Contacts of the helix formed by residues 606 - 618 (chain A) in PDB entry 2XER
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 THR 606 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605A SER* 1.3 72.4 - - - +
607A GLU* 1.3 68.5 + - + +
609A ALA* 3.8 1.6 - - - +
610A ALA* 2.9 28.0 + - + +
643A LEU* 4.1 10.9 - - + +
646A HIS* 3.8 33.6 + - + +
647A LEU* 3.6 28.0 - - + -
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Residues in contact with GLU 607 (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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566A TYR* 5.3 0.2 - - - -
605A SER* 3.2 12.7 + - - +
606A THR* 1.3 86.3 + - + +
608A GLN* 1.3 68.7 + - + +
610A ALA* 3.3 6.9 + - - +
611A ASP* 3.0 22.9 + - - +
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Residues in contact with GLN 608 (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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562A ILE* 4.2 6.0 - - - +
563A CYS* 4.0 25.3 - - - +
566A TYR* 3.6 51.8 - - + +
604A LEU* 3.5 21.9 - - + +
605A SER* 3.1 35.2 + - - +
607A GLU* 1.3 80.9 - - + +
609A ALA* 1.3 62.3 + - - +
611A ASP* 3.3 4.7 + - - +
612A ILE* 3.1 26.8 + - - +
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Residues in contact with ALA 609 (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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601A LEU* 4.1 27.0 - - + +
604A LEU* 4.1 11.3 - - + +
605A SER 3.0 17.4 + - - +
608A GLN* 1.3 74.2 - - - +
610A ALA* 1.3 60.1 + - - +
612A ILE* 3.2 3.8 + - - +
613A LEU 2.9 24.1 + - - -
643A LEU* 3.5 36.1 - - + +
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Residues in contact with ALA 610 (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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606A THR 2.9 20.0 + - - +
607A GLU* 3.6 8.1 - - - +
609A ALA* 1.3 75.2 - - - +
611A ASP* 1.3 58.6 + - - +
613A LEU* 3.3 3.4 + - - +
614A MET* 2.8 38.2 + - + +
643A LEU* 3.9 8.4 - - - +
647A LEU* 4.4 21.8 - - + -
651A SER* 5.9 2.7 - - - +
655A LEU* 4.4 2.6 - - + +
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Residues in contact with ASP 611 (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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566A TYR* 2.5 31.0 + - - +
570A ARG* 3.3 28.2 + - - +
607A GLU 3.0 11.2 + - - +
608A GLN 3.4 5.8 - - - +
609A ALA 3.2 0.2 - - - -
610A ALA* 1.3 77.8 - - - +
612A ILE* 1.3 55.8 + - - +
614A MET* 3.3 5.4 + - - +
615A THR* 2.8 38.1 + - - -
618A ARG* 4.8 4.2 + - - -
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Residues in contact with ILE 612 (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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566A TYR* 4.1 16.6 - - + -
569A LEU* 4.4 13.2 - - + -
570A ARG* 4.2 17.5 - - + -
584A PHE* 3.7 35.0 - - + -
597A VAL* 4.1 17.7 - - + -
601A LEU* 4.1 12.3 - - + -
604A LEU* 4.0 18.8 - - + -
608A GLN 3.1 13.8 + - - +
609A ALA 3.2 7.2 + - - +
611A ASP* 1.3 77.7 - - - +
613A LEU* 1.3 53.4 + - - +
615A THR* 3.5 4.2 + - - -
616A THR* 2.6 40.1 + - - +
640A PHE* 4.5 4.5 - - + -
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Residues in contact with LEU 613 (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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609A ALA 2.9 15.9 + - - +
610A ALA* 3.7 4.0 - - - +
612A ILE* 1.3 74.2 - - - +
614A MET* 1.3 66.1 + - - +
616A THR* 3.3 2.9 + - - -
617A ALA* 3.0 23.1 + - + +
640A PHE* 3.6 46.0 - - + -
643A LEU* 4.1 13.7 - - + -
644A LEU* 3.7 29.8 - - + -
647A LEU* 4.9 0.2 - - + -
655A LEU* 3.6 23.1 - - + +
688A LEU* 4.2 21.5 - - + -
692A LEU* 4.8 6.3 - - + -
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Residues in contact with MET 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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610A ALA* 2.8 26.4 + - + +
611A ASP* 3.6 7.0 - - - +
613A LEU* 1.3 73.8 - - - +
615A THR* 1.3 56.8 + - - +
617A ALA* 3.4 1.2 + - - -
618A ARG* 3.0 42.9 + - - +
654A SER* 3.9 15.0 - - - +
655A LEU* 3.6 39.5 - - + -
658A GLN* 3.3 44.5 - - + +
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Residues in contact with THR 615 (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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570A ARG* 3.4 18.4 + - - +
581A ASP* 4.0 15.5 - - + +
584A PHE* 3.4 28.7 - - + -
611A ASP* 2.8 35.8 + - - -
612A ILE* 3.9 5.2 - - - -
614A MET* 1.3 74.3 - - - +
616A THR* 1.3 64.4 + - - +
618A ARG* 3.2 26.6 + - - +
619A ASN* 2.9 30.5 + - - +
623A LEU* 5.2 0.2 - - - +
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Residues in contact with THR 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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584A PHE* 3.7 19.4 - - - -
588A MET* 4.5 9.2 - - + +
612A ILE 2.6 23.2 + - - -
613A LEU* 3.5 10.1 - - + -
614A MET 3.2 0.2 - - - -
615A THR* 1.3 77.4 - - - +
617A ALA* 1.3 57.7 + - - +
619A ASN 3.2 4.0 + - - -
620A LEU* 2.8 41.3 + - + -
623A LEU* 4.0 18.9 - - + +
633A LEU* 5.8 0.7 - - + -
636A LEU* 5.3 1.1 - - + -
640A PHE* 4.0 17.7 - - + -
684A PHE* 4.5 15.5 - - + -
688A LEU* 5.6 1.6 - - + -
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Residues in contact with ALA 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A LEU* 3.0 17.2 + - + +
614A MET* 3.9 3.8 - - - +
616A THR* 1.3 74.9 - - - +
618A ARG* 1.3 65.7 + - - +
619A ASN 3.2 0.5 + - - -
620A LEU* 3.3 20.7 + - - +
621A PRO* 4.1 4.0 - - - +
655A LEU* 4.4 7.9 - - + +
658A GLN* 4.1 10.8 - - + +
659A LEU* 3.9 39.0 - - + +
688A LEU* 5.1 8.7 - - + +
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Residues in contact with ARG 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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570A ARG* 4.5 3.0 - - - +
581A ASP* 3.1 38.4 + - - -
611A ASP* 4.8 3.6 + - - -
614A MET* 3.0 28.5 + - - +
615A THR* 3.2 41.1 + - - +
616A THR 3.2 0.2 - - - -
617A ALA* 1.3 77.5 - - - +
619A ASN* 1.3 65.5 + - - +
621A PRO* 4.5 5.0 - - - +
658A GLN* 3.2 38.9 + - - +
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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