Contacts of the helix formed by residues 573 - 583 (chain A) in PDB entry 1JQO
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 573 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565A PHE* 5.2 0.7 - - - -
569A ALA 2.9 17.5 + - - -
570A ASP* 3.4 7.4 + - - +
572A GLN* 1.3 73.9 - - - +
574A ALA* 1.3 59.3 + - - +
575A PRO 3.7 0.7 - - - -
576A ALA* 3.5 20.4 - - - +
577A SER* 3.2 22.0 + - - -
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Residues in contact with ALA 574 (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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565A PHE* 4.0 27.1 - - + -
570A ASP 3.1 12.7 + - - +
571A LEU* 3.1 24.5 - - + +
572A GLN 2.7 5.1 + - - -
573A SER* 1.3 75.6 - - - +
575A PRO* 1.4 64.0 - - + +
576A ALA 3.0 5.6 + - - -
577A SER 3.6 0.3 + - - -
578A VAL* 2.9 29.0 + - - +
620A ALA* 4.7 4.0 - - + -
624A MET* 4.1 9.0 - - + -
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Residues in contact with PRO 575 (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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571A LEU 4.0 2.2 - - - +
572A GLN 3.1 14.4 - - - +
574A ALA* 1.4 94.7 - - + +
576A ALA* 1.3 61.9 + - - +
578A VAL* 3.6 9.8 - - + +
579A GLU* 3.1 20.3 + - - +
620A ALA* 4.0 15.3 - - - +
623A GLU* 3.8 34.3 - - + +
624A MET* 4.0 6.1 - - + +
627A VAL* 4.0 24.6 - - + +
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Residues in contact with ALA 576 (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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573A SER* 3.5 23.6 - - - +
574A ALA 3.0 0.8 - - - -
575A PRO* 1.3 76.0 - - - +
577A SER* 1.3 67.9 + - - +
578A VAL 3.0 0.9 - - - -
579A GLU* 2.9 16.8 + - - +
580A ARG* 3.0 24.3 + - + +
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Residues in contact with SER 577 (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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538A THR* 3.7 29.9 + - - -
539A ALA* 5.1 3.3 - - - -
540A PRO* 4.1 5.9 - - - +
565A PHE* 4.5 14.9 - - - -
573A SER* 3.2 16.8 + - - -
574A ALA 4.2 2.0 - - - -
576A ALA* 1.3 77.5 - - - +
578A VAL* 1.3 62.2 + - - +
580A ARG* 3.8 14.9 + - - +
581A LEU* 3.1 24.9 + - - +
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Residues in contact with VAL 578 (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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563A PRO* 6.4 0.2 - - + -
565A PHE* 4.0 13.0 - - + -
574A ALA 2.9 23.6 + - - +
575A PRO* 3.6 7.0 - - + +
576A ALA 2.9 0.6 + - - -
577A SER* 1.3 77.0 - - - +
579A GLU* 1.3 58.9 + - - +
581A LEU* 3.2 12.6 + - - +
582A PHE* 2.6 51.9 + - + -
597A VAL* 5.3 4.3 - - + -
624A MET* 3.5 36.1 - - + +
627A VAL* 4.1 14.8 - - + +
635A LEU* 4.8 6.1 - - + -
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Residues in contact with GLU 579 (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 PRO 3.1 8.8 + - - +
576A ALA* 2.9 5.7 + - - +
578A VAL* 1.3 78.4 - - - +
580A ARG* 1.3 57.9 + - + +
582A PHE* 2.7 27.2 + - - +
583A SER* 3.0 14.2 + - - +
627A VAL* 3.3 18.2 - - + -
630A ARG* 2.6 33.9 + - - -
631A TYR* 2.8 32.2 + - + +
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Residues in contact with ARG 580 (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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483A GLU* 3.6 28.1 - - - +
487A GLN* 4.2 9.1 + - - +
539A ALA* 4.9 5.5 - - - +
540A PRO* 3.7 29.5 - - + +
576A ALA* 3.0 23.5 + - + +
577A SER* 3.8 12.7 + - - +
579A GLU* 1.3 76.7 - - + +
581A LEU* 1.3 57.9 + - - +
583A SER* 3.2 24.6 + - - -
584A VAL* 4.0 9.2 + - - +
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Residues in contact with LEU 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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540A PRO* 3.6 33.6 - - + +
543A VAL* 3.9 30.1 - - + -
544A LEU* 5.3 3.8 - - + -
563A PRO* 5.2 10.5 - - + -
577A SER 3.1 13.7 + - - +
578A VAL* 3.3 13.7 - - - +
579A GLU 2.9 0.8 - - - -
580A ARG* 1.3 74.9 - - - +
582A PHE* 1.3 65.3 + - + +
583A SER 3.0 6.0 + - - -
584A VAL* 3.5 15.5 + - + +
587A TYR* 3.6 49.1 - - + +
595A GLN* 4.5 7.6 - - - +
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Residues in contact with PHE 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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578A VAL* 2.6 51.6 - - + -
579A GLU* 2.7 13.1 + - - +
581A LEU* 1.3 78.5 - - + +
583A SER* 1.3 58.3 + - - +
584A VAL 3.3 2.4 + - - -
587A TYR* 5.3 4.7 - + - -
588A MET* 3.6 35.6 - - + +
591A ILE* 5.8 1.3 - - + -
595A GLN* 3.6 34.1 - - + -
627A VAL 4.7 4.3 - - - -
628A ALA* 4.7 6.7 - - + -
631A TYR* 3.4 32.5 - + + -
633A VAL* 3.0 49.4 - - + -
635A LEU* 4.9 2.0 - - + -
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Residues in contact with SER 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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579A GLU* 3.0 16.3 + - - +
580A ARG* 3.2 16.8 + - - -
581A LEU 3.0 0.8 - - - -
582A PHE* 1.3 78.0 - - - +
584A VAL* 1.3 60.9 + - - +
585A ASP* 3.5 12.1 + - - +
631A TYR* 4.0 14.4 + - - -
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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