Contacts of the helix formed by residues 548 - 559 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547A GLY* 1.3 71.5 - - - -
549A PHE* 1.3 66.6 + - - +
550A ALA* 3.1 3.8 - - - -
551A LYS* 3.0 29.0 + - - +
552A TYR* 3.7 11.7 + - - -
908A ASP* 2.8 22.0 + - - +
996A ASP* 4.7 5.7 - - - +
1007A PHE* 5.9 3.6 - - - -
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Residues in contact with PHE 549 (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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538A TYR* 3.3 32.1 - + - -
539A ALA* 3.5 25.4 - - + -
546A LEU* 3.1 38.4 + - + +
547A GLY 3.3 0.8 + - - -
548A GLY* 1.3 78.8 - - - +
550A ALA* 1.3 62.7 + - - +
552A TYR* 3.1 17.9 + - - +
553A TRP* 3.1 36.2 + + - -
567A VAL* 3.7 8.3 - - + -
619A GLU* 4.0 13.0 - - + -
620A ALA* 3.5 23.1 - - + -
623A GLN* 3.8 20.9 - - + -
624A GLN* 3.7 14.8 - - - -
908A ASP 4.3 1.0 + - - -
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Residues in contact with ALA 550 (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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548A GLY 3.1 1.0 - - - -
549A PHE* 1.3 80.5 - - - +
551A LYS* 1.3 62.5 + - - +
552A TYR 3.1 0.2 - - - -
553A TRP* 3.3 1.8 + - - +
554A GLN* 3.1 23.6 + - - +
619A GLU* 4.9 4.1 + - - +
623A GLN* 3.6 38.8 - - + +
908A ASP 5.3 2.1 + - - +
911A THR* 4.0 16.8 - - + +
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Residues in contact with LYS 551 (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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506A VAL* 3.8 22.9 - - + +
507A ASP* 3.6 22.8 + - - +
548A GLY* 3.0 19.8 + - - +
550A ALA* 1.3 80.0 - - - +
552A TYR* 1.3 63.2 + - - +
554A GLN* 3.6 7.2 + - - +
555A ALA* 3.3 21.5 + - - +
996A ASP* 6.2 0.4 - - - +
1004A SER* 3.0 23.6 + - - -
1006A GLU* 2.7 29.5 + - - -
1007A PHE* 5.7 2.2 - - - -
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Residues in contact with TYR 552 (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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503A TYR* 4.4 4.2 - - - -
504A ALA 2.6 30.2 + - - -
505A ARG* 3.4 9.2 - - - -
506A VAL* 3.5 25.1 - - + -
520A ILE* 4.0 18.4 - - + -
535A LEU* 4.1 5.8 - - + -
538A TYR* 3.6 46.5 - + + +
539A ALA* 4.7 7.4 - - + -
548A GLY 3.7 11.8 + - - -
549A PHE* 3.1 13.8 + + - +
551A LYS* 1.3 77.7 - - - +
553A TRP* 1.3 59.5 + - + +
555A ALA* 3.1 5.4 + - - +
556A PHE* 2.9 44.0 + + + -
996A ASP* 3.3 33.6 + - - +
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Residues in contact with TRP 553 (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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350A LEU* 3.7 30.5 - - + -
351A ILE 3.5 17.3 - - - -
352A ARG* 3.4 28.7 - - + -
538A TYR* 2.9 29.6 + - - -
549A PHE* 3.1 37.7 - + - -
550A ALA 3.3 2.7 + - - +
551A LYS 3.3 0.2 - - - -
552A TYR* 1.3 81.0 - - + +
554A GLN* 1.3 61.4 + - - +
556A PHE* 3.3 21.2 + + + +
557A ARG* 3.0 51.1 + - - +
623A GLN* 3.5 41.5 - - + +
624A GLN* 3.7 19.5 - - + -
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Residues in contact with GLN 554 (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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521A LYS* 4.8 8.1 + - - -
550A ALA 3.1 16.3 + - - +
551A LYS* 3.9 7.6 - - - +
553A TRP* 1.3 76.0 - - - +
555A ALA* 1.3 66.0 + - - +
557A ARG* 3.5 7.2 + - - +
558A GLN* 3.0 50.5 + - - +
623A GLN* 5.1 0.4 + - - -
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Residues in contact with ALA 555 (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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506A VAL* 3.9 21.3 - - + -
520A ILE* 4.8 2.9 - - + -
521A LYS* 3.9 9.9 - - - +
551A LYS 3.3 10.1 + - - +
552A TYR* 3.1 10.4 + - - +
554A GLN* 1.3 83.9 + - - +
556A PHE* 1.3 66.7 + - - +
558A GLN* 4.4 3.4 - - - +
559A TYR* 2.9 33.1 + - - +
562A LEU* 3.8 18.4 - - + -
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Residues in contact with PHE 556 (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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350A LEU* 3.9 17.2 - - + +
520A ILE* 4.1 14.1 - - + -
533A LEU* 5.9 0.9 - - + -
535A LEU* 3.8 22.4 - - + -
538A TYR* 3.8 11.2 - + - -
552A TYR* 2.9 31.9 + + + +
553A TRP* 3.6 51.1 - + + +
555A ALA* 1.3 79.2 - - - +
557A ARG* 1.3 61.8 + - - +
559A TYR 3.4 0.3 - - - +
562A LEU* 3.8 17.9 - - + +
564A GLY* 3.6 45.1 - - - -
3102A NA 2.3 29.6 - - - -
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Residues in contact with ARG 557 (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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350A LEU* 4.4 12.1 - - + +
352A ARG* 3.9 4.8 - - - +
553A TRP* 3.0 43.5 + - + +
554A GLN* 4.0 5.8 - - - +
556A PHE* 1.3 80.1 - - - +
558A GLN* 1.3 62.5 + - - +
559A TYR 4.8 1.0 - - - -
560A PRO* 5.7 0.7 - - - +
623A GLN 2.9 27.1 + - - -
624A GLN 4.1 1.0 - - - -
625A GLN 2.9 28.5 + - - +
628A GLN* 3.2 23.2 - - - +
641A GLU* 2.7 32.0 + - - +
8402A DMS 3.6 19.3 + - - +
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Residues in contact with GLN 558 (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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521A LYS* 5.2 2.9 + - - -
554A GLN* 3.0 43.0 + - - +
555A ALA 3.1 0.4 + - - -
557A ARG* 1.3 79.4 - - - +
559A TYR* 1.3 81.5 + - + +
560A PRO* 3.5 3.2 - - - +
507B ASP 3.0 27.5 + - - +
509B ASP* 3.0 38.1 + - - +
519B SER* 3.7 6.3 - - - -
522B LYS* 3.0 33.3 + - + +
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Residues in contact with TYR 559 (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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521A LYS* 3.6 45.6 + - + +
524A LEU* 4.0 11.2 - - + -
555A ALA* 2.9 23.7 + - - +
556A PHE 3.4 0.7 - - - +
557A ARG 4.8 0.7 - - - -
558A GLN* 1.3 98.6 - - + +
560A PRO* 1.3 63.0 - - + +
561A ARG 3.2 0.4 - - - +
562A LEU* 3.0 26.7 + - + +
3102A NA 2.4 27.6 - - - -
519B SER* 4.1 2.9 + - - -
521B LYS* 3.1 35.3 - - - +
522B LYS* 3.4 25.7 + - + -
525B SER* 3.8 17.7 - - - -
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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