Contacts of the helix formed by residues 769 - 778 (chain A) in PDB entry 1D9F
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 SER 769 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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767A GLY 3.8 0.6 + - - -
768A MET* 1.3 80.5 - - - +
770A ALA* 1.3 59.3 + - - +
771A PHE* 3.9 19.9 + - - +
772A GLY* 2.6 39.0 + - - -
773A LEU* 2.8 11.8 + - - +
788A MET* 4.4 0.9 - - - -
841A ARG* 5.8 0.4 - - - +
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Residues in contact with ALA 770 (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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769A SER* 1.3 72.1 - - - +
771A PHE* 1.3 68.4 + - + +
773A LEU* 3.5 2.3 - - - +
774A ALA 3.2 6.1 + - - -
781A ARG* 5.6 0.4 - - - -
782A LYS 5.9 0.9 - - - +
784A ALA* 3.1 26.7 - - - +
785A GLN* 3.5 41.7 - - + +
788A MET* 3.2 30.9 - - - -
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Residues in contact with PHE 771 (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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769A SER* 2.9 16.8 - - - +
770A ALA* 1.3 79.2 - - + +
772A GLY* 1.3 65.9 + - - +
774A ALA* 3.1 9.6 + - - +
775A ARG* 2.9 30.0 + - + +
781A ARG* 4.3 27.8 - - + +
782A LYS* 3.7 33.2 - - + -
785A GLN* 4.9 11.9 - - - -
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Residues in contact with GLY 772 (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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768A MET* 4.7 14.1 - - - -
769A SER* 2.6 30.0 + - - -
771A PHE* 1.3 71.6 - - - +
773A LEU* 1.3 59.8 + - - -
775A ARG* 3.0 17.8 + - - -
776A GLN* 3.0 26.3 + - - +
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Residues in contact with LEU 773 (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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759A ALA* 3.9 29.8 - - + +
760A ILE* 4.3 20.2 - - + +
763A GLY* 6.4 1.8 - - - -
768A MET* 4.9 5.8 - - + +
769A SER 2.8 9.5 + - - +
770A ALA* 3.5 9.4 - - - +
772A GLY* 1.3 74.7 - - - +
774A ALA* 1.3 61.1 + - - +
776A GLN* 3.0 8.5 + - + -
777A LEU* 2.9 45.3 + - + +
784A ALA* 3.4 40.6 - - + +
787A TYR* 4.7 2.7 - - + -
788A MET* 4.2 18.2 - - + -
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Residues in contact with ALA 774 (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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770A ALA 3.2 11.0 + - - +
771A PHE* 3.1 13.6 + - - +
773A LEU* 1.3 80.1 - - - +
775A ARG* 1.3 58.0 + - + +
778A ASN* 2.8 30.0 + - - -
779A ILE* 3.4 34.6 + - - +
780A PRO 4.3 6.7 - - - +
781A ARG* 4.5 7.2 - - + +
784A ALA* 3.6 12.7 - - + +
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Residues in contact with ARG 775 (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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609A THR 5.4 0.2 - - - +
610A SER* 3.4 44.6 + - - +
611A GLU* 3.4 23.2 - - - +
771A PHE* 2.9 19.8 + - + +
772A GLY* 3.0 11.6 + - - +
774A ALA* 1.3 75.9 - - + +
776A GLN* 1.3 70.7 + - - +
778A ASN* 4.4 10.7 - - - +
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Residues in contact with GLN 776 (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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609A THR* 3.2 25.5 + - - +
610A SER* 4.3 6.5 - - - +
759A ALA* 5.2 11.0 - - + +
768A MET* 6.3 3.4 - - + -
772A GLY* 3.0 26.8 + - - +
773A LEU* 3.0 8.6 + - + +
775A ARG* 1.3 98.7 + - - +
777A LEU* 1.3 65.2 + - - +
778A ASN* 3.5 3.5 + - - -
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Residues in contact with LEU 777 (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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755A ARG* 3.8 13.9 - - + +
756A SER* 3.8 40.2 - - - +
759A ALA* 3.7 22.2 - - + -
773A LEU* 2.9 29.3 + - + +
776A GLN* 1.3 82.2 - - - +
778A ASN* 1.3 68.1 + - - +
779A ILE* 3.5 36.8 + - + +
787A TYR* 4.0 12.3 - - + -
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Residues in contact with ASN 778 (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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616A GLU* 5.6 11.2 + - - +
774A ALA 2.8 9.9 + - - -
775A ARG* 4.4 10.4 - - - +
776A GLN 3.5 3.0 + - - -
777A LEU* 1.3 81.6 - - - +
779A ILE* 1.3 59.6 + - - +
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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