Contacts of the strand formed by residues 724 - 727 (chain A) in PDB entry 1DDJ
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 GLU 724 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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645A LYS* 4.8 6.9 - - - +
707A ASN* 3.4 3.0 - - - +
719A ARG 4.1 3.3 - - - +
720A VAL* 3.8 7.3 - - + -
721A GLN* 2.9 45.4 + - - +
722A SER 3.1 0.4 - - - -
723A THR* 1.3 105.8 + - - +
725A LEU* 1.3 61.8 + - - +
763A LEU* 3.5 40.9 - - + +
773A VAL* 3.7 14.3 - - + +
774A TYR 3.2 7.0 - - - +
775A VAL* 4.6 0.4 - - - +
776A ARG* 2.9 27.7 + - - +
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Residues in contact with LEU 725 (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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674A VAL* 4.5 18.8 - - + -
680A CYS* 6.3 0.2 - - - -
704A VAL* 5.2 4.3 - - + -
707A ASN* 3.6 7.6 - - - +
724A GLU* 1.3 75.8 - - - +
726A CYS* 1.3 77.8 + - - +
727A ALA* 4.4 1.8 - - + -
745A LEU* 3.9 24.2 - - + -
756A GLN* 3.2 32.3 - - + +
757A GLY* 4.4 1.6 - - - -
773A VAL* 3.5 3.4 - - - +
774A TYR* 2.7 43.5 + - + +
776A ARG* 3.6 38.1 - - + +
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Residues in contact with CYS 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A VAL* 3.3 8.8 - - - +
705A ILE* 2.8 43.7 + - + +
707A ASN* 4.2 1.7 - - - +
710A CYS* 2.0 50.9 - - + -
720A VAL* 3.7 21.5 - - - -
725A LEU* 1.3 81.2 - - - +
727A ALA* 1.3 61.7 + - - +
771A PRO* 4.4 5.2 - - + -
772A GLY 3.7 7.0 - - - +
773A VAL* 4.3 7.2 - - - -
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Residues in contact with ALA 727 (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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680A CYS* 5.3 1.3 - - + -
702A LEU* 3.9 24.4 - - + +
703A PRO 3.2 9.9 - - - +
704A VAL* 4.3 6.3 - - + -
705A ILE 4.4 0.2 - - - +
725A LEU* 4.2 2.6 + - + -
726A CYS* 1.3 77.0 - - - +
728A GLY* 1.3 59.5 + - - +
745A LEU* 4.1 20.0 - - + -
771A PRO* 4.3 2.7 - - - -
772A GLY 3.4 21.9 + - - +
774A TYR* 3.9 21.1 - - + -
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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
------------------------------------------------------------
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