61.6 + - - +
676A CYS* 3.1 25.3 + - - +
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Residues in contact with ASP 674 (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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524A TYR* 3.9 6.8 + - - -
529A HIS* 3.0 17.0 + - - -
533A VAL* 3.8 9.9 - - + +
563A HIS* 2.9 5.8 + - - +
633A THR* 3.7 27.7 - - + +
635A LEU* 5.5 4.0 - - - +
670A MET 2.9 18.4 + - - +
671A THR* 3.8 6.5 - - - +
673A CYS* 1.3 76.6 - - - +
675A LEU* 1.3 69.7 + - + +
676A CYS 3.6 0.7 + - - -
677A SER 5.1 0.3 + - - -
900A 2ZX 5.2 2.0 + - - -
901A NI 2.1 45.5 - - - +
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Residues in contact with LEU 675 (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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524A TYR* 5.4 1.1 - - - -
635A LEU* 4.3 15.0 - - + -
671A THR* 3.1 34.3 + - + +
674A ASP* 1.3 83.8 - - + +
676A CYS* 1.3 57.5 + - - +
677A SER* 3.0 10.8 + - - -
678A VAL* 2.9 30.5 + - + +
729A PHE* 3.7 28.9 - - + -
733A VAL* 3.5 29.8 - - + +
734A ALA* 4.3 13.7 - - - -
737A CYS* 5.0 2.9 - - + -
738A TYR* 3.2 10.1 - - + +
900A 2ZX 3.7 21.7 + - + +
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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