Contacts of the helix formed by residues 575 - 586 (chain A) in PDB entry 1PS9
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 575 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A ALA* 4.1 16.2 - - + -
336A GLY 5.3 0.2 - - - +
337A CYS 3.9 9.2 + - - +
338A ASN* 3.9 23.1 - - + +
343A ASP* 4.6 2.5 + - - +
572A GLY* 3.7 16.3 + - - -
573A LYS 3.4 0.2 - - - -
574A THR* 1.3 94.4 - - - +
576A GLY* 1.3 69.4 + - - +
577A TRP 3.2 2.5 - - - -
578A ILE* 3.0 26.6 + - - +
579A HIS* 3.5 20.3 + - - -
703A NAP 4.0 11.8 + - - -
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Residues in contact with GLY 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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568A GLY 4.8 0.4 - - - -
571A LEU* 3.6 30.5 - - - +
572A GLY 2.8 22.4 + - - -
575A THR* 1.3 74.9 + - - +
577A TRP* 1.3 62.2 + - - +
578A ILE 3.2 0.3 + - - -
579A HIS* 3.4 5.2 + - - +
580A ARG* 3.0 32.7 + - - +
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Residues in contact with TRP 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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254A ALA 3.7 11.0 - - - -
255A ARG* 3.5 51.4 - - + +
256A ILE 3.7 25.8 - - - -
257A PRO* 3.7 9.4 - - + -
531A TRP* 5.1 2.5 - + - -
573A LYS 4.1 6.4 + - - -
574A THR 3.3 17.3 + - - -
576A GLY* 1.3 74.8 - - - +
578A ILE* 1.3 85.2 + - + +
580A ARG* 3.8 23.8 + - - +
581A THR* 2.8 44.6 + - - +
704A MDE 3.0 64.0 + - - +
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Residues in contact with ILE 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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257A PRO* 3.4 33.0 - - + -
260A ALA* 3.5 31.6 - - + -
262A PRO* 4.6 12.3 - - + -
531A TRP* 4.2 8.6 - - + -
574A THR 4.0 14.4 - - - +
575A THR* 3.0 12.4 + - - +
577A TRP* 1.3 111.4 - - + +
579A HIS* 1.3 68.0 + - + +
581A THR* 3.2 3.5 + - - -
582A THR* 2.9 34.6 + - - +
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Residues in contact with HIS 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PRO* 4.2 20.4 - - + +
421A LYS* 4.6 21.7 - - - +
507A PHE* 4.4 20.5 - - + +
508A ASP* 4.7 8.7 + - - -
511A MET* 4.1 27.4 - - + -
571A LEU* 4.9 11.4 - - + +
575A THR* 3.5 24.0 + - - -
576A GLY* 3.4 6.3 + - - +
578A ILE* 1.3 85.7 - - + +
580A ARG* 1.3 58.6 + - - +
582A THR* 3.2 2.5 + - - -
583A LEU* 2.9 36.4 + - - +
703A NAP 5.2 7.6 - - - -
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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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507A PHE* 4.3 13.6 - - + -
566A LYS* 2.9 40.7 - - - +
567A PRO 3.4 25.0 + - - -
568A GLY* 3.9 20.2 + - - -
569A GLN* 4.9 2.8 - - - +
576A GLY* 3.0 13.1 + - - +
577A TRP* 3.8 30.5 + - - +
579A HIS* 1.3 77.6 - - - +
581A THR* 1.3 64.1 + - - +
583A LEU* 3.5 0.9 + - - +
584A LEU* 3.0 48.3 + - + +
590A MET* 4.5 12.3 - - - -
704A MDE 4.7 8.9 + - - -
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Residues in contact with THR 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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255A ARG* 5.2 9.2 + - + +
531A TRP* 4.2 23.6 - - + -
548A MET* 4.5 14.1 - - + -
550A ILE* 6.2 0.2 - - + -
577A TRP* 2.8 31.3 + - - +
578A ILE* 3.6 4.0 - - - -
580A ARG* 1.3 79.1 + - - +
582A THR* 1.3 62.6 + - - +
584A LEU* 4.0 6.2 - - - +
585A SER* 2.9 39.9 + - - +
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Residues in contact with THR 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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511A MET* 4.0 15.3 - - + +
530A GLU* 6.0 1.3 - - - +
531A TRP* 3.6 22.5 - - + -
550A ILE* 4.1 9.7 - - + +
578A ILE* 2.9 23.8 + - - +
579A HIS* 3.2 8.6 + - - -
581A THR* 1.3 77.2 - - - +
583A LEU* 1.3 62.9 + - - +
585A SER* 3.3 6.4 + - - -
586A ARG* 3.1 58.4 + - + +
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Residues in contact with LEU 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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507A PHE* 3.5 39.7 - - + +
510A ALA* 3.9 20.9 - - + -
511A MET* 3.7 43.5 - - + +
514A SER* 4.0 11.0 - - - +
559A MET* 4.0 6.1 - - - -
579A HIS 2.9 13.0 + - - +
582A THR* 1.3 78.5 - - + +
584A LEU* 1.3 61.3 + - - +
586A ARG* 3.0 12.4 + - - +
587A GLY 3.3 0.2 + - - -
588A VAL* 3.1 43.5 + - + +
590A MET* 3.5 6.5 - - + -
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Residues in contact with LEU 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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552A ARG* 4.2 1.7 + - - -
566A LYS* 6.1 1.3 - - - -
580A ARG* 3.0 40.1 + - + +
581A THR* 4.0 5.6 - - - +
583A LEU* 1.3 75.7 - - - +
585A SER* 1.3 62.5 + - - +
587A GLY* 3.2 12.0 + - - -
588A VAL 3.6 14.7 - - - +
589A LYS* 5.2 0.7 - - - -
590A MET* 3.3 31.9 - - + +
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Residues in contact with SER 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A MET* 4.5 8.5 - - - +
550A ILE* 3.8 41.2 - - - +
552A ARG* 2.5 23.4 + - - +
581A THR* 2.9 30.6 + - - +
582A THR 3.7 4.3 - - - -
584A LEU* 1.3 77.1 - - - +
586A ARG* 1.3 53.2 + - - +
587A GLY 3.2 1.6 - - - -
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Residues in contact with ARG 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A MET* 3.1 29.0 + - - -
514A SER* 3.0 33.1 + - - -
515A GLN* 2.9 35.2 + - - +
516A PRO* 3.5 14.5 - - + +
530A GLU* 5.3 8.3 + - - -
550A ILE* 3.6 17.2 - - + +
551A PRO* 3.7 13.9 - - - +
552A ARG* 3.2 11.3 + - - +
553A SER* 3.0 34.4 + - - -
582A THR* 3.1 37.9 + - - +
583A LEU* 3.0 12.4 + - - +
585A SER* 1.3 74.6 - - - +
587A GLY* 1.3 58.1 + - - +
588A VAL* 3.4 3.4 - - + -
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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