Contacts of the helix formed by residues 615 - 624 (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 PRO 615 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608A PHE* 5.4 0.4 - - + -
613A PRO 4.5 1.3 - - - +
614A HIS* 1.3 87.4 - - + +
616A ALA* 1.3 62.6 + - - +
617A LEU 3.0 1.0 + - - -
618A THR* 3.1 26.0 + - - +
619A GLU* 4.0 0.3 + - - +
903A GLN* 3.8 17.3 - - + +
904A GLU* 3.5 34.2 - - + +
909A ARG* 3.7 21.9 + - - +
927A THR* 3.7 26.7 - - + +
929A TYR* 3.6 13.5 - - + +
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Residues in contact with ALA 616 (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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541A ALA* 5.4 2.5 - - + -
545A SER 4.0 11.2 - - - +
546A LEU* 3.7 29.6 - - + +
606A LEU* 4.0 17.0 - - + -
614A HIS* 3.1 7.2 + - + -
615A PRO* 1.3 80.4 - - - +
617A LEU* 1.3 63.9 + - - +
619A GLU* 3.1 5.4 + - - +
620A ALA* 3.0 17.8 + - - +
909A ARG* 4.1 15.6 - - - +
929A TYR* 5.2 0.8 + - - +
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Residues in contact with LEU 617 (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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378A LEU* 5.5 2.9 - - + -
382A ASN* 3.5 43.1 - - + +
384A PHE* 4.1 8.7 - - + -
570A TRP* 4.1 22.7 - - + -
606A LEU* 3.9 24.6 + - + +
607A VAL* 4.0 13.7 - - + -
613A PRO* 3.5 30.3 - - + -
614A HIS 3.0 16.5 + - - +
616A ALA* 1.3 80.1 - - - +
618A THR* 1.4 57.6 + - - +
620A ALA* 3.1 2.4 + - + +
621A LYS* 2.9 25.5 + - - +
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Residues in contact with THR 618 (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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382A ASN* 5.0 1.8 - - - -
614A HIS 4.5 0.2 + - - -
615A PRO 3.1 17.8 + - - +
617A LEU* 1.4 74.8 - - - +
619A GLU* 1.3 61.7 + - + +
621A LYS* 3.2 9.5 + - - +
622A HIS* 2.9 30.1 + - - +
717A TRP* 3.8 21.0 - - - -
903A GLN* 3.6 38.4 + - + +
904A GLU 5.7 2.0 - - - +
912A ALA* 3.8 11.6 + - + +
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Residues in contact with GLU 619 (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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546A LEU* 4.4 2.2 - - + -
549A PHE* 4.0 18.3 - - + +
550A ALA* 4.9 5.0 + - - +
615A PRO 4.9 0.2 - - - +
616A ALA* 3.1 9.7 + - - +
618A THR* 1.3 83.6 - - + +
620A ALA* 1.3 64.5 + - - +
622A HIS* 3.8 1.0 - - - +
623A GLN* 3.0 27.1 + - + +
908A ASP 4.7 1.9 - - - +
909A ARG* 3.5 37.5 + - + +
910A LEU* 3.7 8.7 + - - -
911A THR* 2.7 40.2 + - - +
912A ALA* 2.8 28.6 + - - +
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Residues in contact with ALA 620 (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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384A PHE* 4.0 26.7 - - + -
546A LEU* 4.2 7.1 - - + +
549A PHE* 3.5 24.9 - - + -
567A VAL* 5.5 0.9 - - + -
606A LEU* 4.7 4.7 - - + -
616A ALA 3.0 12.3 + - - +
617A LEU* 3.1 9.4 + - - +
619A GLU* 1.3 79.3 - - - +
621A LYS* 1.3 62.4 + - - +
623A GLN 3.4 0.3 + - - -
624A GLN* 3.0 31.1 + - - +
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Residues in contact with LYS 621 (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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381A GLN 3.3 19.3 + - - +
382A ASN* 3.3 44.4 + - - +
383A ASN* 3.0 38.1 + - - +
617A LEU 2.9 7.6 + - - +
618A THR* 3.2 11.4 + - - +
620A ALA* 1.3 78.0 - - - +
622A HIS* 1.3 63.1 + - - +
624A GLN 3.3 1.4 + - - -
625A GLN* 3.3 7.1 + - - +
713A HIS* 3.6 8.4 + - - -
714A ILE* 2.9 31.1 + - - +
715A SER* 4.4 2.0 - - - +
717A TRP* 4.0 25.7 - - + -
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Residues in contact with HIS 622 (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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618A THR 2.9 16.0 + - - +
619A GLU 3.8 1.8 - - - +
621A LYS* 1.3 80.1 - - - +
623A GLN* 1.3 67.0 + - - +
625A GLN* 2.8 47.2 + - - +
717A TRP* 3.1 43.2 + + + -
718A GLN* 4.1 7.4 - - - -
911A THR* 3.3 45.8 + - - -
912A ALA* 3.6 13.5 - - + -
3003A MG 4.0 10.1 - - - -
8402A DMS 3.1 35.3 - - + +
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Residues in contact with GLN 623 (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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549A PHE* 3.8 26.9 - - + -
550A ALA* 3.6 28.7 - - + +
553A TRP* 3.5 26.1 - - + +
557A ARG* 2.9 32.6 + - - -
619A GLU* 3.0 22.0 + - + +
622A HIS* 1.3 86.3 + - - +
624A GLN* 1.3 57.5 + - - +
625A GLN 3.2 0.7 - - - -
911A THR* 2.8 36.6 + - - +
8402A DMS 3.8 22.1 - - - +
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Residues in contact with GLN 624 (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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352A ARG* 2.8 39.1 + - + +
353A GLY 4.4 0.6 + - - -
382A ASN 3.5 8.0 - - - +
383A ASN* 3.4 33.0 - - + +
384A PHE* 3.3 42.2 - - - -
538A TYR* 4.1 3.6 + - - -
549A PHE* 3.7 21.9 - - + -
553A TRP* 3.7 30.4 - - + +
557A ARG* 4.3 0.4 - - - +
567A VAL* 4.4 1.4 - - - +
620A ALA* 3.0 19.0 + - - +
621A LYS 3.5 3.4 - - - -
622A HIS 3.1 0.2 - - - -
623A GLN* 1.3 76.0 - - - +
625A GLN* 1.3 61.8 + - - +
626A PHE* 3.7 1.0 + - - -
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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