Contacts of the helix formed by residues 588 - 600 (chain A) in PDB entry 6X70
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 GLY 588 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584A LYS* 2.8 24.7 + - - +
585A ALA 4.6 0.4 + - - -
586A SER 3.7 0.8 - - - -
587A VAL* 1.3 79.8 - - - +
589A SER* 1.3 60.5 + - - -
590A LYS 3.5 2.0 - - - -
591A LEU 4.3 1.3 - - - -
592A GLY 2.9 22.5 + - - -
12T C 4.0 13.9 - - - -
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Residues in contact with SER 589 (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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584A LYS* 3.7 30.1 + - - +
588A GLY* 1.3 71.3 - - - +
590A LYS* 1.3 64.6 + - - +
593A MET* 3.1 28.8 + - - +
12T C 3.2 11.1 + - - -
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Residues in contact with LYS 590 (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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589A SER* 1.3 80.4 + - - +
591A LEU* 1.3 67.2 + - - +
593A MET* 3.3 8.0 + - + +
594A LYS* 3.0 22.6 + - - +
605A GLU* 5.0 14.6 + - - -
606A GLU* 6.0 5.5 - - + +
11T A 3.7 36.3 + - - +
12T C 3.1 22.9 + - - +
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Residues in contact with LEU 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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551A PRO 4.6 0.2 - - - +
552A GLY* 3.8 24.0 - - - +
557A THR* 3.6 35.0 - - + +
587A VAL* 3.8 28.0 - - + +
588A GLY 4.0 1.4 + - - -
589A SER 3.5 0.2 - - - -
590A LYS* 1.3 77.9 - - - +
592A GLY* 1.3 58.3 + - - +
594A LYS* 3.1 26.9 + - + +
595A ILE* 2.9 44.0 + - + +
10P T 5.8 1.1 - - - -
11T A 5.2 5.1 + - - +
12T C 4.7 1.2 + - - -
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Residues in contact with GLY 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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580A LEU* 4.4 5.4 - - - -
583A LEU* 3.3 31.1 - - - +
584A LYS* 4.3 5.4 - - - -
587A VAL* 3.9 7.0 - - - +
588A GLY 2.9 21.2 + - - -
589A SER 3.9 0.4 - - - -
591A LEU* 1.3 77.5 - - - +
593A MET* 1.3 61.1 + - - +
595A ILE* 4.7 0.4 - - - -
596A HIS* 2.9 20.6 + - - +
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Residues in contact with MET 593 (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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580A LEU* 4.1 21.6 - - + +
584A LYS* 4.4 9.6 - - - +
589A SER 3.1 18.6 + - - +
590A LYS* 3.8 6.3 - - + +
592A GLY* 1.3 75.3 - - - +
594A LYS* 1.3 58.1 + - - +
596A HIS* 3.3 22.1 + - + +
597A LEU* 2.8 64.8 + - + +
604A ASP* 6.2 0.7 - - + -
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Residues in contact with LYS 594 (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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551A PRO* 3.2 46.7 - - - +
552A GLY* 4.7 2.2 - - - +
590A LYS 3.0 13.7 + - - +
591A LEU* 3.3 25.1 - - + +
593A MET* 1.3 76.3 - - - +
595A ILE* 1.3 52.9 + - + +
597A LEU* 3.3 6.0 + - - +
598A ALA* 2.7 39.0 + - + +
604A ASP* 3.0 43.0 + - + +
607A SER* 4.5 8.1 - - - -
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Residues in contact with ILE 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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550A LEU* 3.7 21.1 - - + -
551A PRO 5.5 1.3 - - - +
553A VAL* 3.7 30.3 - - + -
557A THR* 4.6 1.3 - - + -
561A LEU* 4.3 10.8 - - + -
574A LEU* 4.5 6.7 - - + -
583A LEU* 3.7 30.7 - - + -
587A VAL* 4.3 11.9 - - + -
591A LEU* 2.9 29.7 + - + +
592A GLY 3.8 3.4 - - - +
594A LYS* 1.3 77.2 - - + +
596A HIS* 1.3 52.2 + - - +
598A ALA* 3.1 7.3 + - - +
599A LEU* 2.7 51.5 + - + +
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Residues in contact with HIS 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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578A TYR* 2.9 41.4 + - + -
580A LEU* 3.5 30.6 - - + +
583A LEU* 3.9 0.6 - - + +
592A GLY 2.9 17.7 + - - +
593A MET* 3.5 34.2 - - + +
595A ILE* 1.3 77.9 - - - +
597A LEU* 1.3 72.0 + - + +
599A LEU* 3.2 12.6 + - - +
600A GLN* 3.4 24.7 + - + +
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Residues in contact with LEU 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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593A MET* 2.8 54.4 + - + +
594A LYS* 3.6 5.2 - - - +
596A HIS* 1.3 80.6 - - + +
598A ALA* 1.3 63.1 + - - +
600A GLN* 2.9 16.5 + - + -
602A GLN* 3.0 51.1 + - + +
603A ASP 3.9 6.5 - - - +
604A ASP* 3.7 31.2 - - + +
605A GLU 5.1 0.9 - - - +
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Residues in contact with ALA 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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515A VAL* 3.9 22.4 - - + +
542A TRP* 3.3 13.0 - - - -
550A LEU* 3.9 24.4 - - + +
551A PRO* 5.1 3.6 - - + -
594A LYS* 2.7 23.9 + - + +
595A ILE* 3.4 8.1 - - - +
597A LEU* 1.3 72.6 - - - +
599A LEU* 1.3 59.1 + - - +
601A GLY* 2.8 18.5 + - - -
602A GLN 3.4 9.8 + - - +
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Residues in contact with LEU 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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542A TRP* 3.2 18.3 - - + -
550A LEU* 4.3 9.0 - - + -
571A LEU* 4.3 28.9 - - + +
574A LEU* 4.3 12.8 - - + -
575A ARG* 3.2 49.2 + - + -
578A TYR* 3.7 40.4 - - + +
583A LEU* 5.0 0.2 - - + -
595A ILE* 2.7 38.3 + - + +
596A HIS 3.6 5.6 - - - +
597A LEU 3.2 0.2 - - - -
598A ALA* 1.3 73.6 - - - +
600A GLN* 1.3 58.9 + - - +
601A GLY 3.3 0.7 - - - -
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Residues in contact with GLN 600 (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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534A LYS* 5.0 2.9 - - - +
537A LEU* 4.0 13.8 - - - +
542A TRP* 4.9 0.2 - - - -
575A ARG* 3.4 19.0 + - - +
578A TYR* 2.8 31.3 + - - -
596A HIS* 3.5 22.7 + - + +
597A LEU* 2.9 10.8 + - + +
599A LEU* 1.3 81.1 - - - +
601A GLY* 1.3 63.0 + - - +
602A GLN* 3.2 29.0 + - - +
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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