Contacts of the helix formed by residues 565 - 581 (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 ARG 565 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560C PHE* 3.7 50.7 - - + +
563C GLY 4.4 0.2 + - - -
564C VAL* 1.3 75.5 - - - +
566C MET* 1.3 58.2 + - - +
567C GLU* 3.0 29.1 + - - +
568C GLU* 3.0 52.6 + - + +
569C ILE 4.0 0.7 + - - -
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Residues in contact with MET 566 (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* 3.8 53.6 - - + -
543C ALA* 3.6 24.7 - - - +
546C ASP* 2.8 36.3 - - + +
547C THR* 4.2 5.6 - - - +
560C PHE* 5.1 0.6 - - + +
561C VAL* 3.9 11.9 - - + +
564C VAL* 2.9 31.0 - - + +
565C ARG* 1.3 71.1 - - - +
567C GLU* 1.3 60.1 + - - +
568C GLU 3.2 0.7 - - - -
569C ILE* 3.5 13.3 + - + -
570C VAL* 2.9 32.1 + - - +
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Residues in contact with GLU 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547C THR* 3.1 41.2 + - + +
565C ARG* 3.0 20.5 + - + +
566C MET* 1.3 78.2 + - - +
568C GLU* 1.3 60.9 + - + +
570C VAL* 3.8 7.8 - - + +
571C GLU* 3.0 28.9 + - - +
607C ILE* 4.0 30.3 - - + +
610C ILE* 3.9 8.6 - - + +
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Residues in contact with GLU 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508C LYS* 3.7 35.8 + - + +
563C GLY 5.1 1.2 - - - +
564C VAL* 4.3 6.5 - - + +
565C ARG* 3.0 51.3 + - + +
567C GLU* 1.3 77.9 - - + +
569C ILE* 1.3 60.8 + - - +
571C GLU* 3.4 8.8 + - - +
572C GLY* 2.8 24.1 + - - -
17F GLU* 4.7 2.8 - - - +
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Residues in contact with ILE 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504C TRP* 3.6 42.8 - - + -
507C ILE* 4.8 1.3 - - + -
508C LYS* 3.6 39.3 - - + +
511C VAL* 5.2 6.7 - - + -
539C LEU* 4.1 4.7 - - + +
543C ALA* 4.1 14.6 - - + -
564C VAL* 4.3 3.1 - - + -
565C ARG 4.5 2.0 - - - +
566C MET* 3.5 24.9 + - + +
568C GLU* 1.3 74.5 - - - +
570C VAL* 1.3 55.9 + - - +
572C GLY* 2.7 5.3 + - - +
573C CYS* 2.7 52.7 + - - -
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Residues in contact with VAL 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540C LEU* 4.0 17.4 - - + +
543C ALA* 3.3 31.0 - - + +
544C HIS* 3.8 9.2 - - - +
547C THR* 5.0 2.5 - - - +
566C MET 2.9 25.1 + - - +
567C GLU* 3.8 9.4 - - + +
569C ILE* 1.3 76.9 - - - +
571C GLU* 1.3 60.1 + - - +
573C CYS* 5.1 0.7 - - - -
574C THR* 3.0 33.1 + - - +
602C LEU* 3.8 28.9 - - + -
610C ILE* 4.2 13.6 - - + +
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Residues in contact with GLU 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C ARG* 3.8 16.7 + - - +
567C GLU 3.0 20.2 + - - +
568C GLU* 3.6 8.3 - - - +
570C VAL* 1.3 75.5 - - - +
572C GLY* 1.3 58.9 + - - +
574C THR* 4.4 2.0 - - - -
575C GLY* 3.0 25.1 + - - -
607C ILE* 4.5 7.8 - - - +
609C ASN* 3.1 46.7 + - + +
610C ILE* 4.0 20.7 - - + +
613C VAL* 4.5 5.0 - - + +
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Residues in contact with GLY 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511C VAL* 3.4 18.4 - - - +
515C ARG* 4.2 12.4 + - - +
568C GLU 2.8 12.1 + - - -
569C ILE* 2.7 8.1 + - - -
571C GLU* 1.3 75.7 - - - +
573C CYS* 1.3 52.8 + - - -
575C GLY* 3.2 1.9 + - - -
576C ALA* 2.6 36.7 + - - +
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Residues in contact with CYS 573 (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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511C VAL* 3.6 17.4 - - - +
536C LEU* 3.4 36.3 - - + +
539C LEU* 3.9 8.1 - - - -
540C LEU* 3.9 21.8 - - + -
569C ILE* 2.7 39.6 + - - +
570C VAL 4.5 1.1 - - - +
572C GLY* 1.3 69.0 - - - -
574C THR* 1.3 65.6 + - - +
576C ALA* 2.8 6.6 + - - +
577C LEU* 2.7 28.5 + - + +
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Residues in contact with THR 574 (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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540C LEU* 3.3 19.9 - - - +
570C VAL* 3.0 19.2 + - - -
573C CYS* 1.3 76.3 - - - +
575C GLY* 1.3 52.9 + - - +
577C LEU* 3.0 14.5 + - - +
578C HIS* 2.7 35.7 + - - +
599C PHE* 4.3 10.1 - - + -
602C LEU* 3.4 19.1 - - + +
610C ILE* 5.9 1.1 - - + -
613C VAL* 3.5 38.1 - - + +
614C ALA* 4.0 8.7 - - + +
617C VAL* 4.6 1.7 - - + +
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Residues in contact with GLY 575 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C ARG* 3.8 23.8 + - - -
571C GLU 3.0 21.4 + - - -
572C GLY 3.5 0.4 - - - -
573C CYS 3.2 0.2 - - - -
574C THR* 1.3 76.3 - - - +
576C ALA* 1.3 61.2 + - - +
578C HIS* 3.3 8.6 + - - +
579C ILE* 3.1 23.0 - - - +
613C VAL* 3.8 13.9 - - - +
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Residues in contact with ALA 576 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511C VAL* 4.4 7.2 - - + +
514C ILE* 4.7 3.4 - - + -
515C ARG* 4.0 31.3 - - + +
518C ALA* 4.5 1.4 - - - +
536C LEU* 3.9 20.4 - - + -
572C GLY 2.6 20.3 + - - +
573C CYS* 3.4 6.7 - - - +
575C GLY* 1.3 70.8 - - - +
577C LEU* 1.3 65.5 + - - +
579C ILE* 3.4 5.4 + - - +
580C LEU* 3.1 27.1 + - - +
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Residues in contact with LEU 577 (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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533C ILE* 4.2 16.6 - - + -
536C LEU* 4.1 25.6 - - + -
537C VAL* 4.1 26.2 - - + +
540C LEU* 3.9 19.3 - - + -
573C CYS* 2.7 24.2 + - + +
574C THR* 3.4 6.3 - - - +
576C ALA* 1.3 70.1 - - - +
578C HIS* 1.3 67.5 + - - +
580C LEU* 2.7 11.1 + - + +
581C ALA* 2.7 26.3 + - - +
590C ILE* 4.2 16.4 - - + +
599C PHE* 3.9 28.5 - - + -
617C VAL* 4.8 2.2 - - + -
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Residues in contact with HIS 578 (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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574C THR 2.7 16.5 + - - +
575C GLY* 3.3 13.7 + - - +
577C LEU* 1.3 72.4 - - - +
579C ILE* 1.3 71.1 + - + +
581C ALA* 3.4 13.5 + - - +
582C ARG* 4.3 9.9 + - - +
612C ARG* 3.8 15.3 + - - -
613C VAL* 4.0 27.6 - - - +
616C GLY* 3.7 24.8 + - - -
617C VAL* 4.1 16.5 - - - +
620C GLU* 4.1 13.1 + - + +
654C TYR* 3.4 37.9 + + - -
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Residues in contact with ILE 579 (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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515C ARG* 4.5 19.1 - - + +
518C ALA* 3.1 39.3 - - + +
519C LEU* 3.5 28.9 - - + +
524C HIS* 4.0 3.3 + - - -
575C GLY 3.1 17.5 - - - +
576C ALA 3.7 5.8 - - - +
577C LEU 3.0 0.8 - - - -
578C HIS* 1.3 82.1 - - + +
580C LEU* 1.3 64.8 + - - +
581C ALA 3.1 1.8 - - - -
582C ARG* 3.0 49.1 + - - +
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Residues in contact with LEU 580 (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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514C ILE* 4.9 7.9 - - + -
518C ALA* 3.7 21.5 - - + -
524C HIS* 4.1 18.7 - - + +
527C LEU* 4.1 17.3 - - + -
528C ARG 5.9 0.4 - - - +
532C ALA* 5.0 7.4 - - + -
533C ILE* 4.2 21.1 - - + -
536C LEU* 4.1 23.6 - - + -
576C ALA 3.1 14.3 + - - +
577C LEU* 2.7 13.9 + - + +
579C ILE* 1.3 70.9 - - - +
581C ALA* 1.3 53.7 + - - +
582C ARG 2.7 16.5 + - - -
583C ASP* 3.2 5.0 + - - +
586C ASN* 2.9 44.1 + - + +
590C ILE* 5.1 4.0 - - + -
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Residues in contact with ALA 581 (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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577C LEU 2.7 14.9 + - - +
578C HIS* 3.5 12.3 - - - +
579C ILE 3.1 0.8 - - - -
580C LEU* 1.3 74.0 - - - +
582C ARG* 1.3 58.3 - - - +
583C ASP 3.3 1.6 - - - -
586C ASN* 4.5 1.1 - - - -
587C ARG* 2.9 37.4 + - + +
590C ILE* 3.9 19.2 - - + +
617C VAL* 4.5 7.6 - - + -
620C GLU* 3.6 24.3 - - + +
621C LEU* 4.5 2.2 - - + -
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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