Contacts of the helix formed by residues 613 - 628 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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611A PRO* 3.2 15.8 - - + +
612A LEU* 1.3 79.1 - - - +
614A SER* 1.3 63.4 + - - +
615A SER* 3.5 9.2 - - - +
616A ARG* 4.5 7.6 + - + +
617A TYR* 3.8 11.4 + - - +
658A ALA 4.5 1.1 - - - -
659A LEU* 3.4 17.4 - - - +
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Residues in contact with SER 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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613A ASP* 1.3 74.4 - - - +
615A SER* 1.3 60.2 + - - +
616A ARG 3.5 0.2 - - - -
617A TYR 4.0 0.7 - - - -
618A CYS* 2.9 31.6 + - - +
658A ALA 4.6 1.2 + - - -
659A LEU* 4.0 15.1 - - - +
661A ILE* 3.8 16.6 - - - -
662A SER* 3.4 30.9 - - - -
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Residues in contact with SER 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A ASP* 3.5 5.9 - - - +
614A SER* 1.3 75.9 - - - +
616A ARG* 1.3 60.6 + - - +
618A CYS* 3.4 4.8 + - - +
619A ALA* 2.9 30.3 + - - +
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Residues in contact with ARG 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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604A PRO 5.5 0.2 - - - -
608A MET* 4.6 18.6 - - + -
611A PRO* 4.7 13.0 - - + -
613A ASP* 4.5 8.0 + - + +
615A SER* 1.3 78.6 - - - +
617A TYR* 1.3 57.8 + - - +
619A ALA* 3.4 6.4 + - - +
620A LEU* 2.9 30.4 + - - +
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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
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604A PRO* 4.0 21.4 - - + +
605A LEU* 6.1 0.4 - - - -
608A MET* 5.8 1.3 - - - +
613A ASP 3.8 17.5 + - - +
614A SER 3.6 3.4 + - - +
615A SER 3.3 0.4 - - - -
616A ARG* 1.3 79.2 - - - +
618A CYS* 1.3 58.7 + - - +
620A LEU* 3.4 2.1 + - - +
621A LEU* 2.9 31.1 + - - +
659A LEU* 3.9 18.4 - - + -
662A SER* 4.8 3.8 - - - -
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Residues in contact with CYS 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 SER 2.9 20.7 + - - +
615A SER* 3.8 5.4 - - - +
617A TYR* 1.3 76.5 - - - +
619A ALA* 1.3 58.5 + - - +
621A LEU* 3.8 4.2 - - - +
622A LEU* 2.9 32.9 + - - +
662A SER* 4.1 13.9 - - - -
665A LYS* 4.6 13.5 - - + -
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Residues in contact with ALA 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A SER 2.9 18.9 + - - +
616A ARG* 3.8 7.2 - - - +
618A CYS* 1.3 76.7 - - - +
620A LEU* 1.3 60.2 + - - +
622A LEU* 4.0 8.7 + - - +
623A PRO* 4.0 13.3 - - - +
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Residues in contact with LEU 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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604A PRO* 3.8 29.8 - - + +
607A GLN* 3.8 20.0 - - + -
616A ARG 2.9 17.9 + - - +
617A TYR 3.9 0.9 - - - +
618A CYS 3.3 0.2 - - - -
619A ALA* 1.3 77.9 - - - +
621A LEU* 1.3 58.8 + - - +
622A LEU 3.5 0.2 - - - -
623A PRO* 4.3 1.7 - - - +
624A LEU* 3.4 21.3 + - - +
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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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600A VAL 5.7 2.5 - - - +
604A PRO* 3.9 13.2 - - + +
617A TYR 2.9 18.5 + - - +
618A CYS* 4.1 4.5 - - - +
620A LEU* 1.3 78.1 - - - +
622A LEU* 1.3 59.1 + - - +
624A LEU* 4.0 4.7 - - - +
625A LEU* 3.1 30.0 + - - +
666A VAL* 5.9 7.2 - - + -
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Residues in contact with LEU 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 CYS 2.9 17.9 + - - +
619A ALA* 4.5 5.8 - - - +
620A LEU 3.5 0.2 - - - -
621A LEU* 1.3 76.4 - - - +
623A PRO* 1.3 58.0 - - - +
625A LEU* 3.5 3.8 + - - +
626A LYS* 2.9 29.1 + - - +
669A ALA* 5.9 4.9 - - - -
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Residues in contact with PRO 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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619A ALA 4.0 12.4 - - - +
620A LEU 5.0 1.3 - - - +
622A LEU* 1.3 76.3 - - - +
624A LEU* 1.3 60.5 + - - +
626A LYS* 3.8 7.0 - - + +
627A ALA* 2.9 31.7 + - - +
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Residues in contact with LEU 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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600A VAL* 5.5 9.2 - - + +
603A PHE* 5.9 6.7 - - + -
604A PRO* 6.0 1.6 - - + -
620A LEU 3.4 19.8 + - - +
621A LEU* 4.2 5.6 - - - +
622A LEU 3.3 0.6 - - - -
623A PRO* 1.3 77.9 - - - +
625A LEU* 1.3 57.8 + - - +
627A ALA* 5.0 0.2 - - - -
628A TRP* 3.1 46.6 + - + +
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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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621A LEU 3.1 20.5 + - - +
622A LEU* 4.0 3.1 - - - +
624A LEU* 1.3 76.1 - - - +
626A LYS* 1.3 62.0 + - - +
628A TRP* 4.2 2.0 - - - +
629A SER* 3.4 24.8 + - - +
669A ALA* 5.4 12.1 - - + +
673A LEU* 4.4 12.4 - - + +
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Residues in contact with LYS 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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622A LEU 2.9 18.4 + - - +
623A PRO* 3.8 9.0 - - + +
624A LEU 3.3 0.4 - - - -
625A LEU* 1.3 79.0 - - - +
627A ALA* 1.3 61.8 + - - +
629A SER* 3.9 11.4 - - - -
673A LEU* 5.6 3.4 - - - -
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Residues in contact with ALA 627 (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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571A CYS* 5.4 7.6 - - - +
623A PRO 2.9 17.7 + - - +
626A LYS* 1.3 78.4 - - - +
628A TRP* 1.3 70.6 + - + +
629A SER 3.3 5.0 + - - -
630A PRO* 4.7 2.8 - - - +
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Residues in contact with TRP 628 (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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560A THR 4.3 2.7 - - - -
561A LEU* 3.3 44.2 - - + -
564A GLY* 3.6 18.2 - - - -
565A LYS* 3.6 22.5 - - + +
569A ILE* 5.9 2.7 - - + -
571A CYS* 6.5 1.1 - - - -
574A LEU* 3.6 30.7 - - + -
624A LEU* 3.1 35.1 + - + +
625A LEU* 4.0 5.0 - - - -
627A ALA* 1.3 87.2 - - + +
629A SER* 1.3 62.6 + - - +
630A PRO* 3.3 2.9 - - - -
631A VAL* 3.6 17.9 + - + +
632A PHE* 3.2 23.2 + - - +
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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