Contacts of the helix formed by residues 770 - 775 (chain B) in PDB entry 1DQA
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B NAP 4.5 2.0 - - - -
655B MET* 3.4 41.8 - - - +
657B MET* 4.8 1.0 - - - -
690B ASP* 2.9 23.5 + - - +
691B LYS* 3.5 27.9 - - + +
702B ARG* 3.9 9.9 - - - +
761B TYR* 4.6 3.4 - - + -
767B ASP* 2.9 23.5 + - + +
769B ALA* 1.3 74.8 - - - +
771B ASN* 1.3 58.0 + - - +
772B VAL 3.0 2.8 + - - -
773B GLY 3.3 2.6 + - - +
774B SER* 2.8 32.5 + - - +
801B GLU* 3.1 34.1 - - + +
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Residues in contact with ASN 771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768A ALA 4.4 2.5 + - - +
769A ALA* 3.4 14.1 + - - +
771A ASN* 4.8 2.9 - - - +
772A VAL* 3.1 31.6 - - - +
754B ALA* 3.4 9.8 - - - +
757B VAL* 3.6 12.2 - - + +
758B THR* 3.0 28.6 + - - +
761B TYR* 4.8 1.5 - - + -
767B ASP 4.2 0.8 + - - -
768B ALA* 3.1 19.3 + - - +
769B ALA 3.1 0.4 - - - -
770B GLN* 1.3 78.3 - - - +
772B VAL* 1.3 64.9 + - - +
774B SER* 4.3 6.5 - - - -
775B SER* 2.2 45.0 + - - -
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Residues in contact with VAL 772 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693A PRO* 5.4 4.7 - - - +
754A ALA* 3.9 13.9 - - + -
771A ASN* 3.2 37.9 - - - +
772A VAL* 4.4 23.8 - - + +
775A SER* 4.4 3.4 - - - +
691B LYS* 3.8 10.5 - - - +
692B LYS 3.6 7.6 - - - -
693B PRO* 3.6 40.4 - - + +
769B ALA 3.4 9.2 - - - +
770B GLN 3.0 0.2 - - - -
771B ASN* 1.3 81.0 - - - +
773B GLY* 1.3 59.4 + - - +
775B SER* 4.4 4.0 + - - -
776B ASN* 4.2 8.5 - - - +
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Residues in contact with GLY 773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691B LYS* 5.5 2.6 - - - +
692B LYS 5.4 2.4 + - - -
693B PRO* 6.0 1.6 - - - -
697B ASN* 5.1 9.9 - - - -
770B GLN* 3.3 4.0 + - - +
772B VAL* 1.3 78.9 - - - +
774B SER* 1.3 65.5 + - - +
775B SER 3.2 2.7 - - - -
776B ASN* 3.1 21.4 + - - -
799B SER* 2.9 26.3 + - - -
801B GLU* 4.0 9.6 + - - -
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Residues in contact with SER 774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757B VAL* 4.0 8.6 - - - +
761B TYR* 3.0 29.3 + - - -
770B GLN 2.8 19.6 + - - -
773B GLY* 1.3 71.7 - - - +
775B SER* 1.3 58.4 + - - +
776B ASN 3.4 2.1 + - - +
797B MET* 3.2 23.0 - - - +
799B SER 3.2 9.8 - - - +
800B ILE* 4.0 7.6 - - - +
801B GLU* 2.8 40.6 + - - +
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Residues in contact with SER 775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691A LYS 5.3 1.3 - - - -
772A VAL* 4.7 3.8 - - - -
750B ASN* 3.9 5.5 + - - -
753B ALA* 3.6 7.6 - - - +
754B ALA* 3.0 28.6 - - - -
757B VAL* 3.7 10.8 - - - +
771B ASN* 2.2 42.9 + - - -
772B VAL 4.7 2.5 - - - -
773B GLY 3.2 0.2 - - - -
774B SER* 1.3 75.1 - - - +
776B ASN* 1.3 66.2 + - - +
777B CYS* 3.2 12.1 + - - +
797B MET* 4.4 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