Contacts of the helix formed by residues 826 - 845 (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 826 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8221 ARG 4.0 3.6 + - - -
8231 MET 2.8 12.2 + - - +
8241 ALA 2.8 17.7 - - - +
8251 LEU* 1.3 77.2 - - - +
8271 ARG* 1.3 65.3 + - - +
8291 ASN 4.6 2.9 - - - +
8301 TYR* 3.7 6.2 + - - -
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Residues in contact with ARG 827 (chain 1).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8251 LEU 3.9 0.8 + - - -
8261 ASP* 1.3 70.7 - - - +
8281 ARG* 1.3 68.7 + - - +
8291 ASN 4.4 0.2 - - - +
8301 TYR* 2.9 13.3 + - - -
8311 ARG 3.2 7.8 + - - -
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Residues in contact with ARG 828 (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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8271 ARG* 1.3 70.3 - - - +
8291 ASN* 1.3 54.9 + - - +
8311 ARG* 2.6 25.9 + - - +
8321 GLN* 2.8 12.1 + - - -
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Residues in contact with ASN 829 (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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7861 LYS* 6.6 0.2 - - - +
8231 MET* 5.2 9.4 - - - +
8261 ASP* 4.6 2.1 - - - +
8271 ARG 3.2 2.8 - - - +
8281 ARG* 1.3 73.0 - - - +
8301 TYR* 1.3 66.9 + - - +
8321 GLN* 4.5 1.8 - - - +
8331 LEU* 2.9 20.0 + - - +
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Residues in contact with TYR 830 (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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8231 MET 4.8 3.2 + - - -
8241 ALA* 4.7 12.3 - - - +
8261 ASP 3.7 10.6 + - - -
8271 ARG 2.9 11.7 + - - -
8291 ASN* 1.3 78.1 - - - +
8311 ARG* 1.3 67.7 + - - +
8331 LEU* 3.5 0.7 - - - -
8341 VAL* 3.0 13.5 + - - -
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Residues in contact with ARG 831 (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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8271 ARG 3.2 6.3 + - - -
8281 ARG* 2.6 11.9 + - - +
8301 TYR* 1.3 70.7 - - - +
8321 GLN* 1.3 63.7 + - - +
8341 VAL* 2.6 17.9 + - - +
8351 ASP* 3.0 9.0 + - - -
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Residues in contact with GLN 832 (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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8281 ARG 2.8 15.7 + - - -
8291 ASN* 4.0 2.0 - - - +
8311 ARG* 1.3 68.3 - - - +
8331 LEU* 1.3 64.8 + - - +
8351 ASP* 3.2 3.3 + - - +
8361 THR* 2.9 16.6 + - - -
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Residues in contact with LEU 833 (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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8291 ASN 2.9 15.0 + - - -
8301 TYR 3.5 3.6 - - - -
8311 ARG 2.7 0.6 + - - -
8321 GLN* 1.3 74.9 - - - +
8341 VAL* 1.3 65.5 + - - +
8361 THR* 2.6 15.7 + - - +
8371 THR* 3.0 9.9 + - - -
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Residues in contact with VAL 834 (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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8301 TYR 3.0 7.9 + - - -
8311 ARG* 2.6 12.6 + - - +
8331 LEU* 1.3 69.9 - - - +
8351 ASP* 1.3 66.8 + - - +
8371 THR* 3.3 1.7 + - - +
8381 VAL* 2.9 17.3 + - - -
8711 THR* 5.6 11.5 - - - +
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Residues in contact with ASP 835 (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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8311 ARG 3.0 11.2 + - - -
8321 GLN* 3.6 3.6 - - - +
8341 VAL* 1.3 74.1 - - - +
8361 THR* 1.3 66.2 + - - +
8381 VAL* 2.7 13.9 + - - +
8391 GLU* 3.0 8.5 + - - -
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Residues in contact with THR 836 (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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7891 LEU 5.8 2.7 - - - -
7931 LYS* 5.1 17.6 - - - +
8321 GLN 2.9 10.0 + - - -
8331 LEU* 2.6 13.2 + - - +
8351 ASP* 1.3 70.2 - - - +
8371 THR* 1.3 63.1 + - - +
8391 GLU* 2.8 12.9 + - - +
8401 LEU* 3.0 10.6 + - - -
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Residues in contact with THR 837 (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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8331 LEU 3.0 11.0 + - - -
8341 VAL* 3.8 2.2 - - - +
8361 THR* 1.3 75.5 - - - +
8381 VAL* 1.3 64.1 + - - +
8401 LEU* 3.1 4.2 + - - +
8411 ALA* 3.0 17.0 + - - -
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Residues in contact with VAL 838 (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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8341 VAL 2.9 9.4 + - - -
8351 ASP* 2.7 15.9 + - - +
8371 THR* 1.3 71.8 - - - +
8391 GLU* 1.3 56.6 + - - +
8411 ALA* 2.8 18.6 + - - +
8421 ASN* 2.9 10.0 + - - -
8751 ILE* 6.0 6.1 - - - +
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Residues in contact with GLU 839 (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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7931 LYS* 6.4 1.6 - - - +
7961 CYS 5.2 5.4 - - - +
7971 GLY* 5.8 4.4 - - - -
8351 ASP 3.0 7.6 + - - -
8361 THR 2.8 8.0 + - - -
8381 VAL* 1.3 76.1 - - - +
8401 LEU* 1.3 63.0 + - - +
8421 ASN* 3.1 12.8 + - - +
8431 LYS* 3.5 7.4 + - - -
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Residues in contact with LEU 840 (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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7961 CYS 5.7 3.1 - - - -
8361 THR 3.0 12.4 + - - -
8371 THR* 3.1 4.5 + - - +
8391 GLU* 1.3 75.4 - - - +
8411 ALA* 1.3 62.2 + - - +
8431 LYS* 3.4 1.3 + - - +
8441 VAL* 3.0 22.2 + - - -
8451 GLY 4.5 0.2 - - - +
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Residues in contact with ALA 841 (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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8371 THR 3.0 8.4 + - - -
8381 VAL* 2.8 10.8 + - - +
8401 LEU* 1.3 72.3 - - - +
8421 ASN* 1.3 51.4 + - - +
8431 LYS 2.4 19.2 + - - -
8451 GLY* 2.9 40.2 + - - +
8461 ALA* 5.4 0.9 - - - +
8491 ILE* 6.1 3.1 - - - +
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Residues in contact with ASN 842 (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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8381 VAL 2.9 12.2 + - - -
8391 GLU* 3.1 8.0 + - - +
8411 ALA* 1.3 72.1 - - - +
8431 LYS* 1.3 56.6 + - - +
8791 LEU* 6.6 0.9 - - - +
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Residues in contact with LYS 843 (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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8031 ALA* 6.3 0.9 - - - -
8391 GLU 3.5 6.1 + - - -
8401 LEU 3.4 3.1 + - - -
8411 ALA 2.4 9.5 + - - +
8421 ASN* 1.3 76.3 - - - +
8441 VAL* 1.3 53.6 + - - +
8451 GLY* 2.7 17.3 + - - -
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Residues in contact with VAL 844 (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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8031 ALA* 5.8 9.4 - - - +
8401 LEU 3.0 16.0 + - - -
8431 LYS* 1.3 68.9 - - - +
8451 GLY* 1.3 59.2 + - - +
8481 GLU* 5.5 4.3 + - - -
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Residues in contact with GLY 845 (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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8411 ALA* 2.9 28.1 + - - +
8431 LYS 2.7 8.3 + - - -
8441 VAL* 1.3 82.5 - - - +
8461 ALA* 1.3 60.2 + - - +
8481 GLU* 4.6 3.4 - - - -
8491 ILE 4.7 4.0 + - - -
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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