Contacts of the helix formed by residues 713 - 720 (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 PRO 713 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575D LEU 4.1 7.2 - - - +
576D GLY* 3.4 31.0 - - - +
711D VAL* 3.5 5.1 - - + +
712D ILE* 1.4 90.1 - - + +
714D ALA* 1.3 65.8 + - - +
715D LYS* 4.4 5.4 - - + +
716D VAL* 3.0 28.6 + - + +
717D VAL* 3.1 9.9 + - - +
790D ASP* 3.4 12.8 - - - +
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Residues in contact with ALA 714 (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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712D ILE 3.6 1.5 + - - -
713D PRO* 1.3 71.3 - - - +
715D LYS* 1.3 63.3 + - - +
717D VAL* 3.2 14.5 + - - +
718D ARG* 3.2 40.6 + - - +
725D THR* 4.5 0.9 - - - -
789D GLU* 3.2 38.4 - - + +
790D ASP* 2.8 15.6 + - - +
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Residues in contact with LYS 715 (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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713D PRO* 3.2 5.1 - - + +
714D ALA* 1.3 78.4 - - - +
716D VAL* 1.3 61.4 + - + +
718D ARG* 3.3 26.3 + - - +
719D GLU* 2.9 64.0 + - - +
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Residues in contact with VAL 716 (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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572D ALA* 3.7 26.7 - - + +
575D LEU* 3.8 26.5 - - + +
712D ILE* 3.5 20.9 - - + -
713D PRO* 3.0 29.3 + - + +
715D LYS* 1.3 79.3 - - + +
717D VAL* 1.3 61.1 + - - +
719D GLU* 4.8 1.1 - - - -
720D VAL* 2.8 41.9 + - + +
721D LEU* 3.3 4.7 + - - +
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Residues in contact with VAL 717 (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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712D ILE* 3.8 19.3 - - + +
713D PRO 3.1 15.0 + - - +
714D ALA* 3.5 7.2 - - - +
716D VAL* 1.3 75.4 - - - +
718D ARG* 1.3 58.1 + - + +
721D LEU* 3.2 15.8 - - + +
722D LYS 3.1 21.8 + - - -
723D THR* 3.2 29.8 + - + +
724D THR 3.5 22.9 - - - +
725D THR* 3.6 20.6 - - - +
728D MET* 4.6 4.5 - - + -
791D LEU* 4.1 13.5 - - + -
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Residues in contact with ARG 718 (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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714D ALA* 3.2 29.4 + - - +
715D LYS* 3.5 33.9 - - - +
716D VAL 3.2 0.4 - - - -
717D VAL* 1.3 77.5 - - + +
719D GLU* 1.3 65.0 + - + +
722D LYS* 3.2 25.5 - - - +
723D THR 3.3 15.4 + - - +
724D THR* 5.4 4.7 - - - +
789D GLU* 4.7 11.3 + - - -
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Residues in contact with GLU 719 (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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715D LYS* 2.9 50.5 + - + +
716D VAL* 4.4 0.9 - - - +
718D ARG* 1.3 82.7 + - + +
720D VAL* 1.3 65.8 + - + +
722D LYS* 3.0 25.6 + - - +
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Residues in contact with VAL 720 (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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103D COA 3.3 18.8 + - + +
568D ARG* 3.4 33.1 + - + +
571D ARG* 4.1 15.7 - - + +
572D ALA* 4.1 8.5 - - + +
575D LEU* 3.7 29.8 - - + -
716D VAL* 2.8 29.0 + - + +
719D GLU* 1.3 76.8 - - + +
721D LEU* 1.3 60.1 + - + +
722D LYS* 3.1 19.3 + - - +
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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