Contacts of the helix formed by residues 503 - 518 (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 HIS 503 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458C GLU* 3.1 38.3 + - - +
501C PRO 4.3 8.6 + - - -
502C SER* 1.3 72.5 - - - +
504C TRP* 1.3 62.2 + - - +
505C PRO* 3.5 12.8 - - + -
506C LEU 3.4 2.0 + - - -
507C ILE* 2.9 32.1 + - - +
562C GLU* 3.4 27.3 + - - +
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Residues in contact with TRP 504 (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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503C HIS* 1.3 68.6 - - - +
505C PRO* 1.3 70.7 - - + +
506C LEU 3.1 2.0 - - - -
507C ILE* 3.6 33.7 - - + -
508C LYS* 2.8 32.7 + - - +
539C LEU* 4.2 27.1 - - + -
542C ARG* 4.5 18.4 - - + -
543C ALA* 5.2 0.9 - - + -
546C ASP* 5.6 0.4 + - - -
561C VAL* 4.2 7.7 - - + +
562C GLU* 3.8 33.3 + - + -
564C VAL* 4.1 13.4 - - + +
566C MET* 3.8 31.8 - - + -
569C ILE* 3.6 42.4 - - + -
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Residues in contact with PRO 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C GLU* 3.4 30.7 - - - +
503C HIS* 3.6 14.6 - - + -
504C TRP* 1.3 94.6 - - + +
506C LEU* 1.3 58.5 + - - +
508C LYS* 3.7 6.8 - - + +
509C ALA* 3.5 19.1 + - - +
562C GLU* 3.9 27.4 - - + +
564C VAL* 4.0 11.7 - - + -
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Residues in contact with LEU 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C GLU* 3.6 34.1 + - + +
461C THR* 3.7 14.8 - - - +
462C GLU* 3.6 36.3 + - + +
465C ILE* 4.4 8.1 - - + -
497C LEU* 3.7 17.7 - - + +
502C SER* 3.3 29.6 - - - +
503C HIS 3.4 4.0 + - - +
504C TRP 3.1 0.2 - - - -
505C PRO* 1.3 77.9 - - - +
507C ILE* 1.3 56.4 + - - +
508C LYS 3.1 1.1 - - - -
509C ALA* 3.1 5.1 + - + +
510C THR* 2.7 48.9 + - - +
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Residues in contact with ILE 507 (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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497C LEU 4.1 15.7 - - - +
498C LEU* 4.2 16.2 - - + +
499C HIS 5.6 0.4 - - - +
502C SER* 3.4 19.3 - - - +
503C HIS 2.9 25.9 + - - +
504C TRP* 3.6 34.3 - - + +
506C LEU* 1.3 75.9 - - - +
508C LYS* 1.3 65.4 + - - +
510C THR* 3.1 9.1 + - - -
511C VAL* 2.9 35.3 + - + +
535C ARG* 4.9 6.1 - - - +
539C LEU* 3.6 29.4 - - + -
569C ILE* 4.8 0.9 - - + -
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Residues in contact with LYS 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C ARG* 3.9 18.9 + - - +
504C TRP 2.8 19.7 + - - +
505C PRO* 3.7 7.9 - - + +
507C ILE* 1.3 79.1 - - - +
509C ALA* 1.3 64.0 + - - +
511C VAL* 3.2 6.0 + - - +
512C GLY 3.2 15.8 + - - -
564C VAL* 3.7 23.1 - - + -
568C GLU* 3.7 30.2 + - + +
569C ILE* 3.6 26.4 - - + +
17F GLU* 2.9 38.9 + - - -
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Residues in contact with ALA 509 (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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462C GLU* 4.8 2.7 - - + +
465C ILE* 3.8 16.0 - - + +
466C CYS* 3.8 31.2 - - - +
469C ARG* 3.8 17.8 - - - +
505C PRO 3.5 10.7 + - - +
506C LEU* 3.1 9.7 + - + +
508C LYS* 1.3 82.2 - - - +
510C THR* 1.3 57.9 + - - +
512C GLY* 3.3 2.1 + - - -
513C LEU* 3.1 26.2 + - - +
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Residues in contact with THR 510 (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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465C ILE* 4.0 13.5 - - + +
494C VAL* 3.0 35.4 - - + +
497C LEU* 4.0 13.2 - - + +
498C LEU* 3.3 22.7 - - + -
506C LEU* 2.7 37.4 + - - +
507C ILE* 3.1 7.1 + - - -
509C ALA* 1.3 74.6 - - - +
511C VAL* 1.3 64.1 + - - +
513C LEU* 3.5 2.6 + - - +
514C ILE* 3.1 22.8 + - + +
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Residues in contact with VAL 511 (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 12.6 - - + -
507C ILE* 2.9 29.6 + - + +
508C LYS* 3.2 8.5 + - - +
510C THR* 1.3 75.2 - - - +
512C GLY* 1.3 67.6 + - - +
514C ILE* 3.3 7.6 + - - +
515C ARG* 2.9 23.3 + - + +
536C LEU* 4.5 6.3 - - + -
539C LEU* 5.1 0.9 - - + -
569C ILE* 5.0 7.0 - - + +
572C GLY* 3.4 41.5 - - - +
573C CYS* 3.6 20.2 - - - +
576C ALA* 4.4 5.7 - - + +
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Residues in contact with GLY 512 (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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469C ARG* 3.2 40.3 + - - -
508C LYS 3.2 7.5 + - - -
509C ALA 3.3 0.8 + - - -
510C THR 3.3 0.4 - - - -
511C VAL* 1.3 82.2 - - - +
513C LEU* 1.3 58.6 + - - +
515C ARG* 3.4 9.0 + - - +
516C ASN* 3.2 28.8 + - - +
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Residues in contact with LEU 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C ILE* 3.7 26.2 - - + -
468C LEU* 4.0 33.9 - - + -
469C ARG* 4.0 8.4 - - + +
472C THR* 4.0 15.3 - - + +
485C VAL* 5.1 2.5 - - + -
494C VAL* 3.5 30.3 - - + -
509C ALA 3.1 14.0 + - - +
510C THR* 3.6 8.1 - - - +
512C GLY* 1.3 74.3 - - - +
514C ILE* 1.3 65.5 + - - +
516C ASN* 3.1 8.5 + - - +
517C LEU* 2.9 49.9 + - + +
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Residues in contact with ILE 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C VAL* 4.1 17.3 - - + +
495C VAL* 4.9 4.9 - - + -
498C LEU* 3.2 39.5 - - + -
510C THR* 3.1 19.8 + - + +
511C VAL* 3.8 4.0 - - - +
513C LEU* 1.3 75.3 - - - +
515C ARG* 1.3 58.3 + - - +
517C LEU* 3.3 8.5 + - - +
518C ALA* 2.8 30.1 + - + +
527C LEU* 4.1 23.6 - - + -
532C ALA* 5.0 7.6 - - + -
536C LEU* 4.2 26.7 - - + -
576C ALA* 4.7 5.2 - - + -
580C LEU* 4.9 6.3 - - + -
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Residues in contact with ARG 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C ARG* 5.9 3.9 - - - +
511C VAL* 2.9 18.1 + - + +
512C GLY* 3.5 9.2 - - - +
513C LEU 3.2 0.2 - - - -
514C ILE* 1.3 78.2 - - - +
516C ASN* 1.3 70.0 + - - +
518C ALA* 3.4 13.1 + - - +
519C LEU* 3.6 10.9 + - - +
571C GLU* 3.8 26.3 + - - +
572C GLY* 4.2 11.6 - - - +
575C GLY* 3.8 13.2 + - - +
576C ALA* 4.0 26.7 - - + +
579C ILE* 4.5 14.0 - - + +
609C ASN* 6.0 0.2 + - - -
612C ARG* 4.1 8.9 - - - +
613C VAL* 3.7 28.1 - - - +
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Residues in contact with ASN 516 (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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469C ARG* 3.1 40.3 + - - +
472C THR* 3.5 30.1 + - - +
473C SER* 4.0 14.2 + - - -
482C GLN* 2.9 19.3 + - - -
512C GLY 3.2 16.3 + - - +
513C LEU* 3.1 5.6 + - - +
515C ARG* 1.3 80.9 - - - +
517C LEU* 1.3 62.4 + - - +
519C LEU* 2.9 30.0 + - + +
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Residues in contact with LEU 517 (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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472C THR* 4.0 13.9 - - + -
482C GLN* 3.8 15.7 - - - +
485C VAL* 3.6 39.3 - - + -
491C LEU* 3.8 22.9 - - + -
494C VAL* 4.5 8.3 - - + -
513C LEU* 2.9 42.3 + - + +
514C ILE* 3.7 8.7 - - - +
516C ASN* 1.3 74.9 - - - +
518C ALA* 1.3 57.6 + - - +
520C CYS* 2.8 22.2 + - - +
523C ASN* 3.3 26.5 + - - +
527C LEU* 4.4 7.0 - - + -
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Residues in contact with ALA 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514C ILE* 2.8 21.3 + - + +
515C ARG* 3.6 8.1 - - - +
516C ASN 3.2 0.4 - - - -
517C LEU* 1.3 72.1 - - - +
519C LEU* 1.3 57.6 + - - +
520C CYS 3.1 0.7 - - - -
523C ASN* 4.8 0.2 - - - -
524C HIS* 2.7 33.6 + - - -
527C LEU* 4.2 9.4 - - + +
576C ALA 4.5 2.5 - - - +
579C ILE* 3.1 24.1 - - + +
580C LEU* 3.7 27.1 - - + -
582C ARG* 5.3 0.2 + - - -
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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