Contacts of the helix formed by residues 613 - 627 (chain B) in PDB entry 1Q8Z
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 613 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B ASP 3.5 3.0 - - - +
608B GLU* 4.5 4.9 - - - -
611B SER 5.1 2.5 - - - +
612B TYR* 1.3 88.3 - - - +
614B LYS* 1.3 64.8 + - - +
615B ASP* 3.4 11.7 + - - +
616B ASP* 2.6 38.6 + - - +
617B ASP 3.1 16.1 + - - -
643B PHE* 5.2 0.2 - - - -
652B ASN* 5.5 2.2 - - - +
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Residues in contact with LYS 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B ARG* 3.5 39.5 - - - +
569B GLU* 6.1 0.7 - - - -
605B GLU* 5.5 2.0 + - - -
606B PRO* 3.7 35.5 + - + +
607B ASP* 4.1 7.4 - - - +
608B GLU* 3.4 35.0 + - - +
613B THR* 1.3 73.0 - - - +
615B ASP* 1.3 58.2 + - - +
617B ASP* 3.2 2.9 + - - +
618B HIS* 2.7 36.6 + - - +
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Residues in contact with ASP 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B ARG* 2.6 35.6 + - - +
571B ARG* 5.1 2.1 + - - -
576B LEU* 4.4 9.9 - - - +
613B THR* 3.4 7.8 + - - +
614B LYS* 1.3 78.4 - - - +
616B ASP* 1.3 54.2 + - - +
618B HIS* 3.2 0.5 + - - +
619B ILE* 2.8 42.6 + - + +
643B PHE* 3.2 31.8 - - + -
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Residues in contact with ASP 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B TYR* 3.5 12.3 - - + -
613B THR* 2.6 41.6 + - - +
615B ASP* 1.3 76.7 - - - +
617B ASP* 1.3 56.9 + - - +
619B ILE* 3.2 2.5 + - - +
620B ALA* 2.8 30.2 + - - +
642B THR 5.2 0.9 - - - +
643B PHE* 3.5 24.9 - - - +
650B LEU* 3.5 14.4 - - + +
651B ARG* 5.6 0.2 - - - +
652B ASN* 3.4 30.2 + - + -
653B ILE* 4.3 10.1 - - + -
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Residues in contact with ASP 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B GLU 3.8 0.3 - - - +
606B PRO* 3.1 10.6 - - - +
607B ASP* 2.7 50.8 + - - +
612B TYR* 4.0 15.0 + - + -
613B THR 3.1 7.3 + - - +
614B LYS 3.6 2.5 - - - +
616B ASP* 1.3 79.0 - - - +
618B HIS* 1.3 64.1 + - - +
620B ALA* 2.9 10.8 + - - +
621B GLN* 2.9 41.2 + - - +
653B ILE* 5.0 4.5 - - - +
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Residues in contact with HIS 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B ARG* 3.2 42.9 + - - +
569B GLU 4.7 2.2 - - - -
571B ARG 3.6 18.7 + - - -
576B LEU* 3.5 24.9 - - + +
604B PHE* 3.6 35.1 - + + +
606B PRO* 3.3 25.3 - - + +
614B LYS 2.7 22.3 + - - +
615B ASP 3.4 4.5 - - - +
617B ASP* 1.3 74.2 + - - +
619B ILE* 1.3 63.6 + - - +
621B GLN* 3.0 13.0 + - - +
622B ILE* 3.2 16.4 + - + +
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Residues in contact with ILE 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B LEU* 3.6 23.8 - - + +
577B LEU* 3.8 14.4 - - + -
615B ASP 2.8 20.2 + - - +
616B ASP 3.6 3.6 - - - +
618B HIS* 1.3 71.4 - - - +
620B ALA* 1.3 61.2 + - - +
622B ILE* 3.5 8.0 + - + +
623B ILE* 3.3 24.9 + - + +
629B LEU* 4.3 25.8 - - + -
643B PHE* 3.4 52.3 - - + -
644B PHE* 4.3 1.6 - - + -
650B LEU* 3.9 20.6 - - + -
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Residues in contact with ALA 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616B ASP 2.8 14.2 + - - +
617B ASP* 2.9 17.9 + - - +
619B ILE* 1.3 76.9 - - - +
621B GLN* 1.3 58.6 + - - +
623B ILE* 3.5 4.4 + - - +
624B GLU* 2.9 40.4 + - - +
650B LEU* 3.9 15.7 - - + -
653B ILE* 4.2 10.8 - - + -
656B LEU* 4.1 16.3 - - + +
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Residues in contact with GLN 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B LEU 3.9 6.3 + - - -
604B PHE* 3.4 22.4 - - + +
605B GLU* 3.2 37.5 - - - +
606B PRO* 4.7 1.1 - - - -
607B ASP* 5.6 0.2 - - - +
617B ASP* 2.9 40.6 + - - +
618B HIS* 3.0 6.9 + - - +
620B ALA* 1.3 74.1 - - + +
622B ILE* 1.3 67.2 + - - +
624B GLU* 3.4 15.7 - - - +
625B LEU* 3.0 25.3 + - - +
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Residues in contact with ILE 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B SER 5.1 0.4 - - - -
573B PRO* 4.2 16.2 - - + -
576B LEU* 4.0 26.7 - - + -
588B TRP* 4.0 19.5 - - + -
604B PHE* 3.8 21.8 - - + -
618B HIS* 3.2 18.0 + - + +
619B ILE* 3.6 11.4 - - + +
621B GLN* 1.3 76.7 - - - +
623B ILE* 1.3 53.1 + - - +
625B LEU 3.1 1.6 + - - -
626B LEU* 2.6 37.1 + - + +
629B LEU* 4.2 12.8 - - + -
689B LEU* 3.3 31.9 - - + -
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Residues in contact with ILE 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B ILE* 3.3 25.9 + - + +
620B ALA* 3.8 6.5 - - - +
621B GLN 3.3 0.2 - - - -
622B ILE* 1.3 80.7 - - - +
624B GLU* 1.3 59.6 + - - +
627B GLY* 2.6 51.8 + - - +
628B GLU* 3.8 28.9 - - - +
629B LEU* 3.8 29.4 - - + +
644B PHE* 4.5 11.0 - - + -
650B LEU* 5.1 3.4 - - + -
656B LEU* 4.3 22.0 - - + -
658B PHE* 3.9 15.5 - - + -
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Residues in contact with GLU 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B ALA* 2.9 29.9 + - - +
621B GLN* 3.4 20.0 + - - +
622B ILE 3.3 0.2 - - - -
623B ILE* 1.3 76.3 - - - +
625B LEU* 1.3 54.6 + - - +
653B ILE* 5.1 1.6 - - - +
655B LYS 4.1 3.3 - - - +
656B LEU* 3.7 28.0 - - + +
657B LYS* 2.9 35.0 + - - +
658B PHE* 3.4 6.1 - - - +
659B TRP* 2.7 36.0 + - + +
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Residues in contact with LEU 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B LEU* 4.4 19.3 - - + -
604B PHE* 3.4 32.8 - - + -
621B GLN 3.0 15.0 + - - +
622B ILE 3.7 1.3 - - - +
623B ILE 3.0 0.2 - - - -
624B GLU* 1.3 81.3 - - - +
626B LEU* 1.3 77.7 + - + +
627B GLY 3.7 0.7 - - - -
659B TRP 3.6 10.8 - - - +
660B PRO* 4.0 14.4 - - - +
661B LEU* 3.5 40.5 + - + +
664B VAL* 4.0 10.1 - - + -
687B LEU* 4.5 5.6 - - + -
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Residues in contact with LEU 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588B TRP* 3.8 15.5 - - + -
604B PHE* 4.5 0.9 - - + -
622B ILE* 2.6 19.3 + - + +
625B LEU* 1.3 100.2 - - + +
627B GLY* 1.3 61.9 + - - +
628B GLU 4.3 0.9 - - - +
661B LEU* 5.9 3.4 - - + -
684B SER* 5.5 8.1 - - - +
687B LEU* 3.3 42.8 - - + +
689B LEU* 3.4 36.3 - - + +
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Residues in contact with GLY 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623B ILE* 2.6 46.6 + - - +
625B LEU 3.7 1.2 - - - -
626B LEU* 1.3 76.2 - - - +
628B GLU* 1.3 65.9 + - - +
658B PHE* 4.5 15.0 - - - -
689B LEU* 3.8 3.6 - - - +
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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
------------------------------------------------------------
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