Contacts of the helix formed by residues 815 - 824 (chain A) in PDB entry 5M64
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 815 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489A ASN* 3.2 55.9 + - - +
490A ILE 4.5 6.5 - - - +
491A GLU* 5.8 4.1 - - - +
698A GLY 5.1 1.8 - - - +
699A CYS* 2.4 52.6 + - + +
700A ILE 3.7 2.0 + - - -
701A ARG* 4.2 17.1 - - - +
704A ASP* 5.0 3.2 + - - -
706A HIS* 3.0 39.6 + - - -
811A SER* 2.9 24.0 + - - +
812A VAL* 3.6 9.6 - - - +
814A GLY* 1.3 75.5 - - - +
816A LEU* 1.3 62.4 + - - +
818A THR* 3.2 16.9 - - + +
819A ASN* 3.2 12.3 + - - +
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Residues in contact with LEU 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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680A LEU* 4.3 16.2 - - + -
695A TYR* 3.7 18.2 - - + +
696A ILE* 5.3 2.5 - - + -
699A CYS* 3.5 20.9 - - + -
731A ILE* 4.3 22.4 - - + -
732A ILE* 6.5 0.7 - - - -
735A VAL* 5.7 11.7 - - + -
812A VAL 2.9 14.9 + - - +
813A LEU* 3.1 21.0 + - + +
815A ARG* 1.3 78.5 - - - +
817A PHE* 1.3 86.9 + - + +
818A THR 3.2 1.2 + - - -
819A ASN* 3.3 6.6 + - - +
820A TYR* 3.1 23.3 + - + +
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Residues in contact with PHE 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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673A HIS* 3.1 51.9 - - + +
676A ALA* 4.4 5.6 - - + +
677A GLY* 3.5 26.2 - - - -
680A LEU* 3.8 22.9 - - + -
732A ILE* 6.4 0.9 - - + -
781A LEU* 4.3 17.7 - - + -
786A TYR* 4.6 1.1 - - - -
813A LEU* 3.5 49.5 + - + -
816A LEU* 1.3 89.9 - - + +
818A THR* 1.3 59.4 + - - +
820A TYR* 3.7 10.9 - + + +
821A ILE* 2.9 27.2 + - - +
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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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488A PRO* 4.4 23.4 - - + +
489A ASN 5.5 0.4 - - - +
618A TYR* 5.9 0.2 - - - -
673A HIS* 3.5 19.4 - - - -
814A GLY 3.9 1.6 - - - +
815A ARG* 3.2 32.3 - - + +
817A PHE* 1.3 77.6 - - - +
819A ASN* 1.3 69.3 + - - +
820A TYR 3.3 0.2 - - - -
821A ILE* 3.3 11.8 - - - +
822A THR* 3.2 25.8 + - - +
779B THR 5.2 1.4 + - - -
780B GLY* 4.7 10.7 - - - -
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Residues in contact with ASN 819 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A GLN* 5.1 16.4 + - - +
695A TYR* 4.3 12.7 + - + +
698A GLY* 2.9 34.8 + - - +
699A CYS* 3.2 21.6 - - - -
815A ARG* 3.2 6.8 + - - +
816A LEU 3.3 6.4 + - - +
818A THR* 1.3 82.3 - - - +
820A TYR* 1.3 64.2 + - - +
822A THR* 3.2 24.5 - - + +
823A ALA* 3.3 12.1 + - - +
93K ILE* 5.9 2.4 - - - +
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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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676A ALA* 3.3 43.5 - - + -
679A TRP* 3.5 28.3 + - + +
680A LEU* 3.6 29.4 - - + -
685A SER* 4.8 1.7 + - - -
687A PHE* 3.8 12.3 - + - -
695A TYR* 3.4 32.9 - + + -
816A LEU* 3.1 17.7 + - + +
817A PHE* 3.7 11.0 - + + -
818A THR 3.3 0.2 - - - -
819A ASN* 1.3 78.8 - - - +
821A ILE* 1.3 56.9 + - + +
823A ALA* 3.4 0.7 + - - +
824A THR* 2.7 57.9 + - + +
1023B ARG* 3.6 14.2 + - - -
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Residues in contact with ILE 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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672A ASP* 5.1 6.1 - - + +
673A HIS* 6.2 0.9 - - + -
676A ALA* 3.7 26.9 - - + -
817A PHE 2.9 17.8 + - - +
818A THR* 3.3 20.6 - - - +
820A TYR* 1.3 76.2 - - + +
822A THR* 1.3 61.9 + - - +
823A ALA 3.4 0.2 - - - -
824A THR 3.5 3.8 - - - +
825A ALA* 3.3 27.0 + - - +
826A PHE* 3.4 31.9 - - + +
777B SER* 3.2 35.0 - - - +
778B TYR* 3.6 13.6 - - - +
780B GLY* 4.8 7.9 - - - -
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Residues in contact with THR 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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694A GLN* 6.2 1.8 - - - +
818A THR 3.2 16.2 + - - +
819A ASN* 3.2 25.4 - - + +
821A ILE* 1.3 76.8 - - - +
823A ALA* 1.3 59.4 + - + +
778B TYR* 3.1 50.1 + - - -
935B ASP* 6.1 0.2 - - - +
1015B SER* 4.1 1.2 - - - -
1017B ALA* 4.3 11.2 - - + +
1018B THR* 4.0 8.3 + - - +
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Residues in contact with ALA 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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691A GLN* 4.9 6.1 - - - +
694A GLN* 5.9 1.6 - - - +
695A TYR* 3.3 29.4 - - + +
819A ASN 3.3 12.7 + - - +
820A TYR 3.4 0.4 + - - +
822A THR* 1.3 79.5 - - + +
824A THR* 1.3 60.2 + - + +
825A ALA 4.3 0.4 - - - -
778B TYR* 5.2 0.4 - - - -
1015B SER* 3.8 20.9 + - - -
1018B THR* 3.8 21.7 + - + +
1020B GLU* 4.4 14.0 - - - +
1021B GLU 5.3 0.9 - - - +
1022B LEU* 5.0 3.3 - - - +
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Residues in contact with THR 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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687A PHE* 5.7 3.8 - - + -
695A TYR* 4.2 5.8 - - - +
820A TYR* 2.7 61.3 + - + +
821A ILE* 3.5 7.8 - - - +
823A ALA* 1.3 75.9 - - + +
825A ALA* 1.3 62.3 + - - +
1020B GLU* 6.0 4.7 - - - -
1021B GLU 5.6 0.9 - - - -
1022B LEU* 4.8 5.8 - - - -
1023B ARG* 3.1 42.7 + - - +
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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