Contacts of the helix formed by residues 548 - 559 (chain C) in PDB entry 1JZ3
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 548 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547C GLY* 1.3 71.3 - - - -
549C PHE* 1.4 65.7 + - - +
550C ALA* 3.2 3.1 - - - -
551C LYS* 3.1 29.8 + - - +
552C TYR* 3.7 12.5 + - - -
908C ASP* 2.8 20.5 + - - +
996C ASP* 4.7 5.5 - - - +
1004C SER* 6.6 0.4 - - - -
1007C PHE* 5.8 3.4 - - - -
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Residues in contact with PHE 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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538C TYR* 3.4 27.4 - + - -
539C ALA* 3.6 21.3 - - + -
546C LEU* 3.2 38.6 + - + +
547C GLY 3.3 1.0 + - - -
548C GLY* 1.4 76.5 - - - +
550C ALA* 1.3 63.3 + - - +
552C TYR* 3.1 16.9 + - - +
553C TRP* 3.2 36.8 + + - -
567C VAL* 3.6 18.6 - - + -
619C GLU* 4.1 9.6 - - + -
620C ALA* 3.5 27.8 - - + -
623C GLN* 3.8 20.2 - - + -
624C GLN* 3.8 15.0 - - + -
908C ASP 4.3 1.2 + - - -
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Residues in contact with ALA 550 (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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548C GLY* 3.2 1.2 - - - -
549C PHE* 1.3 79.2 - - - +
551C LYS* 1.3 57.4 + - - +
553C TRP* 3.3 2.3 + - - +
554C GLN* 2.9 30.7 + - - +
619C GLU* 4.6 3.6 + - - +
623C GLN* 3.6 37.3 - - + +
908C ASP 5.4 2.6 + - - +
911C THR* 4.0 18.2 - - + +
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Residues in contact with LYS 551 (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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506C VAL* 3.8 24.0 - - + +
507C ASP* 3.7 22.5 + - - +
548C GLY* 3.1 20.8 + - - +
550C ALA* 1.3 80.3 - - - +
552C TYR* 1.3 61.1 + - - +
554C GLN* 3.6 6.9 + - + +
555C ALA* 3.2 22.3 + - - +
1004C SER* 3.0 22.8 + - - -
1006C GLU* 3.0 28.7 + - - -
1007C PHE* 5.5 2.4 - - - -
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Residues in contact with TYR 552 (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 TYR* 4.5 3.1 - - - -
504C ALA 2.6 31.7 + - - -
505C ARG* 3.6 5.0 - - - +
506C VAL* 3.6 25.4 - - + -
520C ILE* 4.1 5.8 - - + -
535C LEU* 3.9 15.9 - - + -
538C TYR* 3.6 43.4 - + + +
539C ALA* 4.8 8.1 + - + -
548C GLY 3.9 11.2 - - - -
549C PHE* 3.1 14.7 + - - +
551C LYS* 1.3 77.9 - - - +
553C TRP* 1.3 61.3 + - + +
555C ALA* 3.1 4.3 + - - +
556C PHE* 2.8 52.7 + + + -
996C ASP* 3.4 31.3 + - - +
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Residues in contact with TRP 553 (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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350C LEU* 3.8 26.5 - - + -
351C ILE 3.6 17.7 - - - -
352C ARG* 3.4 28.9 - - + -
538C TYR* 3.0 27.5 + - - -
549C PHE* 3.2 37.4 - + - -
550C ALA 3.3 1.9 + - - +
552C TYR* 1.3 81.0 - - + +
554C GLN* 1.3 62.7 + - - +
556C PHE* 3.3 25.1 + + + +
557C ARG* 3.0 49.2 + - - +
623C GLN* 3.3 42.4 - - + +
624C GLN* 3.7 18.2 - - + -
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Residues in contact with GLN 554 (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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506C VAL* 5.9 0.2 - - - +
521C LYS* 4.8 7.6 + - - -
550C ALA 2.9 17.2 + - - +
551C LYS* 3.9 8.7 - - - +
552C TYR 3.2 0.2 - - - -
553C TRP* 1.3 77.5 - - - +
555C ALA* 1.3 64.5 + - - +
557C ARG* 3.4 6.9 + - - +
558C GLN* 3.1 52.5 + - - +
623C GLN* 5.0 0.4 + - - -
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Residues in contact with ALA 555 (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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506C VAL* 3.6 21.8 - - + -
520C ILE* 4.8 2.7 - - + -
521C LYS* 4.2 9.6 - - + +
551C LYS 3.2 10.8 + - - +
552C TYR* 3.1 8.6 + - - +
554C GLN* 1.3 85.5 + - - +
556C PHE* 1.3 64.9 + - - +
558C GLN* 3.1 1.8 + - - +
559C TYR* 3.0 34.3 + - - +
562C LEU* 3.9 17.5 - - + -
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Residues in contact with PHE 556 (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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350C LEU* 4.0 18.1 - - + +
520C ILE* 4.0 13.2 - - + -
533C LEU* 6.0 0.7 - - + -
535C LEU* 3.8 22.7 - - + -
538C TYR* 3.7 12.1 - + - -
552C TYR* 2.8 34.9 + + + +
553C TRP* 3.3 55.2 + + + +
555C ALA* 1.3 71.8 - - - +
557C ARG* 1.3 61.8 + - - +
559C TYR 3.3 1.2 - - - +
562C LEU* 3.7 17.9 - - + +
564C GLY* 3.6 42.0 - - - -
3102C NA 2.3 30.8 - - - -
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Residues in contact with ARG 557 (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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350C LEU* 4.6 11.9 - - + +
352C ARG* 3.9 5.7 - - - +
553C TRP* 3.0 41.5 + - - +
554C GLN* 3.9 6.0 - - - +
556C PHE* 1.3 79.5 - - + +
558C GLN* 1.3 63.2 + - - +
559C TYR 3.6 1.2 + - - -
560C PRO* 5.6 0.2 - - - +
623C GLN 2.8 29.2 + - - -
624C GLN 4.1 1.0 - - - -
625C GLN 3.0 27.1 + - - +
628C GLN* 3.3 24.6 - - - +
641C GLU* 2.8 33.0 + - - +
8402C DMS 3.5 19.0 + - - +
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Residues in contact with GLN 558 (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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521C LYS* 5.3 2.8 + - - -
554C GLN* 3.1 41.9 + - - +
555C ALA 3.1 2.9 + - - +
557C ARG* 1.3 80.6 - - - +
559C TYR* 1.3 78.3 + - + +
560C PRO* 3.4 3.3 - - - +
507D ASP 3.1 26.2 + - - +
509D ASP* 3.1 36.6 + - - +
519D SER* 3.8 6.9 + - - -
522D LYS* 2.9 35.7 + - + +
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Residues in contact with TYR 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C LYS* 3.5 47.7 - - + +
524C LEU* 4.1 11.4 - - + -
555C ALA* 3.0 19.5 + - - +
556C PHE 3.3 0.4 - - - +
557C ARG 4.8 1.1 - - - -
558C GLN* 1.3 101.1 - - + +
560C PRO* 1.3 65.2 - - + +
561C ARG 3.3 1.3 - - - +
562C LEU* 3.1 28.0 + - + +
3102C NA 2.4 26.9 - - - -
519D SER* 4.3 2.3 + - - -
521D LYS* 3.1 33.4 - - - +
522D LYS* 3.5 27.4 + - + +
525D SER* 3.8 17.3 - - - -
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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