Contacts of the helix formed by residues 612 - 628 (chain A) in PDB entry 3RJO
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 TYR 612 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A ILE* 3.5 33.1 - - + +
536A THR* 5.4 0.5 - - - -
598A ILE* 3.7 25.6 - - + -
599A LYS* 3.7 8.8 + - + +
600A PHE 2.9 36.7 + - - -
610A VAL* 3.4 30.6 - - + +
611A HIS* 1.3 73.2 - - - +
613A GLU* 1.3 75.5 + - - +
616A GLY* 3.4 32.4 + - - -
617A TRP* 3.2 24.4 - + + +
620A LEU* 3.6 27.4 - - + -
639A LEU* 4.2 8.3 - - + -
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Residues in contact with GLU 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A THR* 3.8 26.4 - - + +
535A ILE 4.2 4.9 - - - +
536A THR* 4.1 18.9 + - + +
538A ARG* 5.8 0.3 + - - -
545A LYS* 5.4 2.8 + - - -
611A HIS* 3.2 35.0 + - + -
612A TYR* 1.3 81.4 - - - +
614A ASP* 1.3 68.5 + - - +
615A ASP* 4.6 3.1 - - + +
617A TRP* 2.8 28.7 + - - -
651A LYS* 5.7 2.1 - - - -
652A LEU* 5.2 0.2 - - - -
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Residues in contact with ASP 614 (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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613A GLU* 1.3 75.0 - - - +
615A ASP* 1.3 62.3 + - - +
617A TRP* 3.5 2.8 + - - +
618A ASP* 2.9 33.1 + - - +
651A LYS 4.7 6.9 - - - +
652A LEU* 4.2 8.3 - - - +
653A SER 5.4 0.5 + - - -
656A LYS* 3.6 31.9 - - - +
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Residues in contact with ASP 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A TYR 5.4 0.2 - - - +
613A GLU* 3.2 3.3 - - + +
614A ASP* 1.3 79.9 - - - +
616A GLY* 1.3 58.4 + - - +
618A ASP* 3.5 10.2 + - - +
619A SER* 3.1 28.9 + - - -
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Residues in contact with GLY 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A VAL* 6.3 3.6 - - - -
598A ILE* 6.6 0.2 - - - -
612A TYR* 3.4 27.2 + - - -
613A GLU 3.3 3.0 + - - -
615A ASP* 1.3 77.2 - - - +
617A TRP* 1.3 57.3 + - - +
619A SER* 3.4 8.2 + - - -
620A LEU* 3.1 33.4 + - - +
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Residues in contact with TRP 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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610A VAL 3.5 22.9 - - - -
611A HIS* 3.0 26.9 - + - -
612A TYR* 3.2 13.9 - + - +
613A GLU 2.8 38.8 + - - +
614A ASP 4.1 2.9 - - - +
616A GLY* 1.3 68.1 - - - +
618A ASP* 1.4 57.5 + - - +
620A LEU* 3.4 10.2 + - + +
621A THR* 2.7 38.0 + - - +
639A LEU* 3.7 50.7 - - + -
642A ASN* 4.2 4.0 - - + -
643A ALA* 3.9 11.0 - - + -
646A LEU* 3.5 16.0 - - + +
652A LEU* 3.8 32.5 - - + +
656A LYS* 5.5 4.7 - - + -
660A LEU* 3.8 24.2 - - + -
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Residues in contact with ASP 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A ASP* 2.9 20.2 + - - +
615A ASP* 3.6 9.1 - - - +
617A TRP* 1.4 73.7 - - - +
619A SER* 1.3 65.6 + - - +
621A THR* 3.2 7.3 + - - -
622A GLY* 2.9 22.2 + - - -
656A LYS* 2.8 31.3 + - - +
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Residues in contact with SER 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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596A GLU 3.4 25.2 + - - +
597A TRP* 4.1 14.0 - - - +
615A ASP 3.1 15.3 + - - -
616A GLY* 3.7 11.5 - - - -
617A TRP 3.4 0.2 - - - -
618A ASP* 1.3 77.7 - - - +
620A LEU* 1.3 58.6 + - - +
622A GLY* 3.5 1.4 + - - -
623A LEU* 3.0 26.5 + - - +
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Residues in contact with LEU 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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597A TRP* 4.3 23.1 - - + -
598A ILE 3.7 17.5 - - - +
599A LYS* 4.8 5.8 - - + -
612A TYR* 3.6 44.4 - - + -
616A GLY 3.1 15.4 + - - +
617A TRP* 3.8 13.7 - - + +
618A ASP 3.2 0.2 - - - -
619A SER* 1.3 74.1 - - - +
621A THR* 1.3 60.6 + - - +
623A LEU* 3.3 10.3 + - + +
624A LEU* 2.9 35.1 + - + +
631A VAL* 5.8 0.4 - - + -
639A LEU* 3.8 29.2 - - + -
660A LEU* 5.4 0.7 - - + -
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Residues in contact with THR 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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617A TRP* 2.7 25.3 + - - +
618A ASP* 3.2 9.3 + - - -
620A LEU* 1.3 74.6 - - - +
622A GLY* 1.3 60.3 + - - +
624A LEU* 3.1 10.9 + - - +
625A LYS* 2.9 62.3 + - + +
656A LYS 4.7 2.8 + - - -
659A ASP* 3.9 16.4 - - + +
660A LEU* 3.9 24.3 + - - +
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Residues in contact with GLY 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 ASP 2.9 14.5 + - - -
619A SER 3.9 1.6 - - - -
621A THR* 1.3 76.2 - - - +
623A LEU* 1.3 55.0 + - - +
625A LYS* 3.2 8.2 + - - +
626A GLY* 2.8 28.1 + - - -
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Residues in contact with LEU 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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597A TRP* 3.7 39.3 - - + +
619A SER 3.0 14.5 + - - +
620A LEU* 3.5 17.0 - - + +
621A THR 3.2 0.2 - - - -
622A GLY* 1.3 76.3 - - - +
624A LEU* 1.3 66.5 + - + +
626A GLY* 3.0 0.8 + - - -
627A THR* 2.9 57.9 + - - +
630A ALA* 3.8 12.6 - - + -
631A VAL* 4.0 32.5 - - + -
639A LEU* 5.8 0.4 - - + -
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Residues in contact with LEU 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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620A LEU 2.9 20.6 + - - +
621A THR* 3.1 4.4 + - - +
623A LEU* 1.3 80.6 - - + +
625A LYS* 1.3 60.4 + - - +
628A HIS* 3.2 34.7 + - + +
631A VAL* 4.5 4.3 - - + -
636A ARG* 3.7 37.2 - - + +
639A LEU* 4.1 25.4 - - + -
660A LEU* 3.9 33.9 - - + -
663A TYR* 3.7 36.4 - - + +
666A HIS* 4.6 2.3 - - - -
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Residues in contact with LYS 625 (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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621A THR* 2.9 33.1 + - + +
622A GLY* 3.8 6.7 - - - +
624A LEU* 1.3 77.0 - - - +
626A GLY* 1.3 58.8 + - - +
659A ASP* 3.0 35.4 + - - +
662A LEU* 4.0 25.9 - - - +
663A TYR* 3.9 19.3 - - + +
665A LYS* 4.9 9.4 - - - +
666A HIS* 4.1 20.3 + - - +
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Residues in contact with GLY 626 (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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622A GLY 2.8 15.5 + - - -
623A LEU* 5.0 0.2 - - - -
625A LYS* 1.3 80.3 - - - +
627A THR* 1.3 65.8 + - - +
628A HIS* 3.9 2.4 + - - -
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Residues in contact with THR 627 (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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623A LEU* 2.9 26.2 + - - +
626A GLY* 1.3 77.9 + - - -
628A HIS* 1.3 65.7 + - - +
629A THR* 3.0 20.8 + - - +
630A ALA* 3.2 25.3 + - + +
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Residues in contact with HIS 628 (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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623A LEU* 3.6 4.8 + - - -
624A LEU* 3.2 28.6 + - - +
626A GLY 5.7 1.3 - - - -
627A THR* 1.3 73.9 - - - +
629A THR* 1.3 79.5 + - + +
630A ALA 3.1 2.1 + - - -
631A VAL* 3.4 13.0 + - - +
636A ARG* 3.2 44.6 + - - -
663A TYR* 4.0 10.3 - + + -
666A HIS* 3.4 42.6 + + + +
667A GLU* 4.1 15.6 + - - -
668A THR* 4.8 6.3 - - + -
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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
------------------------------------------------------------
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