Contacts of the helix formed by residues 947 - 965 (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 VAL 947 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9391 ARG 5.8 2.7 - - - -
9431 LYS 4.9 3.8 + - - -
9441 SER 4.2 2.4 + - - -
9451 ALA* 4.4 1.0 - - - +
9461 LYS* 1.3 71.3 - - - +
9481 ARG* 1.3 68.3 + - - +
9491 GLN 3.4 0.2 - - - -
9501 GLN* 3.2 10.3 + - - +
9511 ALA 3.5 7.3 + - - -
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Residues in contact with ARG 948 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9391 ARG 5.4 0.9 - - - -
9401 LEU* 4.3 22.1 - - - +
9411 ASN 5.4 0.4 - - - -
9451 ALA* 3.6 16.1 + - - +
9461 LYS 3.1 3.4 - - - -
9471 VAL* 1.3 78.8 - - - +
9491 GLN* 1.3 66.7 + - - +
9501 GLN 2.7 2.1 + - - -
9511 ALA* 2.9 10.6 + - - -
9521 ALA* 3.1 8.5 + - - -
9891 VAL* 5.6 0.4 - - - -
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Residues in contact with GLN 949 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9451 ALA 4.3 4.0 + - - -
9461 LYS 3.9 6.5 + - - -
9471 VAL 3.4 0.6 - - - -
9481 ARG* 1.3 73.5 - - - +
9501 GLN* 1.3 64.1 + - - +
9521 ALA* 3.2 3.7 + - - +
9531 ASP* 2.9 16.3 + - - -
9881 GLU 4.1 18.2 - - - -
9891 VAL* 4.4 14.8 - - - +
9921 SER* 4.8 7.8 - - - +
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Residues in contact with GLN 950 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9461 LYS 4.7 2.0 + - - -
9471 VAL* 3.2 8.6 + - - +
9481 ARG 2.7 5.5 + - - -
9491 GLN* 1.3 71.8 - - - +
9511 ALA* 1.3 63.3 + - - +
9531 ASP* 2.7 16.3 + - - -
9541 LEU 2.9 9.4 + - - -
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Residues in contact with ALA 951 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9361 VAL* 5.4 13.6 - - - +
9391 ARG 6.4 0.2 - - - -
9401 LEU* 5.8 6.1 - - - +
9471 VAL 3.5 6.4 + - - -
9481 ARG 2.9 9.1 + - - -
9501 GLN* 1.3 69.0 - - - +
9521 ALA* 1.3 67.0 + - - +
9541 LEU* 2.9 11.9 + - - +
9551 ILE* 3.0 8.7 + - - -
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Residues in contact with ALA 952 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9401 LEU* 6.1 0.8 - - - +
9481 ARG 3.1 10.7 + - - -
9491 GLN* 3.5 6.1 - - - +
9501 GLN 2.8 2.0 + - - -
9511 ALA* 1.3 74.7 - - - +
9531 ASP* 1.3 63.9 + - - +
9551 ILE* 2.7 14.7 + - - -
9561 SER* 3.0 7.8 + - - -
9921 SER 4.6 15.9 - - - +
9931 ILE* 5.4 3.1 - - - +
9961 ALA* 4.9 3.9 - - - +
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Residues in contact with ASP 953 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9491 GLN 2.9 8.5 + - - -
9501 GLN* 2.7 12.2 + - - +
9521 ALA* 1.3 70.1 - - - +
9541 LEU* 1.3 53.0 + - - +
9561 SER* 2.3 30.3 + - - +
9571 ARG 2.9 9.9 + - - -
9921 SER* 4.7 9.0 + - - +
9961 ALA 6.0 0.2 - - - +
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Residues in contact with LEU 954 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9501 GLN 2.9 11.4 + - - -
9511 ALA* 2.9 7.3 + - - +
9531 ASP* 1.3 75.3 - - - +
9551 ILE* 1.3 61.6 + - - +
9571 ARG* 3.3 1.6 + - - -
9581 THR* 3.1 18.4 + - - -
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Residues in contact with ILE 955 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9511 ALA 3.0 6.8 + - - -
9521 ALA 2.7 14.5 + - - -
9541 LEU* 1.3 71.0 - - - +
9561 SER* 1.3 63.4 + - - +
9571 ARG 2.9 1.2 + - - -
9581 THR* 2.9 11.7 + - - +
9591 ALA* 3.0 13.0 + - - -
9961 ALA* 5.1 2.9 - - - +
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Residues in contact with SER 956 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9521 ALA 3.0 6.7 + - - -
9531 ASP* 2.3 20.9 + - - +
9551 ILE* 1.3 69.6 - - - +
9571 ARG* 1.3 58.9 + - - +
9591 ALA* 3.7 6.9 + - - -
9951 GLY 5.0 2.5 - - - -
9961 ALA* 4.1 23.5 - - - +
9991 ALA* 4.9 11.4 - - - +
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Residues in contact with ARG 957 (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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9151 GLY* 5.7 11.0 - - - -
9531 ASP 2.9 9.9 + - - -
9541 LEU* 3.9 1.8 - - - +
9561 SER* 1.3 78.7 - - - +
9581 THR* 1.3 61.0 + - - +
9591 ALA 3.4 0.7 + - - -
9601 VAL 4.5 2.9 + - - -
9611 VAL 5.4 0.2 + - - -
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Residues in contact with THR 958 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9151 GLY* 6.4 0.4 - - - -
9541 LEU 3.1 10.9 + - - -
9551 ILE* 2.9 6.9 + - - +
9571 ARG* 1.3 76.4 - - - +
9591 ALA* 1.3 68.6 + - - +
9601 VAL 3.3 2.0 - - - -
9611 VAL* 3.1 7.6 + - - +
9621 MET* 3.0 15.1 + - - -
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Residues in contact with ALA 959 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9551 ILE 3.0 12.9 + - - -
9561 SER 3.7 5.2 + - - -
9571 ARG 3.2 3.0 - - - -
9581 THR* 1.3 75.1 - - - +
9601 VAL* 1.3 54.9 + - - +
9621 MET* 2.6 26.4 + - - +
9631 LYS* 3.0 9.2 + - - -
9991 ALA 5.1 12.6 - - - -
10001 ILE* 5.8 2.9 - - - +
10031 VAL* 6.4 1.3 - - - -
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Residues in contact with VAL 960 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9571 ARG 4.5 3.2 + - - -
9581 THR 3.3 1.2 - - - -
9591 ALA* 1.3 74.5 - - - +
9611 VAL* 1.3 60.9 + - - +
9631 LYS* 3.1 10.7 + - - +
9641 THR* 3.3 12.5 + - - -
9991 ALA 5.7 0.6 + - - -
10031 VAL* 6.2 4.3 - - - +
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Residues in contact with VAL 961 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9581 THR* 3.1 8.7 + - - +
9591 ALA 3.0 0.8 - - - -
9601 VAL* 1.3 73.8 - - - +
9621 MET* 1.3 66.1 + - - +
9631 LYS 3.0 6.5 + - - -
9651 CYS* 4.1 10.2 + - - -
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Residues in contact with MET 962 (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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9581 THR 3.0 8.3 + - - -
9591 ALA* 2.6 15.6 + - - +
9611 VAL* 1.3 73.6 - - - +
9631 LYS* 1.3 60.7 + - - +
9651 CYS 5.0 0.2 - - - -
9671 GLU* 3.6 26.5 + - - +
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Residues in contact with LYS 963 (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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9591 ALA 3.0 9.8 + - - -
9601 VAL* 3.1 4.4 + - - +
9611 VAL 3.0 2.2 - - - -
9621 MET* 1.3 76.2 - - - +
9641 THR* 1.3 51.2 + - - +
9651 CYS 3.1 1.8 - - - -
9661 GLN* 2.3 38.3 + - - -
10031 VAL* 6.3 3.1 - - - +
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Residues in contact with THR 964 (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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9601 VAL 3.3 12.6 + - - -
9631 LYS* 1.3 71.8 - - - +
9651 CYS* 1.3 61.0 + - - +
9661 GLN* 3.0 2.4 + - - -
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Residues in contact with CYS 965 (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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9611 VAL 4.1 10.5 + - - -
9621 MET 5.2 0.2 - - - -
9631 LYS 2.9 1.4 + - - -
9641 THR* 1.3 73.6 - - - +
9661 GLN* 1.3 63.3 + - - +
9671 GLU 3.5 1.8 - - - -
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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