Contacts of the helix formed by residues 580 - 594 (chain A) in PDB entry 4JWE
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 ASP 580 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532A LEU* 4.3 2.0 - - - -
575A ALA 5.0 0.5 - - - +
578A GLY* 3.6 2.8 - - - -
579A GLU* 1.3 78.3 - - - +
581A LYS* 1.3 61.6 + - - +
582A ALA* 3.3 13.2 + - - +
583A ALA* 3.2 32.5 + - + +
584A ILE* 3.3 23.9 + - - +
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Residues in contact with LYS 581 (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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528A LYS 6.0 0.4 - - - +
531A GLU* 4.0 37.1 + - + +
532A LEU* 4.0 19.7 - - + +
535A THR* 3.4 32.8 - - + +
579A GLU 3.7 4.8 + - - -
580A ASP* 1.3 72.2 + - - +
582A ALA* 1.4 63.5 + - - +
584A ILE* 3.2 6.5 + - - +
585A GLU* 3.0 43.5 + - - +
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Residues in contact with ALA 582 (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 ASP* 3.3 9.4 + - - +
581A LYS* 1.4 77.7 - - - +
583A ALA* 1.4 56.3 + - - +
585A GLU* 3.4 14.6 + - - +
586A ALA* 2.9 31.2 + - - +
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Residues in contact with ALA 583 (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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575A ALA* 4.3 11.2 - - + +
580A ASP* 3.2 35.6 + - + +
581A LYS 3.3 0.2 - - - -
582A ALA* 1.4 75.2 - - - +
584A ILE* 1.4 62.5 + - - +
586A ALA* 3.4 7.1 + - - +
587A LYS* 3.1 29.8 + - + +
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Residues in contact with ILE 584 (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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532A LEU* 3.8 24.7 - - + -
535A THR* 3.7 21.8 - - + +
536A ARG* 3.9 18.8 - - + +
572A LEU* 3.6 9.0 - - + +
575A ALA* 3.3 38.4 - - + +
576A LEU* 3.8 24.9 - - + +
578A GLY 4.3 3.6 - - - +
580A ASP 3.3 13.2 + - - +
581A LYS* 3.2 8.4 + - - +
583A ALA* 1.4 73.2 - - - +
585A GLU* 1.3 61.3 + - - +
587A LYS* 3.1 3.5 + - - -
588A MET* 2.9 31.9 + - - +
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Residues in contact with GLU 585 (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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535A THR* 3.6 16.9 + - + +
581A LYS* 3.0 49.5 + - - +
582A ALA* 3.8 13.8 - - - +
584A ILE* 1.3 73.7 - - - +
586A ALA* 1.4 55.9 + - - +
588A MET* 3.3 16.8 - - - +
589A GLN* 2.8 29.0 + - - +
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Residues in contact with ALA 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A ALA 2.9 18.5 + - - +
583A ALA* 3.6 8.1 - - - +
585A GLU* 1.4 76.3 - - - +
587A LYS* 1.4 62.1 + - + +
589A GLN* 3.3 7.5 + - - +
590A GLU* 2.9 39.6 + - - +
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Residues in contact with LYS 587 (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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568A ALA 4.4 5.0 - - - +
571A ALA* 3.7 35.3 - - + +
572A LEU* 3.8 24.9 - - + +
575A ALA* 3.8 9.4 - - + -
583A ALA* 3.1 16.0 + - - +
584A ILE 3.1 6.9 + - - +
586A ALA* 1.4 74.8 - - + +
588A MET* 1.4 59.3 + - - +
590A GLU* 3.3 32.1 + - + +
591A LEU* 3.1 27.9 + - - +
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Residues in contact with MET 588 (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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535A THR* 4.5 4.5 - - - +
538A GLN* 3.9 31.2 - - + +
539A GLY* 3.8 14.8 - - - -
542A LEU* 3.7 32.6 - - + +
572A LEU* 3.7 18.8 - - + -
584A ILE* 2.9 19.6 + - - +
585A GLU* 3.3 26.0 - - - +
587A LYS* 1.4 76.1 - - - +
589A GLN* 1.4 57.1 + - - +
591A LEU* 3.4 5.4 + - - +
592A ALA* 3.1 27.5 + - - +
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Residues in contact with GLN 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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585A GLU 2.8 16.3 + - - +
586A ALA* 3.5 9.2 - - - +
588A MET* 1.4 73.0 - - - +
590A GLU* 1.3 65.9 + - + +
592A ALA* 3.4 11.1 + - - +
593A GLN* 3.1 56.4 + - - +
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Residues in contact with GLU 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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568A ALA* 4.6 4.9 - - + -
571A ALA* 5.5 1.9 - - - +
586A ALA* 2.9 24.6 + - - +
587A LYS* 3.3 36.4 + - + +
588A MET 3.4 0.2 - - - -
589A GLN* 1.3 75.1 - - + +
591A LEU* 1.3 61.6 + - - +
593A GLN* 3.3 27.0 + - - +
594A VAL* 3.4 18.2 + - - +
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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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542A LEU* 3.8 24.0 - - + +
546A THR* 3.7 25.1 - - + +
565A ILE* 3.9 15.9 - - + +
568A ALA* 3.7 28.4 - - + +
569A LEU* 3.9 24.5 - - + +
572A LEU* 4.1 13.5 - - + -
587A LYS 3.1 18.2 + - - +
588A MET 3.5 3.4 - - - +
590A GLU* 1.3 76.8 - - - +
592A ALA* 1.4 61.2 + - - +
594A VAL* 3.1 13.3 + - - +
595A SER* 2.9 32.4 + - - +
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Residues in contact with ALA 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A LEU* 5.4 7.6 - - + -
588A MET 3.1 16.2 + - - +
589A GLN* 3.4 14.8 + - - +
591A LEU* 1.4 76.9 - - - +
593A GLN* 1.3 59.6 + - - +
594A VAL 3.3 0.2 - - - -
595A SER* 3.5 16.7 + - - -
596A GLN* 3.8 12.0 + - - +
599A MET* 4.3 19.7 - - + +
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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
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589A GLN* 3.1 44.1 + - - +
590A GLU* 3.5 24.1 - - - +
591A LEU 3.2 0.4 - - - -
592A ALA* 1.3 77.9 - - - +
594A VAL* 1.3 61.5 + - + +
595A SER 3.4 0.4 + - - -
596A GLN* 4.3 18.4 + - - +
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Residues in contact with VAL 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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561A ASP* 4.2 14.3 - - - +
564A ALA* 3.5 45.5 - - + +
565A ILE* 3.3 20.3 - - + +
568A ALA* 3.8 11.2 - - + -
590A GLU 3.4 12.1 + - - +
591A LEU 3.1 12.3 + - - +
593A GLN* 1.3 80.1 - - + +
595A SER* 1.4 58.1 + - - +
596A GLN 3.6 2.4 + - - -
597A LYS* 5.3 0.3 + - - +
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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