Contacts of the helix formed by residues 598 - 612 (chain A) in PDB entry 6R4F
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 THR 598 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A ARG* 4.1 35.6 + - + +
546A GLY* 4.6 13.2 - - - -
547A TYR* 5.7 0.8 + - + +
548A HIS* 6.0 0.7 - - - -
594A MET 5.1 0.3 + - - -
596A ASP* 2.9 18.8 + - - +
597A HIS* 1.3 104.7 - - + +
599A TYR* 1.3 63.2 + - - +
600A ALA 3.4 1.3 - - - -
601A LYS* 3.3 19.1 + - + +
602A CYS* 3.0 26.4 + - - -
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Residues in contact with TYR 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A ILE* 4.2 6.1 - - + -
594A MET 3.3 26.7 - - - +
595A ARG* 3.9 15.9 - - + -
596A ASP* 3.1 20.9 + - - +
597A HIS 3.2 1.6 - - - -
598A THR* 1.3 77.8 + - - +
600A ALA* 1.3 69.3 + - + +
602A CYS* 3.2 6.9 + - - +
603A GLN* 2.9 57.0 + - + +
624A ASP* 3.1 34.9 + - - -
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Residues in contact with ALA 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A HIS 4.7 4.2 + - - +
598A THR 3.4 0.2 - - - -
599A TYR* 1.3 85.9 - - + +
601A LYS* 1.3 63.9 + - + +
603A GLN* 3.3 8.4 + - - +
604A ASN* 3.1 19.4 + - - +
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Residues in contact with LYS 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A ARG* 3.6 49.0 + - - +
597A HIS* 5.4 4.5 + - - +
598A THR* 3.3 23.7 + - + +
599A TYR 3.2 0.6 - - - -
600A ALA* 1.3 78.8 - - + +
602A CYS* 1.3 58.2 + - - +
604A ASN* 2.9 24.2 + - - +
605A ALA* 3.0 12.0 + - - +
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Residues in contact with CYS 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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544A GLY* 5.5 0.4 - - - -
545A ARG* 3.6 32.1 - - - +
572A ALA* 5.1 4.5 - - - -
591A MET* 4.5 1.4 - - + +
592A ILE 4.1 17.0 - - - -
593A ILE* 3.9 28.5 - - + +
594A MET 5.4 2.0 - - - -
598A THR* 3.0 25.0 + - - +
599A TYR* 3.2 5.4 + - - +
601A LYS* 1.3 71.7 - - - +
603A GLN* 1.3 61.4 + - - +
605A ALA* 3.2 9.4 + - - +
606A LEU* 2.8 29.5 + - - +
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Residues in contact with GLN 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A ILE* 3.9 14.8 - - - +
599A TYR* 2.9 61.8 + - + +
600A ALA* 3.4 11.4 - - - +
601A LYS 3.2 0.2 - - - -
602A CYS* 1.3 74.7 - - - +
604A ASN* 1.3 57.4 + - - +
606A LEU* 3.4 24.5 + - - +
607A GLN* 3.0 41.6 + - + +
624A ASP* 4.0 9.1 + - - -
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Residues in contact with ASN 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 ALA 3.1 10.6 + - - +
601A LYS* 2.9 16.7 + - - +
603A GLN* 1.3 74.0 - - - +
605A ALA* 1.3 63.8 + - - +
607A GLN* 3.0 11.6 + - - +
608A GLN* 2.4 57.4 + - - +
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Residues in contact with ALA 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A ARG* 6.3 0.4 - - - +
572A ALA* 4.3 18.2 - - + +
575A LEU* 4.0 16.6 - - + +
591A MET* 3.8 15.9 - - + -
601A LYS 3.0 10.0 + - - +
602A CYS* 3.6 10.3 - - - +
604A ASN* 1.3 74.7 + - - +
606A LEU* 1.3 62.6 + - - +
608A GLN* 3.0 17.0 + - - +
609A VAL* 2.9 26.0 + - - +
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Residues in contact with LEU 606 (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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591A MET* 3.7 23.7 - - - +
593A ILE* 4.0 20.0 - - + -
602A CYS 2.8 14.2 + - - +
603A GLN* 3.5 26.9 - - - +
605A ALA* 1.3 76.8 - - - +
607A GLN* 1.3 71.0 + - - +
609A VAL* 3.3 1.2 + - - +
610A VAL* 3.0 35.0 + - + +
616A PRO* 3.9 19.3 - - + -
618A VAL* 4.4 14.1 - - + -
631A THR* 5.1 9.9 - - - +
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Residues in contact with GLN 607 (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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603A GLN* 3.0 32.0 + - + +
604A ASN* 3.0 12.4 + - - +
606A LEU* 1.3 86.0 - - - +
608A GLN* 1.3 58.6 + - + +
610A VAL* 4.4 7.4 - - - +
611A ALA* 3.1 29.3 + - - +
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Residues in contact with GLN 608 (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 ALA 5.3 0.7 - - - +
575A LEU* 4.1 14.4 - - + +
576A LYS* 3.5 42.2 - - + +
580A LEU* 4.2 16.7 - - + +
604A ASN* 2.4 43.4 + - - +
605A ALA* 3.0 16.0 + - - +
607A GLN* 1.3 76.6 - - + +
609A VAL* 1.3 65.6 + - + +
611A ALA* 3.4 5.3 + - - +
612A ARG* 3.4 27.5 + - - +
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Residues in contact with VAL 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A MET* 3.9 24.7 - - + -
575A LEU* 4.4 7.4 - - + -
580A LEU* 4.5 2.7 - - + -
583A VAL* 3.6 27.4 - - + +
589A VAL* 4.5 8.5 - - + -
591A MET* 3.9 18.2 - - + -
605A ALA 2.9 17.4 + - - +
606A LEU 3.8 5.4 - - - +
608A GLN* 1.3 76.4 - - - +
610A VAL* 1.3 63.7 + - - +
612A ARG 3.0 9.9 + - - -
614A GLY* 3.0 28.7 + - - -
616A PRO* 3.9 23.3 - - + -
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Residues in contact with VAL 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A LEU* 3.0 35.5 + - + +
607A GLN* 4.4 8.1 - - - +
609A VAL* 1.3 75.3 - - - +
611A ALA* 1.3 62.7 + - - +
613A GLN* 3.1 17.3 + - - -
614A GLY 3.6 18.6 - - - +
616A PRO* 4.2 9.4 - - + -
631A THR* 4.4 13.5 - - - -
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Residues in contact with ALA 611 (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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607A GLN 3.1 20.6 + - - +
608A GLN* 3.6 8.7 - - - +
609A VAL 3.2 0.4 - - - -
610A VAL* 1.3 77.0 - - - +
612A ARG* 1.3 72.4 + - - +
613A GLN* 3.5 14.9 + - - +
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Residues in contact with ARG 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A LEU* 4.4 26.2 - - + +
583A VAL* 3.5 19.1 - - + +
584A ASP* 3.5 16.5 - - - -
608A GLN 3.4 14.6 + - - +
609A VAL 3.0 7.3 + - - +
611A ALA* 1.3 87.6 + - - +
613A GLN* 1.3 74.0 + - - +
614A GLY 3.1 3.5 + - - -
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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