Contacts of the helix formed by residues 861 - 877 (chain B) in PDB entry 5TWV
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 ASP 861 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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860B LEU* 1.3 76.6 - - - +
862B VAL* 1.3 56.3 + - - +
863B HIS* 3.3 7.4 - - + +
864B LEU* 3.2 10.4 + - + +
865B SER* 2.6 33.5 + - - -
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Residues in contact with VAL 862 (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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861B ASP* 1.3 75.0 - - - +
863B HIS* 1.3 57.4 + - - +
865B SER* 2.4 26.6 + - - +
866B ASP* 2.9 15.2 + - - +
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Residues in contact with HIS 863 (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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861B ASP* 3.3 5.1 - - + +
862B VAL* 1.3 79.2 - - - +
864B LEU* 1.3 58.1 + - - +
866B ASP* 3.2 10.1 + - - +
867B HIS* 2.9 25.3 + - - +
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Residues in contact with LEU 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807B SER* 5.4 9.0 - - - -
860B LEU* 3.7 21.4 - - + +
861B ASP* 3.2 16.5 + - + +
863B HIS* 1.3 75.2 - - - +
865B SER* 1.3 61.4 + - - +
867B HIS* 3.2 10.5 + - + +
868B LEU* 2.8 28.4 + - - +
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Residues in contact with SER 865 (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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857B PHE* 4.2 25.9 - - - +
860B LEU* 4.6 1.9 - - - +
861B ASP 2.6 18.2 + - - -
862B VAL* 2.4 31.8 + - - -
864B LEU* 1.3 72.8 - - - +
866B ASP* 1.3 55.5 + - - +
868B LEU* 3.3 7.5 + - - +
869B MET* 2.8 27.7 + - - +
893B TYR* 3.9 20.7 + - - -
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Residues in contact with ASP 866 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862B VAL 2.9 14.0 + - - +
863B HIS* 3.2 11.9 + - - +
865B SER* 1.3 73.1 + - - +
867B HIS* 1.3 60.1 + - - +
869B MET* 3.3 8.7 - - - +
870B GLN* 3.0 29.5 + - - +
893B TYR* 4.1 7.2 - - - +
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Residues in contact with HIS 867 (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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804B GLU 3.1 22.1 + - - -
805B ALA* 3.1 27.9 + - - -
806B CYS 4.4 0.6 - - - -
807B SER* 3.3 30.1 - - - -
863B HIS 2.9 13.7 + - - +
864B LEU* 3.3 15.0 + - - +
866B ASP* 1.3 76.8 - - - +
868B LEU* 1.3 55.4 + - - +
870B GLN* 3.3 3.4 + - - +
871B ALA* 2.8 47.5 + - + +
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Residues in contact with LEU 868 (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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805B ALA 5.9 0.4 - - - -
856B PRO* 6.1 3.6 - - + +
857B PHE* 4.9 12.1 - - + -
864B LEU 2.8 17.8 + - - +
865B SER* 3.3 8.5 + - - +
867B HIS* 1.3 73.5 + - - +
869B MET* 1.3 58.9 + - - +
871B ALA* 4.9 0.9 - - - -
872B GLY* 2.8 30.8 + - - +
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Residues in contact with MET 869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865B SER 2.8 13.8 + - - +
866B ASP* 3.3 12.6 - - - +
868B LEU* 1.3 76.7 - - - +
870B GLN* 1.3 57.8 + - - +
872B GLY 3.8 0.3 - - - -
873B ILE* 2.9 30.8 + - - +
893B TYR* 3.8 31.4 - - + -
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Residues in contact with GLN 870 (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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866B ASP 3.0 18.3 + - - +
867B HIS* 4.1 3.1 - - - +
869B MET* 1.3 74.0 - - - +
871B ALA* 1.3 58.1 + - - +
873B ILE* 3.2 7.0 + - - +
874B LEU* 3.0 27.5 + - - +
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Residues in contact with ALA 871 (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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805B ALA* 3.3 37.8 - - + +
867B HIS* 2.8 30.1 + - + +
868B LEU* 4.9 1.3 - - - -
870B GLN* 1.3 72.2 - - - +
872B GLY* 1.3 61.0 + - - +
874B LEU* 3.3 8.1 - - - +
875B GLU* 2.9 28.6 + - - +
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Residues in contact with GLY 872 (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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868B LEU* 2.8 24.3 + - - +
869B MET 3.8 0.4 - - - -
871B ALA* 1.3 78.9 - - - +
873B ILE* 1.3 55.8 + - - +
874B LEU 3.0 1.6 - - - -
875B GLU* 3.0 8.4 + - - +
876B LEU* 2.8 37.0 + - - +
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Residues in contact with ILE 873 (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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869B MET 2.9 18.7 + - - +
870B GLN* 3.2 7.8 + - - +
872B GLY* 1.3 75.2 - - - +
874B LEU* 1.3 49.2 + - - +
875B GLU 3.3 0.2 - - - -
876B LEU* 3.6 19.4 - - + +
877B LEU* 2.8 33.8 + - - +
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Residues in contact with LEU 874 (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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870B GLN 3.0 15.8 + - - +
871B ALA* 3.3 10.1 + - - +
872B GLY 3.0 0.4 - - - -
873B ILE* 1.3 75.8 - - - +
875B GLU* 1.3 50.9 + - - +
877B LEU* 3.7 9.0 - - + -
878B ARG* 2.8 29.7 + - - +
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Residues in contact with GLU 875 (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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805B ALA* 6.3 1.8 - - + -
844B LEU* 5.9 6.5 - - + -
871B ALA 2.9 16.1 + - - +
872B GLY* 3.3 11.0 - - - +
874B LEU* 1.3 77.5 - - - +
876B LEU* 1.3 56.0 + - - +
877B LEU 3.2 0.4 - - - -
878B ARG* 3.4 7.2 - - - +
879B ASP* 2.5 32.6 + - - +
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Residues in contact with LEU 876 (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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708B LEU* 5.3 14.8 - - + -
872B GLY 2.8 22.8 + - - +
873B ILE* 3.6 20.2 - - + +
875B GLU* 1.3 75.8 - - - +
877B LEU* 1.3 73.1 + - + +
879B ASP* 2.9 31.8 - - + +
882B ARG 5.4 2.3 - - - +
884B VAL* 4.8 18.8 - - + -
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Residues in contact with LEU 877 (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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873B ILE 2.8 24.9 + - - +
874B LEU* 3.7 8.1 - - + -
876B LEU* 1.3 82.6 - - + +
878B ARG* 1.3 61.5 + - - +
879B ASP 3.5 7.0 + - - +
880B ASP* 5.1 0.5 - - - -
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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