Contacts of the helix formed by residues 812 - 824 (chain A) in PDB entry 5IKP
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 SER 812 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485A GLY* 3.8 1.2 - - - -
486A ILE 3.8 4.7 - - - -
488A PRO* 3.6 7.3 - - - +
513A THR 5.3 0.2 + - - -
515A LEU* 3.7 22.0 + - - +
808A SER 4.1 0.4 + - - -
809A GLY 3.5 17.1 + - - -
810A LYS 2.9 3.8 + - - +
811A PHE* 1.3 78.6 - - - +
813A SER* 1.3 63.0 + - - +
814A ASP* 2.7 32.6 + - - +
815A ARG* 3.3 20.2 + - - +
816A THR* 3.3 12.8 + - - -
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Residues in contact with SER 813 (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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142A CYS* 3.4 18.4 - - - +
143A PHE* 3.9 10.7 - - - -
146A SER* 3.1 20.4 - - - -
485A GLY* 3.1 25.9 + - - -
486A ILE 3.1 22.9 + - - +
487A THR* 3.7 5.4 - - - -
812A SER* 1.3 72.2 + - - +
814A ASP* 1.3 57.8 + - - +
816A THR* 3.2 6.8 + - - -
817A ILE* 2.9 30.3 + - - +
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Residues in contact with ASP 814 (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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146A SER* 3.1 18.8 + - - +
149A THR* 3.2 14.4 + - - -
150A LEU* 3.5 25.4 - - + +
488A PRO* 3.5 7.3 - - - +
489A ARG* 2.8 34.1 + - - -
513A THR 4.0 15.7 - - - +
515A LEU 5.7 0.2 + - - -
812A SER* 2.7 20.9 + - - +
813A SER* 1.3 73.7 - - - +
815A ARG* 1.3 52.3 + - - +
818A THR* 2.8 38.1 + - + +
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Residues in contact with ARG 815 (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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483A THR* 2.8 56.1 + - - +
484A ASN 3.2 16.2 + - - -
809A GLY 5.1 1.1 - - - +
810A LYS* 2.8 50.8 + - + +
811A PHE* 4.4 1.0 - - - +
812A SER* 3.3 17.1 + - - +
813A SER 3.3 0.4 - - - -
814A ASP* 1.3 78.1 - - - +
816A THR* 1.3 62.5 + - - +
818A THR* 3.0 18.3 + - - +
819A GLU* 2.8 62.6 + - + +
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Residues in contact with THR 816 (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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143A PHE* 4.1 16.6 - - + -
482A LYS* 4.1 9.2 - - + +
483A THR 3.0 33.6 + - - +
484A ASN* 3.7 3.2 - - - +
485A GLY 3.4 12.8 + - - -
812A SER 3.3 13.7 + - - -
813A SER 3.2 6.4 + - - -
815A ARG* 1.3 78.0 - - - +
817A ILE* 1.3 60.8 + - - +
819A GLU* 3.2 7.2 + - - +
820A TYR* 2.9 56.4 + - + -
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Residues in contact with ILE 817 (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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143A PHE* 3.8 39.3 - - + +
146A SER* 3.6 24.2 - - - -
147A MET* 3.8 35.0 - - + -
150A LEU* 3.6 18.4 - - + -
152A LEU* 4.2 15.3 - - + -
813A SER 2.9 13.1 + - - +
814A ASP 3.4 3.8 + - - +
816A THR* 1.3 72.2 - - - +
818A THR* 1.3 61.0 + - - +
820A TYR* 3.1 7.2 + - + +
821A ALA* 2.9 28.6 + - - +
825A TRP* 4.0 16.5 - - + -
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Residues in contact with THR 818 (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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150A LEU* 3.8 25.4 - - + -
814A ASP 2.8 27.1 + - - +
815A ARG* 3.0 17.3 + - - +
817A ILE* 1.3 72.0 - - - +
819A GLU* 1.3 56.6 + - - +
821A ALA* 3.5 7.1 + - - +
822A ARG* 3.0 50.4 + - - +
829A PRO* 3.8 22.9 - - + -
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Residues in contact with GLU 819 (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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481A ASN 5.5 1.3 - - - -
482A LYS* 3.4 16.8 - - + -
483A THR 4.7 3.5 + - - -
815A ARG* 2.8 59.4 + - + +
816A THR* 3.5 6.0 - - - +
817A ILE 3.2 0.2 - - - -
818A THR* 1.3 75.9 - - - +
820A TYR* 1.3 58.9 + - - +
822A ARG* 4.6 1.8 - - - +
823A GLU* 2.9 59.7 + - - +
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Residues in contact with TYR 820 (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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84A TYR* 5.3 0.8 + - - -
143A PHE* 3.6 32.1 - + - -
336A GLN* 4.1 20.0 - - + -
375A THR* 3.9 11.8 + - - +
453A ASN* 2.9 39.7 + - - -
455A VAL* 5.9 0.9 - - - +
482A LYS* 3.7 21.1 + - + +
484A ASN* 5.4 1.9 + - - -
816A THR* 2.9 42.7 + - + -
817A ILE* 3.1 11.2 + - + +
819A GLU* 1.3 73.8 - - - +
821A ALA* 1.3 54.4 + - - +
824A ILE* 2.9 28.5 + - + +
825A TRP* 2.8 57.4 + + + -
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Residues in contact with ALA 821 (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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152A LEU* 4.3 14.1 - - + -
817A ILE 2.9 16.0 + - - +
818A THR* 3.7 5.8 - - - +
820A TYR* 1.3 74.8 - - - +
822A ARG* 1.3 56.7 + - - +
825A TRP* 3.7 10.4 - - - -
826A GLY* 3.2 5.5 + - - -
827A VAL* 2.8 58.3 + - + +
829A PRO* 4.2 14.8 - - + -
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Residues in contact with ARG 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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818A THR* 3.0 32.2 + - - +
819A GLU* 4.5 2.5 - - - +
821A ALA* 1.3 80.8 - - - +
823A GLU* 1.3 68.3 + - + +
824A ILE 3.3 2.4 + - - -
826A GLY* 4.4 7.8 + - - -
827A VAL 4.3 5.8 - - - +
828A GLU* 3.1 24.1 + - - +
829A PRO* 3.4 28.4 + - + +
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Residues in contact with GLU 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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480A GLN* 3.1 32.7 + - - +
481A ASN 4.1 3.5 - - - +
482A LYS* 2.8 27.0 + - - +
819A GLU* 2.9 51.4 + - - +
822A ARG* 1.3 75.8 - - + +
824A ILE* 1.3 58.3 + - - +
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Residues in contact with ILE 824 (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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80A LYS* 5.5 0.7 + - - -
336A GLN* 3.9 2.2 - - - +
373A ALA* 3.7 24.2 - - + -
450A HIS* 3.4 27.3 + - + +
451A ALA* 4.1 9.0 - - + +
453A ASN* 4.0 18.2 - - + +
480A GLN* 3.4 26.2 - - - +
482A LYS* 3.9 14.1 - - - -
820A TYR* 2.9 41.6 + - + +
822A ARG 3.3 0.6 - - - -
823A GLU* 1.3 76.7 - - - +
825A TRP* 1.3 79.7 + - + +
826A GLY* 3.3 3.5 + - - -
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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