Contacts of the helix formed by residues 844 - 852 (chain A) in PDB entry 3B7B
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 THR 844 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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813A HIS* 4.4 0.2 - - - -
835A VAL 4.5 3.4 - - - -
836A ASN* 3.7 25.1 - - - +
837A CYS 3.5 1.1 - - - -
838A GLN* 3.7 7.0 - - + -
842A GLY 3.7 0.2 + - - -
843A TRP* 1.3 76.1 - - - +
845A PRO* 1.3 76.9 - - - +
846A MET* 3.6 10.5 + - - +
847A ILE* 3.0 32.2 + - - +
848A TRP* 3.0 14.9 + - - -
870A ILE* 3.4 38.8 - - + +
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Residues in contact with PRO 845 (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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812A LEU* 3.9 27.6 - - + +
813A HIS* 4.0 18.2 - - + +
816A ALA* 4.0 17.1 - - + +
834A ASP 5.0 0.7 - - - +
835A VAL 3.4 20.0 - - - +
837A CYS 3.2 17.3 - - - +
844A THR* 1.3 86.5 - - - +
846A MET* 1.3 55.3 + - - +
848A TRP* 3.2 9.5 + - + +
849A ALA* 2.8 29.8 + - - +
861A LEU* 3.5 18.6 - - + +
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Residues in contact with MET 846 (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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835A VAL 5.2 0.4 + - - -
844A THR* 3.0 9.8 + - - +
845A PRO* 1.3 75.9 - - - +
847A ILE* 1.3 61.0 + - - +
848A TRP 3.0 1.8 - - - -
849A ALA* 3.2 2.1 + - - +
850A THR* 2.8 33.5 + - - -
858A VAL* 3.8 31.4 - - + +
861A LEU* 3.4 11.3 - - + +
862A LEU* 3.7 15.3 - - - -
866A SER* 3.6 34.3 + - - +
867A ASP 4.8 2.0 - - - +
868A ILE* 3.7 32.3 - - + +
878A CYS* 3.7 30.1 - - + -
894A LEU* 4.0 2.9 - - + -
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Residues in contact with ILE 847 (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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842A GLY 4.4 2.5 - - - +
843A TRP* 3.4 36.5 - - + -
844A THR* 3.0 32.5 + - - +
846A MET* 1.3 76.3 - - + +
848A TRP* 1.3 57.9 + - - +
850A THR* 3.7 6.6 - - - +
851A GLU* 3.0 26.0 + - - +
870A ILE* 4.8 9.6 - - + +
872A ASP* 4.3 16.2 - - + +
876A ASN 4.9 0.9 - - - +
878A CYS* 4.3 25.8 - - + +
881A TRP* 3.3 35.8 - - + +
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Residues in contact with TRP 848 (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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809A SER* 4.6 1.6 + - - -
813A HIS* 3.5 30.3 - + + +
817A LYS* 3.4 52.1 - - + +
839A ASP* 2.8 28.7 + - - -
843A TRP* 3.8 35.4 - + + +
844A THR 3.0 12.5 + - - +
845A PRO* 3.4 10.1 - - + +
846A MET 3.0 0.8 - - - -
847A ILE* 1.3 75.9 - - - +
849A ALA* 1.3 64.4 + - - +
850A THR 3.0 2.3 + - - -
851A GLU* 3.2 10.7 + - + +
852A TYR* 3.2 62.1 + + - -
950B LEU* 4.6 11.7 - - + -
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Residues in contact with ALA 849 (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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816A ALA 4.2 7.8 + - - +
845A PRO 2.8 19.4 + - - +
846A MET 4.0 2.9 - - - +
848A TRP* 1.3 73.7 - - - +
850A THR* 1.3 59.7 + - - +
852A TYR 3.7 1.0 + - - -
853A LYS 3.3 1.6 + - - -
854A HIS* 2.8 35.9 + - + +
857A LEU* 3.6 40.6 - - + -
858A VAL* 4.2 10.8 - - + +
861A LEU* 4.5 5.2 - - + -
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Residues in contact with THR 850 (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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846A MET 2.8 20.7 + - - -
847A ILE* 3.7 7.2 - - - -
849A ALA* 1.3 76.6 - - - +
851A GLU* 1.3 68.4 + - - +
853A LYS* 3.0 13.2 + - - -
858A VAL* 3.6 5.5 - - - +
878A CYS* 3.5 17.4 - - - -
881A TRP* 4.0 12.1 - - + +
882A ALA* 3.7 36.6 - - + +
885A SER* 3.9 10.5 + - - -
887A CYS* 6.5 0.4 - - + -
890A ILE* 3.5 28.0 - - + +
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Residues in contact with GLU 851 (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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843A TRP* 3.6 22.4 - - + -
847A ILE 3.0 17.8 + - - +
848A TRP* 3.5 7.4 - - + +
850A THR* 1.3 80.2 - - - +
852A TYR* 1.3 81.4 + - + +
853A LYS* 3.5 9.2 + - - +
881A TRP* 4.5 10.0 - - + +
884A PHE* 5.1 3.7 - - - -
885A SER* 4.5 9.8 + - - -
950B LEU* 4.1 7.9 - - + +
951B ASN* 2.9 38.5 + - - +
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Residues in contact with TYR 852 (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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817A LYS* 3.6 29.7 + - + +
818A LYS* 6.1 2.7 - - - -
848A TRP* 3.2 51.0 + + - +
849A ALA 3.8 0.2 - - - -
850A THR 3.1 0.6 - - - -
851A GLU* 1.3 88.7 - - + +
853A LYS* 1.3 70.4 + - - +
854A HIS* 3.2 37.1 + - + +
950B LEU* 5.5 3.3 - - - +
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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