Contacts of the helix formed by residues 589 - 604 (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 SER 589 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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572A ASN* 3.9 3.7 - - - +
576A GLN* 4.6 2.8 - - - +
588A THR* 1.3 80.1 + - - +
590A THR* 1.3 67.8 + - - +
592A GLU* 3.1 20.0 - - - +
593A GLN* 3.0 23.8 + - - +
631A ILE* 4.3 10.0 - - - +
634A ASP* 2.6 34.8 + - - -
637A LEU* 3.6 18.2 - - - +
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Residues in contact with THR 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A ASN* 3.6 15.6 - - - +
575A LEU* 4.4 11.9 - - + -
576A GLN* 3.0 25.7 + - - +
582A LEU* 3.3 46.4 - - + +
583A ALA* 3.6 5.6 - - + +
586A TYR* 3.0 27.3 + - + +
587A SER 4.1 0.2 + - - -
588A THR 3.7 3.8 - - - -
589A SER* 1.3 77.1 - - - +
591A MET* 1.3 64.9 + - - +
593A GLN* 3.2 1.0 + - - +
594A HIS* 3.1 15.1 + - - +
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Residues in contact with MET 591 (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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567A HIS* 4.1 21.5 - - + +
568A ARG* 4.3 12.3 - - - +
570A PHE* 4.0 15.7 - - - +
572A ASN* 2.9 25.2 + - - +
575A LEU* 3.4 29.6 - - + -
582A LEU* 4.1 15.7 - - - -
590A THR* 1.3 73.2 - - - +
592A GLU* 1.3 61.8 + - - +
594A HIS* 3.0 24.2 + - + +
595A HIS* 2.7 67.4 + - + +
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Residues in contact with GLU 592 (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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572A ASN* 2.9 32.1 + - - +
589A SER* 3.1 19.2 - - - +
591A MET* 1.3 77.0 - - - +
593A GLN* 1.3 61.3 + - - +
595A HIS* 3.1 12.9 + - + -
596A PHE* 3.1 21.0 + - - +
630A ILE* 3.5 27.8 - - - +
631A ILE* 4.2 13.2 - - - +
633A THR* 3.9 6.8 - - - +
634A ASP* 3.8 34.6 - - - +
902A NI 4.0 15.1 - - - +
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Residues in contact with GLN 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A TYR* 3.5 48.8 + - + +
587A SER 4.5 1.0 - - - +
588A THR* 2.9 27.6 + - - +
589A SER* 3.0 19.2 + - - +
590A THR 3.7 0.7 - - - +
592A GLU* 1.3 73.6 - - - +
594A HIS* 1.3 63.8 + - - +
596A PHE* 3.4 7.8 + - - +
597A SER* 3.0 22.7 + - - -
631A ILE* 3.7 21.9 - - + +
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Residues in contact with HIS 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A LEU 4.1 10.8 - - - -
566A ASP* 2.8 28.8 + - + -
568A ARG* 3.7 12.6 + - - -
582A LEU* 3.7 22.6 - - + +
586A TYR* 3.8 16.1 + - + -
590A THR 3.1 10.8 + - - +
591A MET* 3.0 37.3 + - + +
593A GLN* 1.3 78.6 - - - +
595A HIS* 1.3 55.1 + - - +
597A SER* 3.2 7.7 + - - -
598A GLN* 3.0 52.9 + - + +
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Residues in contact with HIS 595 (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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562A CYS 4.0 2.2 - - - +
563A HIS 3.0 33.2 - - - +
564A ASP* 3.2 28.7 + - - -
565A LEU* 2.6 35.3 + - - +
567A HIS* 3.8 11.9 - - + -
591A MET* 2.7 62.1 + - + +
592A GLU* 3.1 10.9 + - - +
594A HIS* 1.3 72.9 - - - +
596A PHE* 1.3 56.7 + - - +
598A GLN* 3.5 3.3 + - - +
599A THR* 2.8 31.5 + - - -
630A ILE* 4.0 4.5 - - + -
902A NI 4.2 5.5 - - + +
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Residues in contact with PHE 596 (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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592A GLU 3.1 12.4 + - - +
593A GLN* 3.7 9.2 - - - +
595A HIS* 1.3 73.2 - - - +
597A SER* 1.3 68.9 + - - +
599A THR* 3.1 8.5 + - + -
600A VAL* 3.1 47.3 + - + +
623A LEU* 3.7 22.0 - - + -
624A GLU* 5.9 0.4 - - - -
626A ILE* 3.8 20.6 - - + -
627A ARG* 3.7 58.3 - - + +
630A ILE* 4.1 12.0 - - + +
631A ILE* 5.6 2.2 - - + -
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Residues in contact with SER 597 (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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586A TYR* 3.7 18.8 + - - -
593A GLN 3.0 14.1 + - - -
594A HIS* 3.4 12.7 + - - -
596A PHE* 1.3 82.9 - - - +
598A GLN* 1.3 57.1 + - - +
600A VAL* 3.4 6.7 + - - +
601A SER* 3.0 33.1 + - - -
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Residues in contact with GLN 598 (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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447A GLY 5.4 5.5 + - - +
448A THR* 4.3 16.4 + - - +
518A ASN* 4.2 18.4 - - - +
565A LEU* 3.9 18.2 - - + +
566A ASP* 3.4 28.6 + - + +
594A HIS* 3.0 47.3 + - + +
595A HIS 3.6 5.4 - - - +
596A PHE 3.3 0.2 - - - -
597A SER* 1.3 73.5 + - - +
599A THR* 1.3 66.0 + - - +
601A SER* 3.4 8.0 + - - -
602A ILE* 3.1 29.6 + - - +
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Residues in contact with THR 599 (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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511A PHE* 4.6 4.6 - - + -
558A ILE* 4.9 4.7 - - + -
562A CYS* 3.2 39.2 - - + +
565A LEU* 3.5 7.8 - - - +
595A HIS 2.8 16.1 + - - -
596A PHE* 3.1 13.6 + - + -
598A GLN* 1.3 74.8 - - - +
600A VAL* 1.3 63.1 + - + +
602A ILE* 3.2 6.8 + - - +
603A LEU* 3.1 33.2 + - + +
623A LEU* 6.0 0.4 - - + -
626A ILE* 4.5 18.8 - - + -
630A ILE* 3.7 7.5 - - - +
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Residues in contact with VAL 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A PHE* 3.1 45.4 + - + +
597A SER* 3.7 8.3 - - - +
599A THR* 1.3 74.8 - - - +
601A SER* 1.3 63.5 + - - +
603A LEU* 3.3 12.0 + - + +
604A GLN* 3.1 51.2 + - - +
623A LEU* 4.2 20.2 - - + -
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Residues in contact with SER 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A THR* 3.6 23.9 + - - -
597A SER* 3.0 19.3 + - - -
598A GLN* 3.6 15.1 + - - -
599A THR 3.2 0.2 - - - -
600A VAL* 1.3 75.3 - - - +
602A ILE* 1.3 63.2 + - - +
604A GLN* 3.3 18.7 + - - +
605A LEU* 3.4 16.2 + - - +
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Residues in contact with ILE 602 (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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448A THR* 3.9 16.6 - - + -
511A PHE* 3.6 27.4 - - + -
514A SER* 4.3 4.5 - - - -
515A VAL* 3.9 17.9 - - + -
518A ASN* 3.6 22.0 - - + +
565A LEU* 3.8 35.0 - - + -
598A GLN* 3.1 12.6 + - + +
599A THR 3.6 6.7 - - - +
601A SER* 1.3 76.3 - - - +
603A LEU* 1.3 61.1 + - - +
605A LEU* 3.0 27.3 + - + +
608A HIS* 3.1 23.5 - - + +
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Residues in contact with LEU 603 (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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511A PHE* 3.7 21.1 - - + -
599A THR* 3.1 27.5 + - + +
600A VAL* 3.6 12.1 - - + +
602A ILE* 1.3 76.5 - - - +
604A GLN* 1.3 58.5 + - + +
605A LEU 3.2 5.8 + - - +
608A HIS 4.0 9.9 - - - +
609A ASN* 3.3 42.9 + - - +
610A ILE* 4.0 17.3 - - + +
611A PHE* 3.8 32.1 - - + -
619A TYR* 5.0 7.2 - - - +
623A LEU* 4.0 27.1 - - + -
626A ILE* 5.3 0.4 - - + -
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Residues in contact with GLN 604 (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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600A VAL* 3.1 42.4 + - - +
601A SER* 3.7 10.0 - - - +
602A ILE 3.2 0.4 - - - -
603A LEU* 1.3 73.3 - - + +
605A LEU* 1.3 64.8 + - - +
606A GLU* 3.7 1.2 + - - -
609A ASN* 5.3 6.1 - - - +
619A TYR* 5.6 4.8 + - - +
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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
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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