Contacts of the helix formed by residues 656 - 671 (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 ASP 656 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A GLN* 3.7 12.0 + - - +
654A GLU 3.2 8.7 + - - +
655A LEU* 1.3 84.1 - - - +
657A ALA* 1.3 63.5 + - - +
658A ARG* 2.8 43.0 + - - +
659A ARG* 3.4 8.6 + - - +
660A ALA* 3.3 7.1 + - - +
701A FAD 3.0 30.6 + - + +
703A NAP 3.4 34.6 + - - +
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Residues in contact with ALA 657 (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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354A LEU* 4.0 11.0 - - + -
383A PRO* 4.7 2.7 - - + -
412A PHE* 3.5 39.0 - - + -
656A ASP* 1.3 70.3 - - - +
658A ARG* 1.3 57.2 + - - +
660A ALA* 3.3 7.0 + - - +
661A ILE* 2.9 33.4 + - - +
701A FAD 2.8 35.2 + - + +
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Residues in contact with ARG 658 (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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339A GLN* 2.5 41.2 + - - +
340A ALA* 3.3 12.4 - - + +
343A ASP* 5.1 0.6 - - - +
344A GLN* 2.7 30.7 + - - +
352A SER* 5.8 3.4 - - - -
353A CYS 4.8 2.2 - - - +
354A LEU* 3.8 40.0 - - + +
357A PRO* 5.2 0.8 - - + +
656A ASP* 2.8 26.5 + - - +
657A ALA* 1.3 74.4 - - - +
659A ARG* 1.3 59.9 + - - +
661A ILE* 3.9 1.2 - - - +
662A ALA* 2.9 38.8 + - + +
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Residues in contact with ARG 659 (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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651A VAL* 6.4 0.4 - - - -
654A GLU* 3.3 50.0 + - - +
655A LEU* 3.2 26.2 - - + -
656A ASP* 3.4 11.6 + - - +
658A ARG* 1.3 84.7 - - - +
660A ALA* 1.3 64.5 + - - +
662A ALA* 4.0 5.5 - - - +
663A GLN* 2.9 39.3 + - - +
666A ARG* 5.9 4.5 - - - +
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Residues in contact with ALA 660 (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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383A PRO* 4.4 2.0 - - + -
384A ALA* 3.8 28.7 - - + +
647A GLY* 4.1 12.8 - - - -
655A LEU* 4.0 3.1 - - + +
656A ASP 3.3 13.3 + - - +
657A ALA* 3.4 11.0 - - - +
658A ARG 3.2 0.2 - - - -
659A ARG* 1.3 80.3 - - - +
661A ILE* 1.3 58.6 + - - +
663A GLN* 3.6 2.3 - - - +
664A GLY 3.0 23.9 + - - -
701A FAD 3.9 23.1 - - - -
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Residues in contact with ILE 661 (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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354A LEU* 3.4 43.7 - - + +
355A VAL* 4.3 9.4 - - + +
357A PRO* 3.7 16.4 - - + -
383A PRO* 3.6 32.3 - - + +
387A ALA* 3.7 12.9 - - + +
412A PHE* 5.1 3.6 - - + -
431A TYR* 3.5 23.3 - - + +
657A ALA* 2.9 19.5 + - + +
658A ARG 4.0 0.7 - - - +
660A ALA* 1.3 69.6 - - - +
662A ALA* 1.3 59.2 + - - +
665A THR* 2.7 45.1 + - - +
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Residues in contact with ALA 662 (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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357A PRO* 3.5 26.9 - - + +
658A ARG* 2.9 29.6 + - + +
659A ARG* 4.0 6.7 - - - +
661A ILE* 1.3 73.9 - - - +
663A GLN* 1.3 57.3 + - - +
665A THR* 3.6 1.6 + - - -
666A ARG* 2.9 42.8 + - + +
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Residues in contact with GLN 663 (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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645A LEU 3.5 3.2 + - - -
646A ILE* 2.7 23.2 - - + +
647A GLY* 2.7 30.7 - - - +
650A ASP* 3.4 24.8 + - - +
651A VAL* 5.9 0.2 - - - +
655A LEU* 4.3 4.7 - - - +
659A ARG* 2.9 34.6 + - + +
660A ALA 3.6 3.4 - - - +
662A ALA* 1.3 74.9 - - - +
664A GLY* 1.3 66.5 + - - +
666A ARG* 3.2 25.8 + - - +
667A LEU* 3.0 24.3 + - - +
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Residues in contact with GLY 664 (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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384A ALA 3.9 20.6 - - - -
388A PHE* 3.4 19.9 - - - -
646A ILE* 3.9 13.4 - - - +
660A ALA 3.0 12.5 + - - -
661A ILE 3.9 0.7 - - - -
663A GLN* 1.3 77.4 - - - +
665A THR* 1.3 56.6 + - - +
667A LEU* 4.6 0.2 - - - -
668A ALA* 2.9 30.8 + - - +
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Residues in contact with THR 665 (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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357A PRO* 4.0 15.1 - - + +
358A ARG* 4.7 7.2 - - + -
365A MET* 4.3 11.2 - - + -
387A ALA* 3.7 13.0 - - - +
391A ASN* 3.7 24.3 + - - +
661A ILE* 2.7 31.2 + - - +
662A ALA 3.8 4.9 - - - -
664A GLY* 1.3 76.8 - - - +
666A ARG* 1.3 61.6 + - - +
668A ALA* 3.5 5.9 + - - +
669A LEU* 3.1 40.8 + - + +
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Residues in contact with ARG 666 (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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357A PRO* 6.4 0.2 - - + -
365A MET* 4.4 19.3 - - + -
659A ARG* 5.9 4.6 - - - +
662A ALA* 2.9 27.8 + - + +
663A GLN* 3.2 31.6 + - - +
665A THR* 1.3 74.0 - - - +
667A LEU* 1.3 68.2 + - - +
669A LEU* 3.5 4.8 + - - +
670A GLU* 3.3 23.3 + - - +
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Residues in contact with LEU 667 (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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388A PHE* 3.5 16.2 - - + -
460A ILE* 3.8 20.9 - - + -
644A HIS* 3.7 39.5 - - + +
646A ILE* 3.8 15.9 - - + -
663A GLN 3.0 16.5 + - - +
664A GLY 3.7 4.0 - - - +
666A ARG* 1.3 77.7 - - - +
668A ALA* 1.3 58.3 + - - +
670A GLU* 2.9 15.4 + - - +
671A ILE* 2.9 52.0 + - + +
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Residues in contact with ALA 668 (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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388A PHE* 3.2 41.2 - - + +
391A ASN* 3.4 20.6 - - + -
392A ALA* 3.8 4.0 - - - +
395A ARG* 2.8 25.6 + - - -
664A GLY 2.9 18.0 + - - +
665A THR 3.7 2.5 - - - +
667A LEU* 1.3 76.7 - - - +
669A LEU* 1.3 58.0 + - - +
670A GLU 3.6 0.2 + - - -
671A ILE* 3.6 9.3 - - - +
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Residues in contact with LEU 669 (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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358A ARG* 4.0 17.0 - - - -
365A MET* 3.8 42.0 - - + +
366A PRO 4.5 8.3 - - - +
367A ILE* 3.5 35.2 - - + -
391A ASN* 4.2 12.1 - - - +
395A ARG* 3.6 33.4 + - + +
665A THR* 3.1 24.2 + - + +
666A ARG* 4.1 4.7 - - - +
667A LEU 3.2 0.4 - - - -
668A ALA* 1.3 75.2 - - - +
670A GLU* 1.3 59.5 + - - +
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Residues in contact with GLU 670 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A VAL* 3.9 15.6 - - - +
666A ARG* 3.3 18.3 + - - +
667A LEU* 2.9 11.6 + - + +
669A LEU* 1.3 79.4 - - - +
671A ILE* 1.3 69.8 + - - +
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Residues in contact with ILE 671 (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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371A VAL* 4.1 13.3 - - - +
374A LYS* 3.6 25.6 + - - +
376A LEU* 3.8 22.7 - - + -
388A PHE* 4.0 17.7 - - + -
392A ALA* 4.8 0.7 - - + -
395A ARG* 3.5 16.1 + - - -
397A HIS* 3.0 31.5 + - + +
458A GLU* 2.9 28.5 - - - +
460A ILE* 4.7 0.9 - - + -
644A HIS* 4.3 9.4 - - + +
667A LEU* 2.9 32.5 + - + +
668A ALA* 3.6 15.5 - - - +
670A GLU* 1.3 83.8 - - - +
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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