Contacts of the helix formed by residues 526 - 543 (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 526 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B TYR* 3.6 15.0 - - - -
520B ARG 3.9 14.8 - - - +
521B ARG* 5.4 1.1 - - - -
522B VAL 3.0 26.1 + - - +
523B PRO 3.3 16.4 + - - -
524B TYR* 2.8 12.3 + - - +
525B HIS* 1.3 75.1 - - - +
527B TRP* 1.3 64.1 + - - +
528B LYS* 3.6 14.1 + - - +
529B HIS* 3.1 19.2 + - - +
530B ALA 3.1 16.3 + - - -
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Residues in contact with TRP 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B GLU* 5.4 1.0 + - - -
486B TRP* 3.7 35.4 - + - +
487B PRO* 4.1 27.3 - - + +
490B PHE* 5.6 0.2 - - + -
512B ILE* 4.1 17.7 - - + -
515B VAL* 4.1 3.8 - - + -
516B LYS* 3.7 63.1 - - + +
519B TYR* 3.8 29.5 - + + +
520B ARG 5.0 0.2 + - - -
526B ASN* 1.3 72.3 - - - +
528B LYS* 1.3 63.4 + - - +
530B ALA* 3.0 16.7 + - + +
531B VAL* 3.1 27.4 + - + +
561B LEU* 3.5 37.5 - - + -
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Residues in contact with LYS 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B ILE* 3.7 11.5 - - + +
480B GLY* 5.3 8.3 - - - -
486B TRP* 3.5 46.5 - - + -
526B ASN* 3.4 13.1 + - - +
527B TRP* 1.3 78.9 - - - +
529B HIS* 1.3 63.4 + - - +
531B VAL* 3.3 1.3 + - - -
532B THR* 3.0 31.8 + - - +
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Residues in contact with HIS 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B TYR* 3.2 54.6 - + + +
525B HIS* 4.5 3.4 - - - -
526B ASN* 3.1 12.2 + - - +
528B LYS* 1.3 78.0 - - - +
530B ALA* 1.3 63.6 + - - +
532B THR* 3.4 10.2 + - + +
533B VAL* 2.9 33.2 + - + +
563B HIS* 3.1 15.1 + + - -
564B ASP* 3.3 10.3 - - + -
674B ASP* 2.9 29.7 + - - -
677B SER* 5.8 1.4 + - - -
901B NI 2.3 37.5 - - + +
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Residues in contact with ALA 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B TYR* 3.5 24.9 - - + +
526B ASN 3.1 6.3 + - - +
527B TRP* 3.0 18.9 + - + +
529B HIS* 1.3 78.4 - - - +
531B VAL* 1.3 57.2 - - - +
533B VAL* 3.5 0.7 + - - +
534B ALA* 3.1 26.7 + - - +
560B CYS 3.8 12.8 - - - +
561B LEU* 3.5 27.6 - - + +
563B HIS* 4.5 6.1 - - - -
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Residues in contact with VAL 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B ILE* 3.8 21.3 - - + -
486B TRP* 3.7 30.5 - - + +
489B ILE* 4.4 16.4 - - + -
490B PHE* 4.9 7.4 - - + -
493B MET* 4.8 2.4 - - + +
527B TRP* 3.1 51.1 + - + +
528B LYS 3.3 0.2 + - - -
530B ALA* 1.3 73.3 - - - +
532B THR* 1.3 58.2 - - - +
534B ALA* 3.3 5.4 + - - +
535B HIS* 2.9 28.4 + - - +
561B LEU* 4.0 6.7 - - + -
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Residues in contact with THR 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B ILE* 3.4 22.4 - - - +
528B LYS* 3.0 23.7 + - - +
529B HIS* 3.5 11.2 - - - +
531B VAL* 1.3 72.7 - - - +
533B VAL* 1.3 67.2 + - + +
535B HIS* 3.3 8.4 + - - +
536B CYS 3.2 17.5 + - - -
676B CYS* 3.5 27.0 - - - -
677B SER* 4.8 12.1 - - - +
680B LYS* 4.5 12.5 + - - +
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Residues in contact with VAL 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B HIS* 2.9 54.3 + - + +
530B ALA 3.8 4.0 - - - +
532B THR* 1.3 73.4 - - + +
534B ALA* 1.3 62.5 + - - +
536B CYS 3.3 2.1 + - - -
537B MET* 3.2 18.5 + - - +
560B CYS* 3.8 20.0 - - + -
563B HIS* 3.6 19.1 - - + +
633B THR* 6.3 0.2 - - + -
670B MET* 5.0 3.6 - - + +
673B CYS* 3.5 42.2 - - + +
674B ASP* 3.7 6.7 - - + +
676B CYS* 5.4 0.2 - - - -
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Residues in contact with ALA 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B PHE* 3.8 35.9 - - + -
493B MET* 4.1 4.5 - - + -
530B ALA 3.1 17.3 + - - +
531B VAL* 3.7 6.3 - - - +
532B THR 3.3 0.2 - - - -
533B VAL* 1.3 77.0 - - - +
535B HIS* 1.3 57.0 + - - +
537B MET* 3.3 3.8 + - - +
538B TYR* 2.9 24.3 + - - +
557B LEU* 3.5 10.0 - - + +
560B CYS* 3.7 19.5 - - + +
561B LEU* 4.4 2.2 - - - +
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Residues in contact with HIS 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B ILE* 2.7 39.9 + - + -
474B LEU 3.2 21.6 + - - -
475B PHE 3.7 13.2 - - - -
477B PHE* 3.5 31.8 + + + +
479B ILE* 4.7 10.5 - - + -
489B ILE* 5.4 0.9 - - + -
493B MET* 3.5 20.3 - - + +
531B VAL 2.9 17.1 + - - +
532B THR* 3.3 6.9 + - - +
534B ALA* 1.3 74.9 - - - +
536B CYS* 1.3 68.7 + - - +
538B TYR* 3.3 2.6 + + - +
539B ALA* 3.1 23.9 + - + +
680B LYS* 4.1 9.5 + - - -
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Residues in contact with CYS 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B PHE* 4.9 4.7 - - - -
532B THR 3.2 7.1 + - - -
533B VAL 3.3 4.9 + - - +
535B HIS* 1.3 81.9 + - - +
537B MET* 1.3 63.9 + - - +
539B ALA* 3.3 6.1 + - - +
540B ILE* 3.0 28.9 + - - +
672B ALA 4.3 1.3 - - - -
673B CYS* 3.6 23.1 - - - -
676B CYS* 3.8 37.9 - - - -
680B LYS* 5.3 1.6 - - - +
751B LEU* 4.0 32.5 - - - -
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Residues in contact with MET 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B VAL 3.2 3.4 + - - +
534B ALA 3.5 8.7 - - - +
535B HIS 3.2 0.2 - - - -
536B CYS* 1.3 79.9 - - - +
538B TYR* 1.3 62.5 + - - +
540B ILE* 3.0 5.4 + - - +
541B LEU* 2.8 47.6 + - + +
556B LEU* 4.1 24.9 - - + +
557B LEU* 4.0 8.5 - - + -
560B CYS* 3.6 23.3 - - - -
669B MET* 3.8 34.5 - - + -
670B MET* 3.5 32.8 - - + -
673B CYS* 3.3 16.5 - - - -
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Residues in contact with TYR 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B ILE* 4.2 22.0 - - + -
473B GLU* 2.5 39.2 + - - -
492B TYR* 4.2 1.9 - + - -
493B MET* 3.4 72.9 - - + -
496B ARG* 3.3 19.8 - - + +
497B SER* 3.9 10.5 - - - -
534B ALA 2.9 9.3 + - - +
535B HIS 3.3 4.0 + - - +
537B MET* 1.3 74.9 - - - +
539B ALA* 1.3 58.7 + - - +
541B LEU* 3.2 4.3 + - - +
542B GLN* 2.8 64.2 + - + +
557B LEU* 3.8 11.3 - - + +
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Residues in contact with ALA 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B ILE 5.3 0.2 - - - +
473B GLU* 4.2 16.4 - - - +
475B PHE* 3.6 35.4 - - + -
535B HIS* 3.1 19.5 + - + +
536B CYS* 3.6 6.7 - - - +
538B TYR* 1.3 76.0 - - - +
540B ILE* 1.3 64.6 + - - +
542B GLN* 4.0 4.2 - - - -
543B ASN* 2.9 32.9 + - - +
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Residues in contact with ILE 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B PHE* 3.9 17.7 - - + -
536B CYS* 3.0 19.9 + - - +
537B MET* 3.0 7.8 + - - +
539B ALA* 1.3 74.5 - - - +
541B LEU* 1.3 62.8 + - - +
544B ASN* 2.8 32.3 + - - +
548B PHE* 5.1 1.6 - - + -
669B MET* 4.1 35.7 - - + +
672B ALA* 4.7 1.1 - - + -
673B CYS* 3.6 27.8 - - - -
741B LEU* 4.2 15.7 - - + -
745B LEU* 4.0 16.8 - - + -
748B THR* 4.0 16.2 - - + -
751B LEU* 4.3 7.4 - - + -
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Residues in contact with LEU 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B SER* 4.3 15.3 - - - +
537B MET* 2.8 40.2 + - + +
538B TYR* 3.5 4.3 - - - +
540B ILE* 1.3 78.4 - - - +
542B GLN* 1.3 57.9 + - - +
544B ASN 3.1 1.9 + - - -
545B HIS* 2.9 35.9 + - - +
548B PHE* 3.6 41.1 - - + -
553B ARG* 4.1 25.6 - - + +
556B LEU* 4.6 7.4 - - + -
557B LEU* 4.0 21.1 - - + -
669B MET* 4.3 12.8 - - + -
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Residues in contact with GLN 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B GLU* 3.3 20.2 + - - +
496B ARG* 4.3 12.2 + - - +
497B SER* 4.0 19.2 + - - -
538B TYR* 2.8 66.1 + - + +
539B ALA* 4.0 5.6 - - - +
541B LEU* 1.3 73.2 - - - +
543B ASN* 1.3 63.3 + - - +
544B ASN 3.2 0.7 + - - -
545B HIS* 3.8 28.1 - - - +
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Residues in contact with ASN 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B GLU 4.2 12.9 + - - -
475B PHE* 3.3 31.4 - - + -
539B ALA* 2.9 27.9 + - - +
540B ILE 3.9 2.5 - - - +
541B LEU 3.2 0.2 - - - -
542B GLN* 1.3 81.0 - - - +
544B ASN* 1.3 69.7 + - - +
545B HIS 3.8 0.4 - - - -
747B PRO* 3.3 27.4 - - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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