Contacts of the helix formed by residues 610 - 626 (chain A) in PDB entry 6O0Z
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 GLU 610 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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609A ASN* 1.3 73.6 - - - +
611A GLU* 1.3 65.8 + - - +
613A GLU* 3.3 18.2 + - - +
614A ASP* 3.6 6.2 - - - +
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Residues in contact with GLU 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A ASN* 4.8 0.8 - - - +
610A GLU* 1.3 75.9 - - - +
612A ASN* 1.3 59.4 + - - +
613A GLU 3.1 0.7 - - - -
614A ASP* 3.0 33.5 - - - +
615A ILE* 3.0 24.5 + - + +
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Residues in contact with ASN 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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606A PHE* 3.3 37.5 - - + +
609A ASN* 3.7 15.6 - - + +
610A GLU 3.3 0.8 - - - +
611A GLU* 1.3 77.1 - - - +
613A GLU* 1.3 58.3 + - - +
615A ILE* 3.6 15.0 - - + +
616A LEU* 2.9 30.8 + - - +
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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
----------------------------------------------------------
513A LEU* 4.8 8.7 - - + +
514A LEU* 5.4 5.4 - - + +
517A TYR* 6.5 1.3 - - + -
606A PHE 4.8 1.1 + - - -
607A LEU 6.5 0.9 - - - -
608A ASP* 6.4 0.2 - - - -
609A ASN 3.6 14.4 + - - +
610A GLU 3.3 13.6 + - - +
611A GLU 3.1 1.0 - - - -
612A ASN* 1.3 76.9 - - - +
614A ASP* 1.3 58.1 + - - +
616A LEU* 3.3 6.2 + - - +
617A GLU* 2.9 26.0 + - - +
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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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514A LEU* 6.0 1.3 - - - -
610A GLU 3.6 4.3 - - - +
611A GLU* 3.0 34.8 - - - +
613A GLU* 1.3 76.9 - - - +
615A ILE* 1.3 72.1 + - - +
617A GLU* 3.3 10.3 + - + +
618A ASP* 3.0 26.0 + - - +
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Residues in contact with ILE 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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611A GLU* 3.0 32.0 + - + +
612A ASN* 3.6 12.6 - - + +
613A GLU 3.3 0.2 - - - -
614A ASP* 1.3 83.6 + - - +
616A LEU* 1.3 57.6 + - - +
618A ASP* 3.0 10.7 + - - +
619A ILE* 2.9 37.9 + - + +
639A TYR* 4.3 36.5 - - + +
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Residues in contact with LEU 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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513A LEU* 4.0 21.6 - - + +
597A LEU* 5.9 8.7 - - + -
606A PHE 5.9 0.9 - - - +
612A ASN 2.9 18.3 + - - +
613A GLU* 3.7 4.7 - - - +
615A ILE* 1.3 76.9 - - - +
617A GLU* 1.3 57.6 + - - +
619A ILE* 3.7 11.4 - - + +
620A VAL* 2.9 30.9 + - - +
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Residues in contact with GLU 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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508A LEU* 6.0 5.3 - - + +
512A SER* 5.3 4.0 - - - +
513A LEU* 5.1 5.1 - - + +
514A LEU* 4.3 21.3 - - + -
613A GLU 2.9 14.5 + - - +
614A ASP* 3.4 15.0 - - + +
615A ILE 3.2 0.2 - - - -
616A LEU* 1.3 75.6 - - - +
618A ASP* 1.3 60.4 + - - +
620A VAL* 3.3 20.9 - - + +
621A LEU* 3.6 10.9 + - - +
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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
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614A ASP 3.0 11.1 + - - +
615A ILE* 3.0 11.5 + - - +
617A GLU* 1.3 77.4 - - - +
619A ILE* 1.3 60.6 + - - +
621A LEU* 3.3 16.9 + - - +
622A THR* 2.8 39.6 + - - -
635A ARG* 5.2 5.2 - - - +
639A TYR* 3.8 29.1 - - - +
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Residues in contact with ILE 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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597A LEU* 5.4 10.1 - - + -
615A ILE* 2.9 24.6 + - + +
616A LEU* 3.2 11.2 + - + +
618A ASP* 1.3 79.7 - - - +
620A VAL* 1.3 57.7 + - - +
622A THR* 3.2 5.8 + - - +
623A LEU* 2.9 42.0 + - + +
635A ARG 5.3 0.2 - - - +
636A LEU* 3.8 27.8 - - + -
639A TYR* 3.7 36.6 - - + -
651A LEU* 4.6 10.3 - - + -
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Residues in contact with VAL 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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509A PRO* 5.0 5.8 - - + -
511A HIS* 3.4 30.1 - - + +
512A SER* 4.2 18.8 - - - -
513A LEU* 4.8 6.3 - - + +
593A THR* 5.2 2.0 - - - +
597A LEU* 6.0 4.0 - - + -
616A LEU 2.9 20.1 + - - +
617A GLU* 3.3 17.3 - - - +
619A ILE* 1.3 76.7 - - - +
621A LEU* 1.3 56.1 + - - +
623A LEU* 3.3 8.6 + - - +
624A THR* 2.5 43.9 + - - +
656A TYR* 4.6 18.4 - - + -
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Residues in contact with LEU 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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489A GLN* 4.7 10.3 - - - +
493A GLU* 5.1 5.2 - - - +
509A PRO* 4.1 25.8 - - + -
617A GLU 3.6 10.5 + - - +
618A ASP* 3.3 19.0 + - - +
619A ILE 3.2 0.4 - - - -
620A VAL* 1.3 79.5 - - - +
622A THR* 1.3 59.7 + - - +
624A THR* 3.2 4.0 + - - -
625A LEU* 2.9 55.7 + - + +
659A TRP* 4.3 13.0 - - + -
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Residues in contact with THR 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* 2.8 27.4 + - - -
619A ILE* 3.4 11.1 - - - +
621A LEU* 1.3 78.1 - - - +
623A LEU* 1.3 61.5 + - + +
624A THR 3.5 0.3 + - - -
625A LEU* 3.6 10.6 + - - +
626A PHE* 3.6 21.4 + - + +
632A ILE* 4.6 15.5 - - + +
635A ARG* 3.7 45.4 + - + +
636A LEU* 4.3 16.2 - - + +
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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 LEU* 5.3 10.5 - - + -
619A ILE* 2.9 33.6 + - + +
620A VAL* 3.8 7.0 - - - +
621A LEU 3.3 0.4 - - - -
622A THR* 1.3 77.2 - - - +
624A THR* 1.3 61.6 + - - +
626A PHE 4.1 3.7 - - - +
627A GLU* 5.6 0.2 - - - -
632A ILE* 4.5 22.6 - - + +
636A LEU* 4.8 10.1 - - + -
651A LEU* 4.0 28.0 - - + +
652A LYS* 5.1 1.6 - - - +
654A ARG* 4.6 20.2 - - + +
655A ARG* 4.0 22.4 - - - -
656A TYR* 4.0 36.4 + - + +
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Residues in contact with THR 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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509A PRO* 3.8 25.2 - - + +
511A HIS* 6.1 0.4 - - - +
620A VAL* 2.5 29.2 + - - +
621A LEU 3.2 3.6 + - - -
623A LEU* 1.3 79.7 - - - +
625A LEU* 1.3 66.3 + - - +
626A PHE 4.2 1.9 - - - +
627A GLU* 4.3 7.3 - - - -
656A TYR* 4.3 25.8 - - + +
657A THR* 4.5 8.7 - - - +
658A GLY 4.1 19.3 - - - +
659A TRP* 4.6 19.3 + - + +
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Residues in contact with LEU 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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488A ALA 5.7 0.4 - - - +
489A GLN* 3.7 39.5 - - + +
492A ILE* 3.8 35.3 - - + +
493A GLU* 4.3 8.1 - - + +
621A LEU* 2.9 36.4 + - + +
622A THR* 4.2 5.2 - - - +
623A LEU 3.5 0.4 - - - -
624A THR* 1.3 80.8 - - - +
626A PHE* 1.3 81.5 + - + +
627A GLU* 3.9 6.9 + - - -
635A ARG* 6.4 0.7 - - - -
659A TRP* 3.7 32.8 - - + -
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Residues in contact with PHE 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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485A GLY* 3.7 20.0 - - - -
488A ALA* 3.7 34.3 - - + -
489A GLN* 3.9 15.7 - - + -
622A THR* 3.6 13.2 + - + -
623A LEU 4.1 9.9 - - - +
625A LEU* 1.3 97.7 - - + +
627A GLU* 1.3 70.0 + - - +
628A ASP 3.8 0.7 - - - +
631A MET* 3.9 31.0 - - + -
632A ILE* 3.7 36.2 - - + +
635A ARG* 3.4 40.2 - - - -
655A ARG* 4.2 2.9 - - - -
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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