Contacts of the helix formed by residues 531 - 549 (chain C) in PDB entry 1JPW
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 531 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495C VAL* 4.0 5.7 - - - +
499C HIS* 4.7 3.5 + - - -
528C ARG 2.7 13.8 + - - -
529C GLU 3.3 1.2 - - - -
530C GLN* 1.3 81.0 - - - +
532C ALA* 1.3 62.4 + - - +
533C ILE 3.6 1.3 - - - -
534C PRO* 3.9 20.4 - - - +
535C ARG* 3.9 13.2 + - - +
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Residues in contact with ALA 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C VAL* 3.9 24.2 - - + +
498C LEU* 4.9 1.3 - - - +
514C ILE* 5.0 8.1 - - + -
527C LEU* 3.1 33.2 + - + +
528C ARG 3.9 0.6 + - - -
530C GLN 3.6 1.0 - - - -
531C GLY* 1.3 75.4 - - - +
533C ILE* 1.3 67.2 + - - +
535C ARG* 3.3 3.9 + - - +
536C LEU* 3.0 37.1 + - + +
580C LEU* 5.0 5.2 - - + -
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Residues in contact with ILE 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528C ARG* 3.8 24.6 - - + +
532C ALA* 1.3 74.3 - - + +
534C PRO* 1.3 73.0 - - + +
536C LEU* 2.9 19.4 + - - +
537C VAL* 3.0 22.1 + - + +
577C LEU* 4.2 9.0 - - + -
580C LEU* 4.2 18.2 - - + -
586C ASN* 3.7 36.6 - - + +
589C VAL* 3.7 31.9 - - + -
590C ILE* 3.8 23.8 - - + +
593C LEU* 4.5 0.9 - - + -
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Residues in contact with PRO 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528C ARG* 5.6 1.3 - - + +
531C GLY* 3.9 19.1 - - - +
532C ALA 3.8 1.6 - - - +
533C ILE* 1.3 95.9 - - + +
535C ARG* 1.3 61.0 + - - +
537C VAL* 3.5 2.6 + - - +
538C GLN* 3.1 27.6 + - - +
589C VAL* 4.6 8.5 - - + -
593C LEU* 3.6 24.4 - - + +
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Residues in contact with ARG 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C LEU* 2.9 43.0 + - + -
499C HIS* 3.5 38.4 - - + +
500C PRO* 4.1 19.7 - - - +
507C ILE* 4.9 4.9 - - - +
531C GLY 3.9 9.4 + - - +
532C ALA 3.3 3.0 + - - +
533C ILE 3.2 0.8 - - - -
534C PRO* 1.3 77.4 - - - +
536C LEU* 1.3 65.1 + - - +
538C GLN* 3.5 15.0 + - - +
539C LEU* 3.1 52.4 + - + +
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Residues in contact with LEU 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C LEU* 4.1 20.4 - - + -
511C VAL* 4.5 18.6 - - + -
514C ILE* 4.2 16.8 - - + -
532C ALA 3.0 18.7 + - - +
533C ILE 2.9 7.7 + - - +
535C ARG* 1.3 78.7 - - - +
537C VAL* 1.3 56.2 + - - +
539C LEU* 3.3 2.6 + - + -
540C LEU* 3.0 26.9 + - - +
573C CYS* 3.4 25.9 - - + +
576C ALA* 3.9 23.8 - - + -
577C LEU* 4.1 17.5 - - + -
580C LEU* 4.1 24.0 - - + -
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Residues in contact with VAL 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C ILE* 3.0 17.2 + - + +
534C PRO 3.7 6.7 - - - +
536C LEU* 1.3 77.0 - - - +
538C GLN* 1.3 61.6 + - - +
540C LEU* 3.0 16.3 - - + +
541C VAL* 2.9 36.2 + - + +
577C LEU* 4.1 20.0 - - + -
590C ILE* 5.2 1.6 - - + -
593C LEU* 3.9 27.1 - - + +
595C THR* 3.6 32.8 - - + -
598C LEU* 5.5 1.8 - - + -
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Residues in contact with GLN 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534C PRO 3.1 17.9 + - - +
535C ARG* 4.0 20.2 - - - +
537C VAL* 1.3 80.9 - - - +
539C LEU* 1.3 63.2 + - - +
541C VAL* 3.4 23.4 + - - +
542C ARG* 3.2 22.7 + - - +
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Residues in contact with LEU 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C LEU* 4.0 19.1 - - + +
504C TRP* 4.2 21.4 - - + -
507C ILE* 3.6 31.0 - - + -
511C VAL* 5.1 1.6 - - + -
535C ARG* 3.1 65.0 + - + +
536C LEU* 3.8 4.9 - - - +
538C GLN* 1.3 74.6 - - - +
540C LEU* 1.3 65.2 + - - +
542C ARG* 4.0 6.8 - - + +
543C ALA* 3.1 24.8 + - - +
569C ILE* 4.1 3.4 - - + +
573C CYS* 3.9 15.3 - - - -
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Residues in contact with LEU 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C LEU 3.0 13.6 + - - +
537C VAL* 3.0 16.8 - - + +
539C LEU* 1.3 77.3 - - - +
541C VAL* 1.3 60.9 + - - +
543C ALA* 3.2 6.6 + - - +
544C HIS* 2.9 22.3 + - + +
570C VAL* 4.0 24.5 - - + +
573C CYS* 3.9 10.1 - - + -
574C THR* 3.3 21.3 - - - +
577C LEU* 3.9 16.6 - - + -
595C THR* 5.5 0.4 - - + -
598C LEU* 3.5 28.5 - - + -
599C PHE* 3.7 26.2 - - + -
602C LEU* 4.4 6.1 - - + -
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Residues in contact with VAL 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C VAL* 2.9 20.5 + - + +
538C GLN* 3.6 29.2 - - - +
540C LEU* 1.3 75.4 - - - +
542C ARG* 1.3 66.2 + - - +
544C HIS* 2.9 15.8 + - - +
545C GLN* 3.1 38.9 + - + +
598C LEU* 4.3 22.0 - - + -
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Residues in contact with ARG 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504C TRP* 4.5 20.0 - - + -
538C GLN 3.2 13.4 + - - +
539C LEU* 4.0 9.0 - - + +
541C VAL* 1.3 78.8 - - - +
543C ALA* 1.3 62.3 + - - +
545C GLN* 3.7 25.9 + - - +
546C ASP* 2.5 50.5 + - - +
549C ARG* 6.0 1.8 - - - +
566C MET* 6.0 0.2 - - - -
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Residues in contact with ALA 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504C TRP* 5.2 1.3 - - + -
539C LEU 3.1 20.7 + - - +
540C LEU* 3.4 2.9 - - - +
541C VAL 3.1 0.8 - - - -
542C ARG* 1.3 76.5 - - - +
544C HIS* 1.3 64.5 + - - +
546C ASP* 3.1 21.2 + - - +
547C THR* 3.4 11.6 + - - -
566C MET* 3.6 20.5 - - + +
569C ILE* 4.1 15.0 - - + -
570C VAL* 3.3 23.9 - - + +
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Residues in contact with HIS 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540C LEU* 2.9 16.4 + - + +
541C VAL* 2.9 10.1 + - - +
543C ALA* 1.3 77.0 - - - +
545C GLN* 1.3 65.4 + - + +
547C THR* 3.3 8.0 + - - +
548C GLN* 3.3 41.3 + - - +
570C VAL* 3.8 10.3 - - + +
598C LEU* 3.7 28.9 - - + +
601C GLN* 4.6 17.5 - - + +
602C LEU* 4.0 30.1 - - + +
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Residues in contact with GLN 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C VAL* 3.1 28.8 + - + +
542C ARG* 3.7 33.6 + - - +
544C HIS* 1.3 80.0 - - + +
546C ASP* 1.3 58.7 + - - +
548C GLN* 2.9 29.3 + - + +
549C ARG* 3.2 21.5 + - - +
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Residues in contact with ASP 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504C TRP* 5.6 0.7 + - - -
542C ARG* 2.5 45.6 + - - +
543C ALA 3.1 14.7 + - - +
544C HIS 3.1 0.2 - - - -
545C GLN* 1.3 80.6 - - - +
547C THR* 1.3 58.0 + - - +
548C GLN 3.1 0.6 + - - -
549C ARG* 4.0 12.0 + - - +
561C VAL* 4.6 8.5 - - - +
566C MET* 2.8 38.0 - - + +
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Residues in contact with THR 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543C ALA 3.4 9.2 + - - -
544C HIS* 3.3 10.7 + - - -
545C GLN 3.3 0.2 - - - -
546C ASP* 1.3 75.5 - - - +
548C GLN* 1.3 64.8 + - - +
549C ARG 3.9 4.5 - - - +
566C MET* 4.2 8.0 - - - +
567C GLU* 3.1 46.8 + - + +
570C VAL* 5.0 2.1 - - - +
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Residues in contact with GLN 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544C HIS* 3.3 34.5 + - + +
545C GLN* 2.9 23.7 + - + +
547C THR* 1.3 78.4 - - - +
549C ARG* 1.3 71.4 + - + +
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Residues in contact with ARG 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542C ARG* 6.0 1.6 - - - +
545C GLN* 3.2 19.7 + - - +
546C ASP 4.3 8.8 - - - +
547C THR 3.7 7.3 - - - +
548C GLN* 1.3 91.0 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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