Contacts of the helix formed by residues 589 - 604 (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 589 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B ASN* 3.7 4.4 + - - +
588B THR* 1.3 76.9 - - - +
590B THR* 1.3 57.0 + - - +
592B GLU* 3.2 23.9 - - - +
593B GLN* 2.9 33.0 + - - +
631B ILE* 4.4 10.2 - - - +
634B ASP* 2.7 30.1 + - - -
637B LEU* 3.8 16.6 - - - +
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Residues in contact with THR 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B ASN* 3.4 23.9 + - - +
575B LEU* 3.7 19.3 - - + -
576B GLN* 5.6 1.9 + - - +
582B LEU* 3.3 41.1 - - + +
583B ALA* 3.6 9.8 - - - +
586B TYR* 3.0 30.4 + - + +
587B SER 4.2 7.1 + - - -
588B THR 3.1 1.4 + - - -
589B SER* 1.3 74.7 + - - +
591B MET* 1.3 64.5 + - - +
593B GLN 3.4 0.2 + - - -
594B HIS* 3.2 17.2 + - - +
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Residues in contact with MET 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B ASP 4.1 2.0 - - - +
567B HIS* 3.9 27.4 - - + +
568B ARG* 4.4 7.4 - - + +
570B PHE* 3.8 22.0 - - - +
572B ASN* 2.9 26.3 - - - +
575B LEU* 3.6 23.6 - - + -
582B LEU* 4.2 14.8 - - + -
590B THR* 1.3 73.6 - - - +
592B GLU* 1.3 63.7 + - - +
594B HIS* 3.1 23.3 + - + +
595B HIS* 2.8 65.8 + - + +
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Residues in contact with GLU 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B ASN* 2.9 26.5 + - - +
589B SER* 3.2 16.5 - - - +
591B MET* 1.3 83.2 - - - +
593B GLN* 1.3 64.7 + - - +
594B HIS 3.1 0.2 - - - -
595B HIS* 3.3 10.9 + - + -
596B PHE* 3.2 19.6 + - - +
630B ILE* 3.5 34.7 - - - +
631B ILE* 3.9 16.6 - - + +
633B THR* 3.7 6.2 - - - +
634B ASP* 3.6 32.0 - - + +
902B NI 4.1 14.0 - - - +
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Residues in contact with GLN 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B TYR* 3.4 46.7 - - + +
587B SER 4.9 0.4 - - - +
588B THR* 3.1 27.2 + - - +
589B SER* 2.9 19.7 + - - +
592B GLU* 1.3 76.3 - - - +
594B HIS* 1.3 62.8 + - - +
596B PHE* 3.5 5.1 + - - +
597B SER* 3.3 21.1 + - - -
631B ILE* 3.9 18.6 - - + +
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Residues in contact with HIS 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B LEU 4.0 12.1 - - - -
566B ASP* 2.9 33.5 + - - +
582B LEU* 4.9 21.1 - - + +
586B TYR* 3.9 24.3 + + + -
590B THR 3.2 12.6 + - - +
591B MET* 3.1 34.0 + - + +
593B GLN* 1.3 75.2 - - - +
595B HIS* 1.3 65.9 + - - +
596B PHE 3.4 0.2 + - - -
597B SER* 3.4 4.5 + - - -
598B GLN* 3.1 40.4 + - + +
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Residues in contact with HIS 595 (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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562B CYS 4.0 1.1 - - - +
563B HIS 2.9 34.1 - - - +
564B ASP* 3.2 15.5 + - - -
565B LEU* 2.6 35.7 + - - +
567B HIS* 3.3 35.5 - + + -
591B MET* 2.8 52.1 + - + +
592B GLU* 3.3 11.4 + - + +
594B HIS* 1.3 73.7 - - - +
596B PHE* 1.3 57.2 + - - +
598B GLN* 3.5 4.9 - - - +
599B THR* 2.8 30.0 + - - -
630B ILE* 4.0 5.2 - - + -
902B NI 4.2 5.3 - - + +
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Residues in contact with PHE 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592B GLU 3.2 12.2 + - - +
593B GLN* 3.9 8.3 - - - +
594B HIS 3.3 0.2 - - - -
595B HIS* 1.3 74.4 - - - +
597B SER* 1.3 61.8 + - - +
599B THR* 2.9 10.1 + - - -
600B VAL* 2.9 43.9 + - + +
623B LEU* 3.6 38.6 - - + -
626B ILE* 4.2 12.8 - - + -
627B ARG* 3.5 63.5 - - + +
630B ILE* 4.1 11.8 - - + +
631B ILE* 5.4 1.8 - - + -
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Residues in contact with SER 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B TYR* 3.9 17.3 - - - -
593B GLN 3.3 11.5 + - - -
594B HIS* 3.7 9.4 - - - -
596B PHE* 1.3 79.4 - - - +
598B GLN* 1.3 53.0 + - - +
600B VAL* 3.2 10.2 + - - +
601B SER* 2.8 35.1 + - - -
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Residues in contact with GLN 598 (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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518B ASN* 4.0 24.8 + - - +
565B LEU* 3.9 15.2 - - + +
566B ASP* 3.5 29.0 + - + +
594B HIS* 3.1 39.9 + - + +
595B HIS 3.5 9.9 - - - +
597B SER* 1.3 75.9 - - - +
599B THR* 1.3 59.9 + - - +
601B SER* 3.5 14.3 + - - -
602B ILE* 3.2 30.2 + - - +
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Residues in contact with THR 599 (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* 5.0 2.6 - - + -
558B ILE* 5.1 2.5 - - + -
562B CYS* 3.4 38.3 - - + +
565B LEU* 3.4 6.7 - - - +
595B HIS 2.8 18.4 + - - -
596B PHE* 2.9 16.4 + - + -
598B GLN* 1.3 73.0 - - - +
600B VAL* 1.3 67.2 + - - +
602B ILE* 3.2 6.6 + - - +
603B LEU* 3.0 38.2 + - + +
623B LEU* 5.5 0.2 - - + -
626B ILE* 4.3 18.6 - - + -
630B ILE* 3.7 6.4 - - - +
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Residues in contact with VAL 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B PHE* 2.9 51.0 + - + +
597B SER* 3.5 9.9 - - - +
599B THR* 1.3 74.4 - - - +
601B SER* 1.3 64.3 + - - +
603B LEU* 3.1 18.4 + - - +
604B GLN* 3.1 44.8 + - + +
623B LEU* 4.2 9.6 - - + -
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Residues in contact with SER 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B SER 2.8 17.0 + - - -
598B GLN* 3.6 20.2 + - - -
599B THR 3.1 0.2 - - - -
600B VAL* 1.3 78.4 - - - +
602B ILE* 1.3 61.9 + - - +
604B GLN* 3.5 17.1 + - - +
605B LEU* 3.6 19.0 + - - +
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Residues in contact with ILE 602 (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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449B SER 5.0 1.1 - - - +
511B PHE* 4.0 25.4 - - + -
514B SER* 4.2 8.1 - - - -
515B VAL* 4.0 22.7 - - + -
518B ASN* 3.4 41.5 - - + +
565B LEU* 4.3 10.8 - - + -
598B GLN* 3.2 17.2 + - - +
599B THR* 3.2 6.9 + - - +
601B SER* 1.3 77.0 - - - +
603B LEU* 1.3 61.9 + - - +
604B GLN 3.1 5.6 + - - -
605B LEU* 3.3 23.8 + - + +
608B HIS* 3.3 25.5 - - + +
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Residues in contact with LEU 603 (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* 3.6 23.1 - - + -
558B ILE* 5.8 0.2 - - + -
599B THR* 3.0 30.4 + - + +
600B VAL* 3.8 7.0 - - - +
602B ILE* 1.3 75.4 - - - +
604B GLN* 1.3 61.3 + - + +
605B LEU 3.4 1.1 - - - +
608B HIS 4.0 8.7 - - - +
609B ASN* 3.2 44.2 + - - +
610B ILE* 3.8 23.6 - - + -
611B PHE* 3.9 18.2 - - + -
619B TYR* 4.4 4.7 - - - +
623B LEU* 4.2 35.0 - - + -
626B ILE* 5.2 1.8 - - + -
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Residues in contact with GLN 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B VAL* 3.1 38.1 + - + +
601B SER* 3.8 10.0 - - - +
602B ILE 3.1 1.6 - - - -
603B LEU* 1.3 80.4 - - + +
605B LEU* 1.3 64.7 + - - +
606B GLU* 3.8 0.9 + - - -
609B ASN* 5.2 0.9 - - - +
619B TYR* 5.5 5.5 + - - +
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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