Contacts of the helix formed by residues 606 - 617 (chain A) in PDB entry 6T8G
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 LYS 606 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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601A MET* 5.2 7.0 - - + -
605A GLY* 1.3 77.3 - - - +
607A LYS* 1.3 59.1 + - - +
608A VAL 3.5 2.0 - - - -
609A GLU* 3.4 14.2 - - + +
610A GLU* 2.9 29.8 + - - +
1H A 4.9 29.6 + - - +
2H T 3.7 29.5 + - - +
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Residues in contact with LYS 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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529A ARG* 4.3 21.5 - - - +
604A VAL* 4.1 15.0 - - + -
605A GLY 3.7 0.8 - - - -
606A LYS* 1.3 76.7 - - - +
608A VAL* 1.3 60.8 + - + +
610A GLU* 3.1 21.1 + - + +
611A LEU* 3.0 42.5 + - + +
1H A 5.7 1.0 + - - -
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Residues in contact with VAL 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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525A ALA* 4.2 16.6 - - + -
528A LEU* 5.0 4.7 - - + -
597A PHE* 6.6 0.2 - - + -
600A MET* 4.4 32.8 - - + +
601A MET* 5.2 4.9 - - + +
604A VAL* 3.7 36.9 - - + +
605A GLY 5.2 0.4 - - - +
606A LYS* 4.6 0.2 - - - +
607A LYS* 1.3 74.4 - - + +
609A GLU* 1.3 59.7 + - - +
611A LEU* 3.1 22.1 + - + +
612A ILE* 2.9 43.0 + - + +
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Residues in contact with GLU 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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597A PHE* 5.4 1.2 - - - -
601A MET* 3.6 32.5 - - + +
605A GLY 4.3 1.6 + - - +
606A LYS* 3.4 24.5 + - + +
607A LYS 3.2 0.6 - - - -
608A VAL* 1.3 78.8 - - - +
610A GLU* 1.3 60.6 + - - +
612A ILE* 3.5 11.1 + - - +
613A ALA 3.6 4.2 + - - -
637A VAL 3.5 14.3 - - - +
639A THR* 2.9 28.0 + - + +
641A LEU* 3.3 35.0 - - + +
642A ILE* 3.3 30.7 - - - +
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Residues in contact with GLU 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 LYS 2.9 13.8 + - - +
607A LYS* 3.1 24.4 + - + +
609A GLU* 1.3 74.4 - - - +
611A LEU* 1.3 70.2 + - - +
613A ALA* 3.5 3.3 + - - +
614A ARG* 2.9 46.0 + - - +
641A LEU* 4.5 12.3 - - + -
602B MET* 5.5 17.1 - - + +
603B ILE* 5.5 6.9 - - - +
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Residues in contact with LEU 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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525A ALA* 4.4 7.6 - - + +
528A LEU* 3.7 21.5 - - + -
529A ARG* 3.6 39.3 - - + +
532A VAL* 4.2 17.7 - - + +
607A LYS* 3.0 25.3 + - + +
608A VAL* 3.1 32.5 + - + +
610A GLU* 1.3 86.8 - - - +
612A ILE* 1.3 56.2 + - - +
614A ARG* 3.7 7.4 - - + +
615A ILE* 2.9 33.6 + - - +
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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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528A LEU* 4.0 26.9 - - + -
594A VAL* 5.9 1.6 - - + -
597A PHE* 5.4 11.2 - - + -
608A VAL* 2.9 28.7 + - + +
609A GLU* 3.9 8.1 - - - +
610A GLU 3.3 0.4 - - - -
611A LEU* 1.3 77.0 - - - +
613A ALA* 1.3 57.7 + - - +
615A ILE* 3.3 6.5 + - + +
616A ALA* 2.9 27.2 + - + +
626A LEU* 4.0 30.6 - - + +
628A LEU* 4.4 17.9 - - + -
642A ILE* 3.8 30.3 - - + -
646A ILE* 5.1 1.1 - - + -
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Residues in contact with ALA 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 GLU 3.6 2.2 + - - -
610A GLU* 3.5 5.4 + - - +
612A ILE* 1.3 80.4 - - - +
614A ARG* 1.3 58.4 + - - +
616A ALA* 3.6 3.8 - - - +
617A GLN* 2.9 35.7 + - - +
641A LEU* 3.3 45.5 - - + +
642A ILE* 4.7 3.1 - - + +
645A ASN* 4.0 10.7 + - - +
632B ARG* 6.0 0.2 - - - +
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Residues in contact with ARG 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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532A VAL* 3.4 36.3 - - - +
535A MET* 4.1 13.5 - - - +
536A GLU* 3.5 29.3 + - - +
610A GLU* 2.9 34.7 + - - +
611A LEU* 3.3 9.6 + - + +
613A ALA* 1.3 76.6 - - - +
615A ILE* 1.3 63.4 + - - +
617A GLN* 4.1 6.6 + - - +
618A LYS* 3.4 43.8 + - + +
599B ASP* 5.6 7.3 + - - +
603B ILE* 5.1 18.1 - - + +
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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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461A HIS* 5.4 0.2 - - + -
528A LEU* 3.9 15.9 - - + -
531A SER* 4.2 12.1 - - - -
532A VAL* 3.7 35.9 - - + +
535A MET* 3.4 27.6 - - + +
592A VAL* 6.0 2.0 - - + -
611A LEU 2.9 18.8 + - - +
612A ILE* 3.6 9.0 - - + +
614A ARG* 1.3 76.9 - - - +
616A ALA* 1.3 60.5 + - + +
617A GLN 3.0 6.6 + - - -
618A LYS 3.1 12.6 + - - -
619A ALA* 3.3 17.2 - - + +
624A ILE* 4.3 18.2 - - + +
626A LEU* 5.3 17.0 - - + -
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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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461A HIS* 4.2 19.1 + - + +
612A ILE* 2.9 22.3 + - + +
613A ALA* 3.3 2.4 + - - +
615A ILE* 1.3 72.8 - - - +
617A GLN* 1.3 58.0 + - - +
618A LYS 3.5 0.2 - - - -
619A ALA* 4.3 3.2 + - - +
626A LEU* 4.8 9.4 - - + -
642A ILE* 6.1 0.7 - - + -
645A ASN* 3.4 44.0 - - + +
646A ILE* 4.4 11.9 - - + -
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Residues in contact with GLN 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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613A ALA 2.9 17.4 + - - +
614A ARG* 4.6 4.7 - - - +
615A ILE 3.0 0.4 + - - -
616A ALA* 1.3 78.6 - - - +
618A LYS* 1.3 80.2 + - - +
619A ALA 3.8 1.7 + - - -
645A ASN* 3.8 14.1 - - - +
500B LYS* 3.3 46.7 + - - +
596B GLU* 4.1 15.2 - - - +
598B ALA* 5.8 7.5 - - + +
599B ASP* 3.6 19.6 + - - +
602B MET* 5.9 2.4 - - + +
631B GLN* 4.0 32.2 - - + +
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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