Contacts of the helix formed by residues 606 - 618 (chain A) in PDB entry 6EJ9
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 GLN 606 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A GLN* 5.2 1.0 - - - +
344A ARG* 3.7 26.0 + - - +
602A ALA* 3.9 19.7 + - + +
605A ASN* 1.3 71.2 - - - +
607A GLU* 1.3 66.0 + - - +
608A ILE 3.2 2.9 - - - -
609A ILE* 2.9 20.4 + - + -
610A GLY* 3.0 11.4 + - - +
627A LEU 3.8 7.7 + - - -
628A ARG* 3.8 20.8 + - - +
629A SER 3.3 27.4 + - - +
630A TYR* 3.6 25.0 - - + +
693A ASP* 2.8 16.6 + - - +
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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
----------------------------------------------------------
581A PRO* 3.6 21.1 - - + +
605A ASN* 3.3 6.2 + - - +
606A GLN* 1.3 76.2 - - - +
608A ILE* 1.3 56.7 + - - +
610A GLY* 3.2 3.3 + - - -
611A GLN* 3.0 47.5 + - + +
693A ASP* 3.2 19.3 + - - +
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Residues in contact with ILE 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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579A PHE* 3.6 24.7 - - + +
580A LYS 3.8 23.8 - - - +
581A PRO* 3.9 5.8 - - + -
584A PHE* 3.9 33.7 - - + -
587A PHE* 3.9 23.8 - - + -
600A PHE* 4.2 17.9 - - + -
605A ASN* 3.1 27.8 + - - +
607A GLU* 1.3 73.8 - - - +
609A ILE* 1.3 68.5 + - - +
611A GLN* 3.4 8.4 + - - -
612A LEU* 3.1 21.8 + - - +
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Residues in contact with ILE 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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341A GLN* 3.8 38.6 - - - +
344A ARG* 3.9 21.3 - - - +
427A TYR* 4.1 18.1 - - + -
600A PHE* 3.9 34.8 - - + -
601A GLU 4.3 0.2 - - - -
602A ALA* 4.1 20.6 - - + +
605A ASN 4.0 16.8 - - - +
606A GLN* 2.9 10.0 + - + +
608A ILE* 1.3 76.8 - - - +
610A GLY* 1.3 61.7 + - - +
612A LEU* 3.2 6.4 + - - +
613A ASP* 3.0 22.0 + - - +
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Residues in contact with GLY 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ARG* 3.7 21.4 - - - +
606A GLN* 3.0 12.9 + - - -
607A GLU* 3.2 4.0 + - - -
609A ILE* 1.3 77.6 - - - +
611A GLN* 1.3 62.3 + - - +
612A LEU 3.2 0.2 + - - -
613A ASP 3.3 0.5 + - - -
614A TYR* 2.9 44.5 + - - -
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Residues in contact with GLN 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A PRO* 3.4 30.5 + - - +
584A PHE* 3.7 39.3 - - + +
607A GLU* 3.0 34.4 + - + +
608A ILE* 3.7 10.2 - - - +
610A GLY* 1.3 74.1 - - - +
612A LEU* 1.3 57.8 + - - +
614A TYR* 4.1 5.9 - - - +
615A TYR* 3.1 30.0 + - - +
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Residues in contact with LEU 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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427A TYR* 3.8 14.8 - - + -
428A PRO 3.5 26.5 - - - +
429A ILE* 3.8 22.9 - - + +
584A PHE* 4.2 11.2 - - + -
587A PHE* 4.2 19.3 - - + -
600A PHE* 3.8 31.4 - - + -
608A ILE 3.1 16.2 + - - +
609A ILE* 3.7 4.5 - - - +
610A GLY 3.1 0.4 - - - -
611A GLN* 1.3 75.0 - - - +
613A ASP* 1.3 64.5 + - - +
615A TYR* 3.4 7.1 + - + +
616A LEU* 3.2 40.5 + - + +
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Residues in contact with ASP 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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344A ARG* 4.6 15.0 + - - +
348A ALA* 3.9 13.9 - - - +
427A TYR* 2.6 35.0 + - - +
609A ILE 3.0 16.1 + - - +
610A GLY 4.0 2.5 - - - +
612A LEU* 1.3 77.3 - - - +
614A TYR* 1.3 72.0 + - + +
616A LEU* 3.4 5.4 + - - +
617A TYR* 3.0 36.8 + - - +
618A GLY 4.0 1.9 + - - +
620A TYR* 4.5 12.1 + - - -
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Residues in contact with TYR 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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344A ARG* 3.3 28.5 + - - -
610A GLY* 2.9 25.9 + - - +
611A GLN* 4.3 4.0 - - - +
613A ASP* 1.3 83.3 - - + +
615A TYR* 1.3 63.1 + - - +
618A GLY* 2.7 43.4 + - - +
619A ASN* 3.5 29.1 + - - +
620A TYR* 4.1 22.7 - + - -
627A LEU* 3.9 34.1 + - + +
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Residues in contact with TYR 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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429A ILE 5.3 3.1 - - - -
584A PHE* 3.7 26.0 - + + -
587A PHE* 6.1 3.1 - - + -
588A GLN* 3.4 37.9 + - + +
611A GLN 3.1 19.8 + - - +
612A LEU* 3.7 8.5 - - + +
613A ASP 3.3 0.2 - - - -
614A TYR* 1.3 78.7 - - - +
616A LEU* 1.3 81.1 + - + +
618A GLY 4.8 0.3 + - - -
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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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427A TYR* 5.2 2.2 - - + -
428A PRO* 3.4 35.7 - - + +
429A ILE* 3.6 25.1 - - - +
430A ARG* 3.8 17.3 - - - +
431A THR* 3.8 18.6 - - + +
612A LEU* 3.2 24.2 + - + +
613A ASP* 3.9 3.6 - - - +
614A TYR 3.2 0.2 - - - -
615A TYR* 1.3 96.7 - - + +
617A TYR* 1.3 87.7 + - + +
618A GLY 3.7 0.4 - - - -
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Residues in contact with TYR 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ALA* 3.5 35.7 + - + -
428A PRO* 5.6 1.7 - - + +
430A ARG 4.4 1.4 + - - -
431A THR* 3.4 23.4 - - + -
432A ASN* 3.1 30.4 + - + +
613A ASP* 3.0 25.1 + - - +
616A LEU* 1.3 98.8 - - + +
618A GLY* 1.3 66.5 + - - +
619A ASN 4.8 0.5 - - - +
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Residues in contact with GLY 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A ASP* 4.4 1.6 - - - +
614A TYR* 2.7 40.6 + - - -
615A TYR 4.6 0.4 + - - -
616A LEU 3.7 0.6 - - - -
617A TYR* 1.3 77.3 - - - +
619A ASN* 1.3 67.8 + - - -
620A TYR* 3.8 3.3 + - - -
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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
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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