Contacts of the helix formed by residues 586 - 604 (chain 1) in PDB entry 6AH0
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 586 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5841 ASP* 3.2 12.0 - - - +
5851 GLU* 1.3 76.2 - - - +
5871 TYR* 1.3 66.5 + - - +
5881 TYR 3.5 1.3 - - - +
5891 ALA* 3.5 8.8 + - - +
5901 ARG* 3.4 11.4 + - - -
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Residues in contact with TYR 587 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5841 ASP 5.4 0.2 - - - -
5851 GLU 3.3 6.0 + - - -
5861 ASP* 1.3 65.3 - - - +
5881 TYR* 1.3 58.9 + - - +
5891 ALA 2.9 1.8 - - - -
5901 ARG* 2.4 29.4 + - - +
5911 VAL 3.1 8.1 + - - -
152G C 5.9 3.1 - - - -
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Residues in contact with TYR 588 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5861 ASP* 3.5 0.6 - - - +
5871 TYR* 1.3 72.2 - - - +
5891 ALA* 1.3 63.5 + - - +
5911 VAL* 3.3 2.3 + - - +
5921 GLU* 3.1 18.0 + - - -
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Residues in contact with ALA 589 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5811 LEU* 4.6 8.5 - - - +
5841 ASP* 6.5 0.2 - - - +
5861 ASP* 3.5 11.8 + - - +
5871 TYR 2.8 2.0 + - - -
5881 TYR* 1.3 76.7 - - - +
5901 ARG* 1.3 64.0 + - - +
5921 GLU* 3.2 1.6 + - - -
5931 GLY* 3.0 17.8 + - - -
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Residues in contact with ARG 590 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5811 LEU 4.2 14.4 + - - -
5821 LEU* 5.0 9.3 - - - +
5861 ASP 3.4 7.7 + - - -
5871 TYR* 2.4 14.2 + - - +
5891 ALA* 1.3 71.1 - - - +
5911 VAL* 1.3 64.1 + - - +
5931 GLY* 2.7 14.2 + - - +
5941 ARG* 2.9 11.8 + - - -
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Residues in contact with VAL 591 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5871 TYR 3.1 10.1 + - - -
5881 TYR* 3.3 3.9 + - - +
5891 ALA 3.2 0.4 - - - -
5901 ARG* 1.3 75.4 - - - +
5921 GLU* 1.3 63.1 + - - +
5941 ARG* 3.5 2.0 + - - +
5951 GLU* 3.0 18.5 + - - -
926 GLY* 3.9 11.9 - - - -
936 SER 5.0 3.1 + - - +
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Residues in contact with GLU 592 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5881 TYR 3.1 13.8 + - - -
5891 ALA 3.6 3.1 - - - -
5911 VAL* 1.3 75.9 - - - +
5931 GLY* 1.3 64.4 + - - +
5951 GLU* 2.8 13.8 + - - +
5961 ILE* 2.9 10.7 + - - -
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Residues in contact with GLY 593 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5781 ILE 6.0 1.8 - - - -
5811 LEU* 5.5 11.0 - - - -
5821 LEU* 5.7 1.6 - - - -
5891 ALA 3.0 9.4 + - - -
5901 ARG* 2.7 14.1 + - - -
5921 GLU* 1.3 68.9 - - - +
5941 ARG* 1.3 63.0 + - - -
5961 ILE* 3.0 3.9 + - - -
5971 ILE* 2.9 20.1 + - - -
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Residues in contact with ARG 594 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5821 LEU* 6.3 0.4 - - - +
5901 ARG 2.9 11.4 + - - -
5911 VAL* 4.0 2.7 - - - +
5931 GLY* 1.3 73.7 - - - +
5951 GLU* 1.3 65.9 + - - +
5971 ILE* 2.9 12.4 + - - +
5981 SER* 3.0 12.3 + - - -
6341 VAL* 6.1 2.1 - - - +
926 GLY* 4.6 3.8 - - - -
936 SER 5.4 3.1 - - - +
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Residues in contact with GLU 595 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5911 VAL 3.0 7.6 + - - -
5921 GLU* 2.8 15.4 + - - +
5941 ARG* 1.3 72.0 - - - +
5961 ILE* 1.3 62.2 + - - +
5981 SER* 3.4 1.2 + - - -
5991 ASN* 3.0 17.5 + - - -
916 LEU 3.7 11.4 - - - +
926 GLY* 3.6 24.9 - - - +
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Residues in contact with ILE 596 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5571 ASP* 5.8 8.3 - - - +
5921 GLU 2.9 12.5 + - - -
5931 GLY* 3.0 2.6 + - - -
5951 GLU* 1.3 77.1 - - - +
5971 ILE* 1.3 59.0 + - - +
5991 ASN* 4.2 2.9 - - - +
6001 LEU* 2.8 26.2 + - - -
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Residues in contact with ILE 597 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5931 GLY 2.9 14.6 + - - -
5941 ARG* 2.9 2.4 + - - +
5961 ILE* 1.3 74.3 - - - +
5981 SER* 1.3 66.1 + - - +
6001 LEU* 3.8 0.8 - - - +
6011 ALA* 2.8 20.4 + - - -
6341 VAL* 5.8 1.1 - - - -
6351 VAL* 5.4 5.8 - - - -
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Residues in contact with SER 598 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5941 ARG 3.0 12.0 + - - -
5951 GLU 3.8 2.7 - - - -
5971 ILE* 1.3 74.8 - - - +
5991 ASN* 1.3 55.4 + - - +
6011 ALA* 2.6 24.9 + - - +
6021 LYS* 2.9 14.8 + - - +
6341 VAL* 5.4 12.8 - - - +
6351 VAL* 5.7 1.6 - - - +
6381 ALA* 5.6 8.1 - - - +
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Residues in contact with ASN 599 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5601 LEU* 4.8 11.5 - - - +
5951 GLU 3.0 14.9 + - - -
5961 ILE* 3.2 4.4 + - - +
5981 SER* 1.3 72.5 - - - +
6001 LEU* 1.3 57.0 + - - +
6021 LYS* 5.6 0.2 - - - +
6031 ALA* 2.9 24.9 + - - +
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Residues in contact with LEU 600 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5961 ILE 2.8 15.6 + - - -
5971 ILE* 3.8 1.3 - - - +
5981 SER 2.8 2.6 + - - -
5991 ASN* 1.3 73.5 - - - +
6011 ALA* 1.3 54.7 + - - +
6031 ALA* 2.8 1.2 + - - +
6041 ALA* 2.4 37.3 + - - +
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Residues in contact with ALA 601 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5971 ILE 2.8 12.6 + - - -
5981 SER* 2.6 11.2 + - - +
6001 LEU* 1.3 71.4 - - - +
6021 LYS* 1.3 50.2 + - - +
6041 ALA* 2.6 31.5 - - - +
6051 GLY 4.3 7.2 - - - +
6061 LEU* 4.8 0.7 + - - -
6091 MET* 6.3 2.9 - - - +
6351 VAL* 5.5 9.2 - - - +
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Residues in contact with LYS 602 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5981 SER* 2.9 11.4 + - - +
5991 ASN* 5.6 0.2 - - - +
6011 ALA* 1.3 72.5 - - - +
6031 ALA* 1.3 57.0 - - - +
6041 ALA 2.6 15.1 - - - +
6351 VAL* 6.1 0.6 - - - +
6381 ALA* 5.7 10.5 - - - +
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Residues in contact with ALA 603 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5601 LEU 5.9 1.8 - - - -
5631 LEU 5.6 2.0 - - - -
5641 ASP* 4.1 24.4 - - - +
5991 ASN* 2.9 18.9 + - - +
6001 LEU* 2.8 11.9 + - - +
6021 LYS* 1.3 72.1 - - - +
6041 ALA* 1.3 61.3 + - - +
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Residues in contact with ALA 604 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5641 ASP 4.7 7.2 - - - -
5651 ASP* 6.2 0.7 - - - +
5671 VAL 6.4 0.4 - - - -
5681 ARG* 6.1 6.3 - - - +
6001 LEU 2.4 23.3 + - - -
6011 ALA* 2.6 20.5 - - - +
6021 LYS* 2.6 15.9 - - - +
6031 ALA 1.3 68.7 - - - +
6051 GLY* 1.3 58.6 + - - +
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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