Contacts of the helix formed by residues 907 - 922 (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 907 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9051 THR 3.9 3.0 + - - -
9061 GLU* 1.3 75.2 - - - +
9081 SER* 1.3 68.3 + - - +
9091 VAL 3.1 4.7 + - - +
9101 MET 4.1 2.3 + - - -
9111 LEU* 3.9 10.9 + - - -
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Residues in contact with SER 908 (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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9071 ASP* 1.3 73.9 - - - +
9091 VAL* 1.3 66.3 + - - +
9111 LEU* 3.2 1.8 + - - +
9121 ASN* 2.9 21.0 + - - -
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Residues in contact with VAL 909 (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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8691 MET 6.5 0.4 - - - -
8701 GLU* 6.1 4.7 - - - +
9071 ASP* 3.1 5.5 - - - +
9081 SER* 1.3 79.4 - - - +
9101 MET* 1.3 63.7 + - - +
9121 ASN* 3.8 0.2 - - - -
9131 GLY* 2.8 21.2 + - - -
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Residues in contact with MET 910 (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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8661 LYS* 6.3 0.8 - - - +
8691 MET* 6.4 3.1 - - - +
9001 PHE* 6.3 3.1 - - - +
9071 ASP 4.1 3.4 + - - -
9091 VAL* 1.3 71.1 - - - +
9111 LEU* 1.3 62.8 + - - +
9131 GLY* 4.6 1.6 - - - +
9141 PHE* 2.8 20.3 + - - -
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Residues in contact with LEU 911 (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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9071 ASP 3.9 6.2 + - - -
9081 SER* 3.2 7.7 + - - +
9091 VAL 2.9 2.6 + - - -
9101 MET* 1.3 75.8 - - - +
9121 ASN* 1.3 62.8 + - - +
9141 PHE* 2.9 5.0 + - - -
9151 GLY* 2.9 17.2 + - - -
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Residues in contact with ASN 912 (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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9081 SER 2.9 17.6 + - - -
9091 VAL 3.8 0.9 - - - -
9111 LEU* 1.3 68.6 - - - +
9131 GLY* 1.3 56.0 + - - +
9151 GLY* 2.6 25.6 + - - +
9161 THR* 2.9 12.0 + - - -
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Residues in contact with GLY 913 (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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8691 MET 5.1 8.1 - - - -
8701 GLU* 5.7 2.5 - - - -
8731 GLU* 4.6 23.1 - - - -
9091 VAL 2.8 19.1 + - - -
9101 MET* 3.9 1.8 - - - -
9121 ASN* 1.3 69.1 - - - +
9141 PHE* 1.3 64.7 + - - +
9161 THR* 3.6 1.4 + - - -
9171 VAL* 3.0 14.7 + - - -
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Residues in contact with PHE 914 (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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9101 MET 2.8 16.2 + - - -
9111 LEU 3.4 3.8 - - - -
9121 ASN 2.9 0.2 + - - -
9131 GLY* 1.3 74.4 - - - +
9151 GLY* 1.3 54.3 + - - +
9171 VAL* 2.3 33.6 + - - +
9181 VAL 3.0 4.5 + - - -
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Residues in contact with GLY 915 (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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9111 LEU 2.9 9.3 + - - -
9121 ASN* 2.6 13.6 + - - -
9141 PHE* 1.3 67.9 - - - +
9161 THR* 1.3 62.3 + - - -
9181 VAL* 3.0 3.7 + - - -
9191 ASN* 2.9 21.7 + - - -
9571 ARG* 5.7 11.9 - - - -
9581 THR* 6.4 0.4 - - - -
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Residues in contact with THR 916 (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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8731 GLU* 5.9 5.4 - - - +
8761 MET 5.5 4.7 - - - +
9121 ASN 2.9 10.6 + - - -
9131 GLY* 4.0 1.8 - - - -
9151 GLY* 1.3 75.0 - - - +
9171 VAL* 1.3 66.9 + - - +
9191 ASN* 4.6 1.3 - - - +
9201 ALA* 3.0 19.4 + - - -
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Residues in contact with VAL 917 (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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8731 GLU* 5.9 1.6 - - - +
9131 GLY 3.0 10.7 + - - -
9141 PHE* 2.3 21.2 + - - +
9161 THR* 1.3 71.0 - - - +
9181 VAL* 1.3 61.8 + - - +
9201 ALA* 3.2 1.2 + - - -
9211 LEU* 2.9 17.3 + - - -
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Residues in contact with VAL 918 (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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9141 PHE 3.0 5.3 + - - -
9151 GLY* 3.0 6.5 + - - -
9171 VAL* 1.3 75.0 - - - +
9191 ASN* 1.3 57.2 + - - +
9211 LEU* 2.6 25.7 + - - +
9221 GLY* 3.0 10.7 + - - +
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Residues in contact with ASN 919 (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 2.9 14.5 + - - -
9161 THR* 3.9 1.8 - - - +
9181 VAL* 1.3 74.9 - - - +
9201 ALA* 1.3 59.3 + - - +
9221 GLY* 4.1 6.0 + - - -
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Residues in contact with ALA 920 (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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8761 MET 5.5 5.6 - - - -
8811 ALA* 4.8 18.5 + - - +
9161 THR 3.0 12.9 + - - -
9171 VAL 3.6 3.1 - - - -
9181 VAL 2.7 1.6 + - - -
9191 ASN* 1.3 77.2 - - - +
9211 LEU* 1.3 64.4 + - - +
9221 GLY* 3.1 3.6 + - - -
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Residues in contact with LEU 921 (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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8811 ALA* 5.5 4.5 - - - +
9171 VAL 2.9 10.2 + - - -
9181 VAL* 2.6 14.0 + - - +
9201 ALA* 1.3 73.2 - - - +
9221 GLY* 1.3 67.5 + - - +
9241 ARG* 3.1 15.8 + - - +
9251 VAL* 4.5 4.3 - - - +
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Residues in contact with GLY 922 (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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9181 VAL 3.0 11.0 + - - +
9191 ASN* 4.6 5.6 - - - -
9201 ALA 3.1 4.3 - - - -
9211 LEU* 1.3 75.5 - - - +
9231 LYS* 1.3 52.2 + - - -
9251 VAL* 2.6 31.2 + - - -
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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