Contacts of the helix formed by residues 548 - 559 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547D GLY* 1.3 73.3 - - - -
549D PHE* 1.4 64.7 + - - +
550D ALA* 3.3 3.4 - - - -
551D LYS* 3.0 30.7 + - - +
552D TYR* 3.7 11.9 + - - -
908D ASP* 2.8 22.3 + - - +
996D ASP* 4.7 5.0 - - - +
1004D SER* 6.6 0.4 - - - -
1007D PHE* 5.8 3.6 - - - -
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Residues in contact with PHE 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538D TYR* 3.3 22.4 - + - -
539D ALA* 3.4 32.3 - - + -
546D LEU* 3.2 38.4 + - + +
547D GLY 3.3 0.6 + - - -
548D GLY* 1.4 77.4 - - - +
550D ALA* 1.3 62.8 + - - +
552D TYR* 3.1 19.6 + + - +
553D TRP* 3.3 34.7 + + - -
567D VAL* 3.6 12.3 - - + -
619D GLU* 4.1 8.3 - - + -
620D ALA* 3.6 26.5 - - + -
623D GLN* 3.8 20.9 - - + -
624D GLN* 3.6 15.5 - - - -
908D ASP 4.4 1.4 + - - -
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Residues in contact with ALA 550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548D GLY 5.1 0.7 - - - -
549D PHE* 1.3 78.2 - - - +
551D LYS* 1.3 62.2 + - - +
553D TRP* 3.3 1.4 + - - -
554D GLN* 3.0 24.9 + - - +
619D GLU* 4.8 4.0 + - - +
623D GLN* 3.5 40.3 - - + +
908D ASP 5.5 2.2 + - - +
911D THR* 3.9 17.7 - - + +
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Residues in contact with LYS 551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506D VAL* 3.9 27.7 - - + +
507D ASP* 3.6 22.6 + - + +
548D GLY* 3.0 22.4 + - - +
550D ALA* 1.3 80.2 - - - +
552D TYR* 1.3 62.7 + - - +
554D GLN* 3.6 6.3 + - - +
555D ALA* 3.3 19.6 + - - +
996D ASP* 6.1 1.1 - - - +
1004D SER* 2.9 24.2 + - - -
1006D GLU* 2.7 29.7 + - - -
1007D PHE* 5.5 3.1 - - - -
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Residues in contact with TYR 552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503D TYR* 4.4 3.8 - - - -
504D ALA 2.6 30.7 + - - -
505D ARG* 3.5 9.0 - - - -
506D VAL* 3.5 26.0 - - + -
520D ILE* 4.1 6.1 - - + -
535D LEU* 4.0 12.3 - - + -
538D TYR* 3.6 45.3 - + + +
539D ALA* 4.6 8.7 - - + -
548D GLY 3.9 10.8 - - - -
549D PHE* 3.1 13.4 + - - +
551D LYS* 1.3 79.0 - - - +
553D TRP* 1.3 52.6 + - + +
555D ALA* 3.0 5.1 + - - +
556D PHE* 2.8 57.7 + + + -
996D ASP* 3.3 33.1 + - - +
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Residues in contact with TRP 553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D LEU* 3.7 29.4 - - + -
351D ILE 3.5 18.4 - - - -
352D ARG* 3.4 33.4 - - + -
538D TYR* 2.9 30.1 + - - -
549D PHE* 3.3 36.9 - + - -
550D ALA 3.3 2.7 + - - +
552D TYR* 1.3 74.6 - - + +
554D GLN* 1.3 67.4 + - - +
556D PHE* 3.3 22.4 + + + +
557D ARG* 3.0 48.8 + - - +
623D GLN* 3.4 40.2 - - + +
624D GLN* 3.7 17.3 - - + -
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Residues in contact with GLN 554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521D LYS* 5.0 6.8 + - - -
550D ALA 3.0 17.1 + - - +
551D LYS* 4.0 6.3 - - - +
552D TYR 3.3 0.2 - - - -
553D TRP* 1.3 77.9 - - - +
555D ALA* 1.3 65.0 + - - +
557D ARG* 3.8 7.0 - - - +
558D GLN* 3.0 53.9 + - - +
623D GLN* 5.0 0.4 + - - -
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Residues in contact with ALA 555 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506D VAL* 4.0 18.8 - - + -
520D ILE* 4.7 4.3 - - + -
521D LYS* 4.4 11.0 - - + +
551D LYS 3.3 10.3 + - - +
552D TYR 3.0 9.2 + - - +
554D GLN* 1.3 84.0 + - - +
556D PHE* 1.3 68.5 + - - +
557D ARG 3.2 0.2 + - - -
558D GLN* 4.4 0.4 - - - +
559D TYR* 3.0 34.2 + - + +
562D LEU* 3.8 18.2 - - + -
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Residues in contact with PHE 556 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D LEU* 3.8 17.9 - - + +
520D ILE* 4.0 14.8 - - + -
533D LEU* 6.0 1.1 - - + -
535D LEU* 3.9 22.2 - - + -
538D TYR* 3.7 9.9 - + - -
552D TYR* 2.8 32.4 + + + +
553D TRP* 3.5 52.5 - + + +
555D ALA* 1.3 78.9 - - - +
557D ARG* 1.3 61.1 + - - +
559D TYR 3.3 0.5 - - - +
562D LEU* 3.8 16.4 - - + +
564D GLY* 3.6 44.0 - - - -
3102D NA 2.3 30.5 - - - -
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Residues in contact with ARG 557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D LEU* 4.5 11.4 - - + +
352D ARG* 3.9 5.3 - - - +
553D TRP* 3.0 45.2 + - + +
554D GLN* 3.8 6.0 - - - +
556D PHE* 1.3 80.4 - - + +
558D GLN* 1.3 61.5 + - - +
559D TYR 4.8 1.7 - - - -
623D GLN 2.9 27.1 + - - -
624D GLN 4.1 0.4 - - - -
625D GLN 2.9 28.1 + - - +
628D GLN* 3.2 25.9 + - - +
641D GLU* 2.8 31.1 + - - +
8402D DMS 3.6 17.8 + - - +
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Residues in contact with GLN 558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507C ASP 3.0 27.6 + - - +
509C ASP* 3.1 36.8 + - - +
519C SER* 3.8 6.9 + - - -
522C LYS* 2.9 36.4 + - + +
521D LYS* 5.3 3.6 + - - -
554D GLN* 3.0 42.3 + - - +
555D ALA 3.2 0.4 + - - -
557D ARG* 1.3 80.2 - - - +
559D TYR* 1.3 76.5 + - + +
560D PRO* 3.6 2.5 - - - +
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Residues in contact with TYR 559 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519C SER* 4.4 1.7 + - - -
521C LYS* 3.1 32.7 - - - +
522C LYS* 3.3 26.1 + - + +
525C SER* 3.8 19.3 - - - -
521D LYS* 3.5 45.4 - - + +
524D LEU* 4.0 11.7 - - + -
555D ALA* 3.0 15.4 + - - +
556D PHE 3.3 0.5 - - - +
557D ARG 3.5 0.9 - - - -
558D GLN* 1.3 98.4 - - + +
560D PRO* 1.3 64.4 - - + +
561D ARG 4.5 0.2 - - - +
562D LEU* 3.0 35.0 + - + +
3102D NA 2.4 27.3 - - - -
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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