Contacts of the strand formed by residues 724 - 730 (chain A) in PDB entry 1L8A
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 GLY 724 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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721A GLY 3.3 9.6 - - - +
722A SER 3.4 3.4 + - - -
723A LYS* 1.3 79.4 - - - +
725A LYS* 1.3 62.5 + - - +
750A GLY 3.7 2.4 + - - -
751A VAL* 4.1 11.4 - - - -
752A GLY* 2.8 23.9 + - - -
856A LEU* 4.3 6.1 - - - -
861A GLU* 4.3 9.2 - - - -
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Residues in contact with LYS 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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718A THR* 3.5 19.2 - - - +
719A ILE 5.0 0.6 + - - -
721A GLY 5.6 0.2 - - - +
724A GLY* 1.3 74.8 - - - +
726A VAL* 1.3 71.8 - - - +
751A VAL* 4.3 1.4 - - - +
752A GLY* 3.3 5.4 - - - -
753A SER* 3.8 15.3 - - - +
754A ASP* 3.2 43.8 + - - +
793A ASN* 5.0 5.2 - - - +
795A ALA* 3.6 22.9 - - + +
796A PRO* 3.6 10.0 - - - +
856A LEU* 4.1 4.7 - - - +
861A GLU* 4.5 7.2 + - - +
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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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725A LYS* 1.3 82.8 - - - +
727A GLN* 1.3 66.2 + - - +
728A LEU* 4.1 10.5 - - + -
745A LEU* 3.9 22.4 - - + -
751A VAL* 4.1 3.8 - - + -
752A GLY 3.1 5.8 + - - +
753A SER* 2.9 39.1 - - - -
754A ASP 3.0 3.6 + - - -
795A ALA* 4.2 2.5 - - - -
796A PRO* 3.2 19.1 - - + +
797A ALA* 5.4 0.2 - - - -
798A VAL* 5.8 0.2 - - + -
852A ALA* 4.5 14.6 - - + +
855A GLU* 4.8 2.5 - - - +
856A LEU* 3.9 30.3 - - + -
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Residues in contact with GLN 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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726A VAL* 1.3 78.0 - - - +
728A LEU* 1.3 64.3 + - - +
729A LEU* 4.3 0.9 - - - -
754A ASP* 3.3 8.3 - - + +
756A TYR* 2.7 39.9 + - + -
792A MET* 3.2 21.0 - - + +
793A ASN* 2.8 61.2 + - - +
795A ALA* 3.0 18.4 - - + +
796A PRO 2.9 7.0 + - - +
797A ALA* 3.2 10.9 - - + +
798A VAL 2.9 26.3 + - - +
817A ALA* 4.1 0.7 - - - +
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Residues in contact with LEU 728 (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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726A VAL* 4.1 15.9 - - + -
727A GLN* 1.3 81.0 - - - +
729A LEU* 1.3 59.9 + - - +
738A VAL* 4.0 18.6 - - + +
741A ALA 4.7 0.2 - - - -
742A ALA* 3.4 42.2 - - + +
745A LEU* 4.1 11.4 - - + -
753A SER* 3.6 15.5 - - - +
754A ASP 2.8 11.4 + - - +
755A VAL* 3.5 6.7 - - + +
756A TYR* 2.7 33.8 + - - +
798A VAL* 3.4 14.4 - - + -
848A VAL* 3.8 23.8 - - + -
852A ALA* 4.6 3.1 - - + -
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Residues in contact with LEU 729 (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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713A ILE* 4.4 5.4 - - + -
727A GLN 4.2 5.6 - - - +
728A LEU* 1.3 82.6 - - - +
730A GLY* 1.3 58.7 + - - +
738A VAL* 3.6 11.7 - - - +
756A TYR* 3.6 17.7 - - + -
758A VAL* 3.6 27.4 - - + -
761A PHE* 4.0 15.5 - - + -
788A ILE* 4.9 4.7 - - + -
792A MET* 3.8 37.9 - - + -
797A ALA* 4.6 4.5 - - + -
798A VAL 2.8 15.8 + - - +
799A ALA* 3.3 14.0 - - + -
800A SER 3.0 24.5 + - - -
820A TYR* 4.4 11.7 - - + +
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Residues in contact with GLY 730 (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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729A LEU* 1.3 76.7 - - - +
731A SER* 1.3 59.6 + - - -
735A LEU* 3.8 26.0 - - - +
738A VAL* 4.0 2.9 - - - -
756A TYR 3.2 9.0 + - - +
757A SER* 3.7 3.8 - - - -
758A VAL* 2.9 27.0 + - - -
761A PHE* 5.1 1.3 - - - -
800A SER 3.4 11.7 - - - -
801A THR* 5.0 0.7 - - - -
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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