Contacts of the helix formed by residues 822 - 832 (chain B) in PDB entry 1MQB
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 822 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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782B ARG* 4.0 2.0 - - - +
820B GLU 3.5 1.0 + - - -
821B LEU* 1.3 77.5 - - - +
823B ASN* 1.3 65.0 + - - +
824B HIS* 3.7 13.4 + - - -
825B GLU* 2.7 43.9 + - - +
826B VAL* 3.1 19.8 + - - +
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Residues in contact with ASN 823 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779B ILE 5.8 0.6 + - - -
781B ILE* 4.0 36.9 + - + +
782B ARG* 2.9 30.8 + - - +
816B ARG* 4.9 1.9 + - - +
822B SER* 1.3 70.5 - - - +
824B HIS* 1.3 67.9 + - - +
826B VAL* 2.9 17.9 + - - +
827B MET* 3.0 16.1 + - - +
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Residues in contact with HIS 824 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822B SER* 3.4 12.8 + - - +
823B ASN* 1.3 75.5 - - - +
825B GLU* 1.3 81.4 + - + +
827B MET* 3.3 13.2 + - - +
828B LYS* 3.0 35.9 + - + +
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Residues in contact with GLU 825 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820B GLU 4.4 1.7 - - - +
821B LEU* 3.6 22.3 - - + +
822B SER* 2.7 51.4 + - - +
823B ASN 3.1 0.2 - - - -
824B HIS* 1.3 91.9 + - + +
826B VAL* 1.3 60.7 + - - +
828B LYS* 3.5 4.3 + - - +
829B ALA* 2.9 31.6 + - - +
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Residues in contact with VAL 826 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781B ILE* 4.3 7.2 - - + +
782B ARG* 3.6 53.2 - - + +
818B TYR* 3.8 35.1 - - + -
821B LEU* 3.9 7.4 - - + +
822B SER 3.1 21.7 + - - +
823B ASN* 2.9 9.8 + - - +
825B GLU* 1.3 75.2 - - - +
827B MET* 1.3 57.9 - - + +
829B ALA* 3.2 8.7 + - - +
830B ILE* 2.9 38.1 + - + +
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Residues in contact with MET 827 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781B ILE* 3.6 33.4 - - + -
789B ILE* 3.9 39.3 - - + -
823B ASN* 3.0 11.6 + - - +
824B HIS* 3.8 13.0 - - - +
826B VAL* 1.3 74.2 - - + +
828B LYS* 1.3 66.4 + - - +
830B ILE* 3.2 9.1 + - - +
831B ASN* 2.9 37.4 + - - +
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Residues in contact with LYS 828 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824B HIS* 3.0 29.5 + - + +
825B GLU* 3.8 6.5 - - - +
827B MET* 1.3 74.3 - - - +
829B ALA* 1.3 65.2 + - - +
831B ASN* 3.1 11.4 + - - +
832B ASP* 3.0 40.4 + - - +
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Residues in contact with ALA 829 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818B TYR* 5.7 0.7 - - + -
821B LEU* 4.9 8.7 - - + -
825B GLU 2.9 19.4 + - - +
826B VAL* 3.4 7.2 - - - +
828B LYS* 1.3 77.5 - - - +
830B ILE* 1.3 55.1 + - + +
832B ASP* 3.4 8.1 + - - +
833B GLY 3.3 3.6 + - - -
834B PHE* 2.7 58.8 + - + +
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Residues in contact with ILE 830 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784B THR 6.0 2.0 - - - +
786B PRO* 3.8 36.6 - - + -
789B ILE* 6.2 4.3 - - + -
801B TRP* 4.0 17.3 - - + -
818B TYR* 3.3 30.5 - - + +
826B VAL* 2.9 26.5 + - + +
827B MET* 3.4 11.2 - - - +
828B LYS 3.2 0.2 - - - -
829B ALA* 1.3 72.9 - - - +
831B ASN* 1.3 60.9 + - - +
833B GLY* 2.7 25.8 + - - -
834B PHE* 3.6 19.7 - - + +
835B ARG* 3.7 11.7 + - - +
856B GLN* 4.8 5.3 - - - +
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Residues in contact with ASN 831 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786B PRO* 4.8 8.0 - - - +
827B MET* 2.9 29.4 + - - +
828B LYS* 3.6 11.7 - - + +
830B ILE* 1.3 80.2 - - - +
832B ASP* 1.3 62.8 + - - +
833B GLY 3.2 0.7 + - - -
856B GLN* 5.6 3.8 + - - +
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Residues in contact with ASP 832 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828B LYS* 3.0 40.0 + - - +
829B ALA* 3.8 10.7 - - - +
830B ILE 3.1 0.4 - - - -
831B ASN* 1.3 77.5 - - - +
833B GLY* 1.3 61.9 + - - +
834B PHE* 3.4 0.9 - - + +
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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