Contacts of the strand formed by residues 721 - 726 (chain A) in PDB entry 6DGD
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 LYS 721 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639A ARG 3.9 0.5 - - - +
640A ALA* 3.1 4.1 - - - -
641A GLU* 3.1 52.8 + - + +
720A VAL* 1.3 70.4 - - - +
722A TRP* 1.3 59.9 + - - +
723A VAL* 4.3 3.1 + - + +
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Residues in contact with TRP 722 (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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13A PRO* 6.2 4.5 - - + -
638A ILE* 5.3 10.1 - - + -
639A ARG 3.4 7.0 - - - +
640A ALA* 4.1 3.1 - - + -
651A PHE* 4.2 26.2 - + + -
655A LEU* 6.0 2.9 - - + -
708A LEU* 4.6 24.2 - - + -
711A ILE* 5.2 21.5 - - + -
717A ALA* 3.4 21.9 + - + -
720A VAL* 3.6 16.4 - - + +
721A LYS* 1.3 72.3 - - - +
723A VAL* 1.3 78.0 + - - +
724A LEU* 5.3 10.5 - - + -
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Residues in contact with VAL 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ARG* 4.0 25.1 - - - +
637A LEU 4.0 0.3 - - - +
638A ILE* 3.5 7.8 - - - +
639A ARG* 2.8 56.2 + - + +
721A LYS* 5.2 3.4 - - + +
722A TRP* 1.3 84.6 - - - +
724A LEU* 1.3 61.9 + - - +
725A ASP* 5.6 2.0 - - + +
804A SO4 3.7 33.4 - - - +
805A SO4 4.1 12.6 - - - +
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Residues in contact with LEU 724 (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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87A TYR 4.6 5.9 - - - +
88A HIS* 3.4 51.0 - - + +
89A HIS* 6.0 1.9 - - - -
333A ARG* 4.4 14.4 + - - +
636A VAL* 3.9 14.6 - - + -
638A ILE* 3.0 39.3 - - + -
704A VAL* 5.2 5.2 - - + -
708A LEU* 3.8 20.0 - - + -
722A TRP* 5.3 11.1 - - + -
723A VAL* 1.3 74.5 - - - +
725A ASP* 1.3 61.6 + - - +
726A VAL* 4.1 7.7 + - + -
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Residues in contact with ASP 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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327A LYS* 3.4 14.0 + - - -
329A GLN* 5.2 6.2 - - - +
333A ARG* 3.6 35.9 + - - +
636A VAL* 3.6 3.2 - - - +
637A LEU* 2.8 51.5 + - + +
723A VAL* 4.2 2.7 - - + -
724A LEU* 1.3 72.5 - - - +
726A VAL* 1.3 75.8 + - - +
727A ASP 3.8 0.3 + - - -
728A PRO* 3.5 26.6 - - - +
729A ILE 4.9 1.0 + - - -
730A GLU 5.7 0.5 + - - -
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Residues in contact with VAL 726 (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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86A TYR* 3.5 48.7 - - + +
87A TYR* 3.4 46.8 - - + +
88A HIS* 3.7 11.9 - - + +
327A LYS* 3.8 9.6 + - - +
333A ARG* 5.1 1.0 + - - +
635A HIS 4.5 0.7 - - - +
636A VAL* 3.7 21.3 - - + -
700A LEU* 5.6 1.6 - - + -
724A LEU* 4.1 5.6 + - + -
725A ASP* 1.3 78.4 + - - +
727A ASP* 1.3 79.4 + - - +
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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