Contacts of the helix formed by residues 821 - 830 (chain A) in PDB entry 5LIA
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 ARG 821 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A TYR* 3.2 20.7 + - - -
433A HIS* 4.5 0.4 + - - -
504A GLU* 3.7 29.9 + - - +
506A ILE* 4.3 3.8 - - - +
507A GLU* 3.9 17.4 + - - -
524A ASN 4.9 3.4 + - - -
526A THR* 4.6 1.0 + - - -
788A SER* 4.6 0.2 - - - -
820A ALA* 1.3 75.4 - - - +
822A VAL* 1.3 67.3 + - - +
823A ARG* 3.7 29.9 - - - +
824A ASP* 2.9 50.1 + - - +
825A ILE* 3.3 14.0 + - - +
827A HIS* 4.5 6.9 + - - -
848A LYS 3.5 12.8 - - - +
849A THR* 3.3 37.7 - - - +
850A TYR 3.5 11.9 - - - +
851A LEU* 3.7 13.0 - - + +
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Residues in contact with VAL 822 (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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766A ILE* 3.9 15.7 - - + -
786A VAL* 3.8 26.2 - - + -
788A SER* 3.5 18.6 + - - +
820A ALA 4.0 1.0 + - - -
821A ARG* 1.3 71.7 - - - +
823A ARG* 1.3 63.3 + - - +
825A ILE* 3.0 11.8 + - - +
826A GLU* 2.9 22.1 + - - +
833A PHE* 3.8 26.0 - - + -
834A TYR* 4.1 12.8 - - + +
847A LEU 4.8 0.4 - - - +
848A LYS* 3.4 32.4 + - + +
850A TYR 4.5 1.6 + - - -
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Residues in contact with ARG 823 (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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524A ASN 5.9 0.7 - - - +
525A GLY 5.4 3.6 + - - -
526A THR* 3.2 40.3 + - - +
821A ARG* 3.1 24.7 - - - +
822A VAL* 1.3 77.6 - - - +
824A ASP* 1.3 61.6 + - - +
826A GLU* 3.0 38.3 + - - +
827A HIS* 3.0 61.1 + - - +
832A ASP* 5.1 3.0 + - - -
845A LEU* 6.0 0.9 - - - -
848A LYS* 3.0 27.9 + - - +
849A THR* 4.8 0.2 - - + -
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Residues in contact with ASP 824 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LYS* 5.8 1.3 - - + +
431A ARG* 4.2 14.4 - - - +
433A HIS* 2.8 34.3 + - + +
790A ILE* 4.0 15.3 - - + -
820A ALA* 3.9 5.9 - - - +
821A ARG* 2.9 58.3 + - - +
823A ARG* 1.3 76.4 - - - +
825A ILE* 1.3 63.4 + - - +
827A HIS* 3.4 10.2 + - - +
828A LEU* 3.1 30.0 + - + +
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Residues in contact with ILE 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A ILE* 4.6 1.6 - - + -
764A TYR* 3.7 45.8 - - + -
765A SER 4.4 0.2 - - - +
766A ILE* 3.5 27.1 - - + -
788A SER* 3.7 21.1 - - - +
789A PHE 4.1 4.9 - - - +
790A ILE* 3.7 25.8 - - + -
820A ALA* 4.8 0.7 - - + -
821A ARG 3.8 7.6 - - - +
822A VAL* 3.0 7.0 + - - +
824A ASP* 1.3 74.6 - - - +
826A GLU* 1.3 64.4 + - - +
828A LEU* 3.1 4.2 + - - +
829A THR* 2.8 35.4 + - + +
833A PHE* 4.1 12.8 - - + -
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Residues in contact with GLU 826 (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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822A VAL* 2.9 17.8 + - - +
823A ARG* 3.0 44.9 + - - +
825A ILE* 1.3 76.8 - - - +
827A HIS* 1.3 58.9 + - - +
829A THR* 3.8 2.7 - - - -
830A GLY* 2.9 31.0 + - - -
831A LEU 3.2 19.3 + - - +
832A ASP* 3.3 6.3 - - - +
833A PHE* 2.9 29.3 + - + -
848A LYS* 2.6 44.1 + - - +
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Residues in contact with HIS 827 (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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221A TYR* 5.5 2.1 + - - -
433A HIS* 5.3 2.5 - + + -
524A ASN* 5.2 7.6 + - - +
740A GLY 3.4 16.2 - - - +
741A LEU* 3.5 14.0 - - + +
742A ARG* 3.0 21.1 + - - +
821A ARG* 4.5 8.6 + - - -
823A ARG* 3.0 63.8 + - + +
824A ASP* 3.6 10.3 - - - +
825A ILE 3.2 0.2 - - - -
826A GLU* 1.3 77.2 - - - +
828A LEU* 1.3 59.9 + - - +
829A THR 3.4 0.3 + - - -
830A GLY* 4.0 1.7 + - - -
1B NAG 3.6 30.4 + - + -
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Residues in contact with LEU 828 (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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430A LYS* 4.4 17.7 - - + -
433A HIS* 6.1 2.7 - - + -
733A ILE* 4.0 33.7 - - + +
734A PHE 4.4 5.9 + - - +
735A ASP* 3.5 31.4 - - + +
740A GLY* 3.3 31.6 - - - +
741A LEU 3.7 2.9 - - - +
742A ARG* 3.3 21.3 - - - +
790A ILE* 3.7 26.7 - - + -
824A ASP* 3.1 18.5 + - + +
825A ILE 3.1 5.5 + - - +
827A HIS* 1.3 80.2 - - - +
829A THR* 1.3 58.4 + - - +
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Residues in contact with THR 829 (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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601A TYR* 3.5 19.2 + - - -
625A LEU* 5.3 1.2 - - - +
732A PRO 4.0 5.8 - - - +
733A ILE* 3.8 21.1 - - + +
742A ARG* 3.5 10.6 - - - +
764A TYR* 3.8 22.9 - - + -
825A ILE* 2.8 27.7 + - + +
826A GLU* 3.8 0.5 - - - -
828A LEU* 1.3 77.6 - - - +
830A GLY* 1.3 65.6 + - - +
831A LEU* 3.3 34.0 + - + +
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Residues in contact with GLY 830 (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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599A VAL* 3.9 1.6 - - - -
600A LEU* 2.9 38.5 + - - +
601A TYR* 3.9 8.7 - - - -
742A ARG* 4.1 13.8 - - - +
826A GLU 2.9 13.0 + - - -
827A HIS 4.0 3.9 + - - -
828A LEU 3.8 0.6 - - - -
829A THR* 1.3 78.9 - - - +
831A LEU* 1.3 59.0 + - - +
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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