Contacts of the helix formed by residues 613 - 628 (chain B) in PDB entry 6O81
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 ASP 613 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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611B PRO* 3.2 16.2 - - + +
612B LEU* 1.3 79.4 - - - +
614B SER* 1.3 62.5 + - - +
615B SER* 3.5 9.2 - - - +
616B ARG* 4.5 8.1 + - + +
617B TYR* 3.8 11.6 + - - +
658B ALA 4.5 1.1 - - - -
659B LEU* 3.4 17.9 - - - +
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Residues in contact with SER 614 (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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613B ASP* 1.3 74.3 - - - +
615B SER* 1.3 60.0 + - - +
617B TYR 4.0 0.4 - - - -
618B CYS* 2.9 31.9 + - - +
658B ALA 4.6 1.3 + - - -
659B LEU* 4.0 15.6 - - - +
661B ILE* 3.8 16.8 - - - -
662B SER* 3.4 31.3 - - - -
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Residues in contact with SER 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B ASP* 3.5 5.8 - - - +
614B SER* 1.3 76.4 - - - +
616B ARG* 1.3 60.4 + - - +
618B CYS* 3.4 4.4 + - - +
619B ALA* 2.9 30.2 + - - +
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Residues in contact with ARG 616 (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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604B PRO 5.5 0.4 - - - -
608B MET* 4.6 20.6 - - + -
611B PRO* 4.7 13.0 - - + -
613B ASP* 4.5 7.1 + - + +
615B SER* 1.3 78.5 - - - +
617B TYR* 1.3 58.1 + - - +
619B ALA* 3.4 5.9 + - - +
620B LEU* 2.9 30.3 + - - +
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Residues in contact with TYR 617 (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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604B PRO* 4.0 21.2 - - + +
605B LEU* 6.1 0.9 - - - -
608B MET* 5.8 1.7 - - - +
613B ASP 3.8 17.3 + - - +
614B SER* 3.6 3.2 + - - +
615B SER 3.3 0.4 - - - -
616B ARG* 1.3 80.1 - - - +
618B CYS* 1.3 56.5 + - - +
620B LEU* 3.4 2.1 + - - +
621B LEU* 2.9 30.5 + - - +
659B LEU* 3.9 18.8 - - + -
662B SER* 4.8 4.3 - - - -
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Residues in contact with CYS 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B SER 2.9 20.3 + - - +
615B SER* 3.8 5.6 - - - +
617B TYR* 1.3 75.7 - - - +
619B ALA* 1.3 58.2 + - - +
621B LEU* 3.8 5.0 - - - +
622B LEU* 2.9 32.4 + - - +
662B SER* 4.1 14.5 - - - -
665B LYS* 4.6 13.5 - - + -
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Residues in contact with ALA 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B SER 2.9 18.2 + - - +
616B ARG* 3.8 6.7 - - - +
618B CYS* 1.3 77.0 - - - +
620B LEU* 1.3 60.9 + - - +
622B LEU* 4.0 8.0 + - - +
623B PRO* 4.0 13.7 - - - +
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Residues in contact with LEU 620 (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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604B PRO* 3.8 30.7 - - + +
607B GLN* 3.8 19.3 - - + -
616B ARG 2.9 17.7 + - - +
617B TYR 3.9 0.2 - - - +
619B ALA* 1.3 79.2 - - - +
621B LEU* 1.3 58.5 + - - +
623B PRO* 4.6 1.3 - - - +
624B LEU* 3.4 22.3 + - - +
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Residues in contact with LEU 621 (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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600B VAL 5.7 2.0 - - - +
604B PRO* 4.1 13.5 - - + -
617B TYR 2.9 18.5 + - - +
618B CYS* 4.1 4.7 - - - +
620B LEU* 1.3 77.5 - - - +
622B LEU* 1.3 59.0 + - - +
624B LEU* 4.0 4.9 - - - +
625B LEU* 3.1 30.0 + - - +
666B VAL* 5.9 7.4 - - + -
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Residues in contact with LEU 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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618B CYS 2.9 18.2 + - - +
619B ALA* 4.0 5.4 + - - +
620B LEU 3.5 0.2 - - - -
621B LEU* 1.3 77.2 - - - +
623B PRO* 1.3 59.9 - - - +
625B LEU* 3.5 3.5 + - - +
626B LYS* 2.9 28.7 + - - +
669B ALA* 5.9 5.6 - - - -
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Residues in contact with PRO 623 (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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619B ALA 4.0 12.6 - - - +
620B LEU 4.3 1.5 - - - +
621B LEU 3.6 0.2 - - - -
622B LEU* 1.3 75.5 - - - +
624B LEU* 1.3 61.2 + - - +
626B LYS* 3.8 6.9 - - + +
627B ALA* 2.9 31.9 + - - +
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Residues in contact with LEU 624 (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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600B VAL* 5.5 9.6 - - + +
603B PHE* 5.9 7.2 - - + -
604B PRO* 6.0 1.1 - - + -
620B LEU 3.4 20.5 + - - +
621B LEU* 4.2 4.7 - - - +
622B LEU 3.3 0.6 - - - -
623B PRO* 1.3 79.6 - - - +
625B LEU* 1.3 58.2 + - - +
628B TRP* 3.1 46.2 + - + +
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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
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621B LEU 3.1 19.5 + - - +
622B LEU* 4.0 3.8 - - - +
624B LEU* 1.3 76.1 - - - +
626B LYS* 1.3 61.5 + - - +
628B TRP* 4.2 1.8 - - - -
629B SER* 3.4 24.4 + - - +
669B ALA* 5.4 12.6 - - + +
673B LEU* 4.4 12.8 - - + +
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Residues in contact with LYS 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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622B LEU 2.9 18.0 + - - +
623B PRO* 3.4 8.7 + - + +
624B LEU 3.3 0.2 - - - -
625B LEU* 1.3 79.2 - - - +
627B ALA* 1.3 62.5 + - - +
629B SER* 3.9 11.2 - - - -
673B LEU* 5.6 3.1 - - - -
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Residues in contact with ALA 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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571B CYS* 5.4 7.3 - - - +
623B PRO 2.9 17.7 + - - +
626B LYS* 1.3 79.0 - - - +
628B TRP* 1.3 70.2 + - + +
629B SER* 3.3 5.1 + - - -
630B PRO* 4.7 2.9 - - - +
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Residues in contact with TRP 628 (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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560B THR 4.3 2.2 - - - -
561B LEU* 3.3 46.0 - - + -
564B GLY* 3.6 18.4 - - - -
565B LYS* 3.6 22.1 - - - +
569B ILE* 5.9 2.5 - - + -
571B CYS* 6.5 0.9 - - - -
574B LEU* 3.6 29.8 - - + -
624B LEU* 3.1 34.4 + - + +
625B LEU* 4.0 5.2 - - - -
627B ALA* 1.3 87.1 - - + +
629B SER* 1.3 60.6 + - - +
630B PRO 3.3 2.9 - - - -
631B VAL* 3.6 17.7 + - + +
632B PHE* 3.2 23.6 + - - +
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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
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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