Contacts of the helix formed by residues 615 - 624 (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 PRO 615 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608C PHE* 5.5 0.2 - - + -
613C PRO 4.5 1.1 - - - +
614C HIS* 1.3 88.7 - - + +
616C ALA* 1.3 61.2 + - - +
617C LEU 3.0 1.4 + - - -
618C THR* 3.1 24.9 + - - +
619C GLU 4.0 0.3 + - - -
903C GLN* 3.8 16.4 - - + +
904C GLU* 3.4 44.3 - - + +
909C ARG* 3.7 13.0 + - - +
927C THR* 3.7 33.0 - - + +
929C TYR* 3.7 7.6 - - - +
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Residues in contact with ALA 616 (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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541C ALA* 5.5 2.9 - - + -
545C SER 3.8 11.7 - - - +
546C LEU* 3.7 33.7 - - + +
606C LEU* 4.1 12.6 - - + -
614C HIS* 3.2 8.5 + - + +
615C PRO* 1.3 79.3 - - - +
617C LEU* 1.3 64.0 + - - +
618C THR 3.2 0.2 - - - -
619C GLU* 3.1 13.6 + - - +
620C ALA* 3.1 10.0 + - - +
909C ARG* 4.1 14.1 - - - +
929C TYR* 5.2 1.3 + - - +
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Residues in contact with LEU 617 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C LEU* 5.1 3.6 - - + -
382C ASN* 3.5 43.3 - - + +
384C PHE* 3.9 17.9 - - + -
570C TRP* 3.9 16.8 - - + -
606C LEU* 3.9 25.2 + - + +
607C VAL* 3.9 14.6 - - + -
613C PRO* 3.6 27.4 - - + -
614C HIS 3.1 13.2 + - - +
615C PRO 3.0 2.2 + - - -
616C ALA* 1.3 78.7 - - - +
618C THR* 1.3 56.5 + - - +
620C ALA* 3.2 3.7 + - - +
621C LYS* 2.9 25.1 + - - +
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Residues in contact with THR 618 (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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382C ASN* 5.0 2.0 - - - -
614C HIS 4.5 0.4 + - - -
615C PRO 3.1 18.0 + - - +
617C LEU* 1.3 74.5 - - - +
619C GLU* 1.3 67.3 + - + +
621C LYS* 3.2 7.8 + - - +
622C HIS* 2.9 20.1 + - - +
717C TRP* 3.9 20.3 - - - -
903C GLN* 3.7 40.1 + - + +
904C GLU 5.7 1.8 - - - +
912C ALA* 3.5 16.1 + - + +
8415C DMS 4.5 8.3 + - - +
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Residues in contact with GLU 619 (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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546C LEU* 4.2 3.1 - - + -
549C PHE* 4.2 20.4 - - + -
550C ALA* 4.6 7.1 + - - +
616C ALA 3.1 9.7 + - - +
618C THR* 1.3 81.6 - - + +
620C ALA* 1.3 65.8 + - - +
622C HIS* 3.3 1.6 + - - +
623C GLN* 3.0 26.3 + - + +
908C ASP 4.7 1.6 - - - +
909C ARG* 3.5 41.3 + - + +
910C LEU* 3.7 6.2 + - - -
911C THR* 2.7 37.5 + - - +
912C ALA* 2.9 28.0 + - - +
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Residues in contact with ALA 620 (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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384C PHE* 3.9 28.3 - - + -
546C LEU* 4.2 6.6 - - + +
549C PHE* 3.5 24.2 - - + -
567C VAL* 5.7 0.2 - - + -
606C LEU* 4.7 4.3 - - + -
616C ALA 3.1 8.7 + - - +
617C LEU* 3.5 11.0 - - - +
619C GLU* 1.3 80.0 - - - +
621C LYS* 1.3 63.4 + - - +
624C GLN* 3.0 32.2 + - - +
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Residues in contact with LYS 621 (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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381C GLN 3.2 19.8 + - - +
382C ASN* 3.4 43.9 + - - +
383C ASN* 3.1 32.0 + - - +
617C LEU 2.9 8.8 + - - +
618C THR* 3.2 10.3 + - - +
620C ALA* 1.3 78.3 - - - +
622C HIS* 1.3 63.2 + - - +
624C GLN 3.4 0.9 + - - -
625C GLN* 3.3 6.6 + - - +
713C HIS* 3.7 8.8 - - - -
714C ILE 2.8 28.5 + - - +
715C SER* 4.4 7.0 - - - +
717C TRP* 4.0 15.7 - - + -
8415C DMS 2.7 31.3 + - - +
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Residues in contact with HIS 622 (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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618C THR 2.9 15.5 + - - +
619C GLU 3.7 1.3 - - - +
621C LYS* 1.3 78.9 - - - +
623C GLN* 1.3 63.2 + - - +
625C GLN* 2.8 49.0 + - - +
717C TRP* 3.2 37.9 + + + -
718C GLN* 4.1 8.5 - - - -
911C THR* 3.1 50.2 + - - -
912C ALA* 3.6 13.0 - - + -
3003C MG 4.0 9.3 - - - -
8402C DMS 3.1 37.6 - - + +
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Residues in contact with GLN 623 (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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549C PHE* 3.8 27.6 - - + -
550C ALA* 3.6 27.4 - - + +
553C TRP* 3.3 27.7 - - + +
554C GLN 5.0 0.3 + - - -
557C ARG* 2.8 31.9 + - - -
619C GLU* 3.0 19.3 + - + +
622C HIS* 1.3 83.9 - - - +
624C GLN* 1.4 58.5 + - - +
625C GLN 3.3 0.7 - - - -
911C THR* 2.9 32.8 + - - +
8402C DMS 3.8 21.8 - - - +
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Residues in contact with GLN 624 (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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352C ARG* 2.8 43.7 + - + +
353C GLY 4.5 2.0 + - - -
382C ASN 3.3 17.5 - - - +
383C ASN* 3.4 27.6 - - + +
384C PHE* 3.4 37.5 - - - -
538C TYR* 4.3 2.4 + - - -
549C PHE* 3.8 20.3 - - + -
553C TRP* 3.7 30.7 - - + +
557C ARG* 4.1 1.6 - - - +
567C VAL* 4.6 0.2 - - - +
620C ALA 3.0 18.3 + - - +
621C LYS 3.7 2.5 - - - -
622C HIS 3.2 0.2 - - - -
623C GLN* 1.4 75.4 - - - +
625C GLN* 1.4 59.7 + - - -
626C PHE* 3.7 0.9 + - - -
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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