Contacts of the helix formed by residues 770 - 775 (chain D) in PDB entry 1DQ8
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 GLN 770 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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655D MET* 3.5 40.9 - - - +
657D MET* 4.0 4.8 - - - +
690D ASP* 3.1 20.3 + - - +
691D LYS* 3.6 27.8 - - + +
702D ARG* 4.1 2.4 - - - +
761D TYR* 4.6 3.4 - - + -
767D ASP* 3.0 28.0 + - - +
768D ALA 3.0 1.4 - - - -
769D ALA* 1.3 75.6 - - - +
771D ASN* 1.3 54.6 + - - +
772D VAL* 2.9 7.1 + - - -
773D GLY 3.3 2.0 + - - +
774D SER* 2.8 34.8 + - - +
801D GLU* 3.1 33.0 - - - +
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Residues in contact with ASN 771 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769C ALA 3.5 3.8 + - - -
771C ASN* 3.0 22.1 + - - +
772C VAL* 3.2 20.3 - - - +
754D ALA* 3.3 8.6 - - - +
757D VAL* 3.1 28.6 - - + +
758D THR* 2.9 30.6 + - - +
761D TYR* 4.9 1.5 - - + -
767D ASP 4.3 0.6 + - - -
768D ALA* 3.0 19.7 + - - +
770D GLN* 1.3 78.0 - - - +
772D VAL* 1.3 62.9 + - - +
774D SER* 3.9 0.4 - - - -
775D SER* 2.4 48.0 + - - -
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Residues in contact with VAL 772 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693C PRO* 5.4 2.4 - - - +
754C ALA* 4.0 17.9 - - + -
771C ASN* 4.0 26.2 - - - +
772C VAL* 4.3 23.1 - - + +
775C SER* 4.4 3.1 - - - +
691D LYS* 4.1 7.0 - - - +
692D LYS 3.6 11.4 - - - +
693D PRO* 3.6 41.0 - - + +
769D ALA 3.4 15.7 + - - +
770D GLN 2.9 1.0 - - - -
771D ASN* 1.3 81.7 - - - +
773D GLY* 1.3 59.8 + - - +
775D SER* 4.2 5.0 + - - -
776D ASN* 4.1 10.4 + - - -
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Residues in contact with GLY 773 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691D LYS* 5.5 2.6 - - - +
692D LYS 5.4 2.7 - - - -
693D PRO* 6.0 1.6 - - - -
697D ASN* 5.0 10.8 - - - -
770D GLN* 3.3 3.8 + - - +
772D VAL* 1.3 79.2 - - - +
774D SER* 1.3 65.1 + - - +
775D SER 3.1 2.7 - - - -
776D ASN* 3.0 21.6 + - - -
799D SER* 2.9 25.7 + - - -
801D GLU* 4.0 8.9 + - - -
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Residues in contact with SER 774 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757D VAL* 4.1 9.4 - - - +
761D TYR* 3.0 26.5 + - - -
770D GLN 2.8 16.1 + - - -
773D GLY* 1.3 77.7 - - - +
775D SER* 1.3 56.4 + - - +
776D ASN 3.5 1.7 + - - +
797D MET* 3.2 22.5 - - - +
799D SER 3.1 11.1 - - - +
800D ILE* 3.9 9.8 - - - +
801D GLU* 2.8 41.0 + - - +
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Residues in contact with SER 775 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691C LYS 5.3 2.0 - - - -
693C PRO* 6.0 2.9 - - - -
772C VAL* 4.5 5.6 - - - -
750D ASN* 3.9 5.5 + - - -
753D ALA* 3.6 7.8 - - - +
754D ALA* 3.2 22.9 - - - +
757D VAL* 4.2 9.8 - - - +
771D ASN* 2.4 46.9 + - - -
772D VAL 4.2 4.5 - - - -
773D GLY 3.1 0.2 - - - -
774D SER* 1.3 73.5 - - - +
776D ASN* 1.3 69.4 + - - +
777D CYS* 3.1 11.3 + - - +
797D MET* 4.3 1.1 - - - -
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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