Contacts of the helix formed by residues 861 - 877 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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860F LEU* 1.3 77.3 - - - +
862F VAL* 1.3 56.6 + - - +
863F HIS* 3.3 7.4 - - + +
864F LEU* 3.2 9.7 + - + +
865F SER* 2.6 34.2 + - - -
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Residues in contact with VAL 862 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861F ASP* 1.3 74.2 - - - +
863F HIS* 1.3 58.2 + - - +
865F SER* 2.4 27.2 + - - +
866F ASP* 2.9 14.2 + - - +
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Residues in contact with HIS 863 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861F ASP* 3.3 5.2 - - + +
862F VAL* 1.3 78.6 - - - +
864F LEU* 1.3 56.3 + - - +
866F ASP* 3.2 10.1 + - - +
867F HIS* 2.9 25.3 + - - +
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Residues in contact with LEU 864 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807F SER* 5.4 9.6 - - - -
860F LEU* 3.7 21.4 - - + +
861F ASP* 3.2 16.1 + - + +
863F HIS* 1.3 75.3 - - - +
865F SER* 1.3 60.6 + - - +
867F HIS* 3.2 10.7 + - + +
868F LEU* 2.8 28.6 + - - +
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Residues in contact with SER 865 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857F PHE* 4.2 25.0 - - - +
860F LEU* 4.6 1.4 - - - +
861F ASP 2.6 17.6 + - - -
862F VAL* 2.4 32.4 + - - +
864F LEU* 1.3 72.4 - - - +
866F ASP* 1.3 55.5 + - - +
868F LEU* 3.3 7.8 + - - +
869F MET* 2.8 27.7 + - - +
893F TYR* 3.9 21.8 + - - -
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Residues in contact with ASP 866 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862F VAL 2.9 13.8 + - - +
863F HIS* 3.3 12.8 - - - +
865F SER* 1.3 73.6 + - - +
867F HIS* 1.3 59.8 + - - +
869F MET* 3.3 8.4 - - - +
870F GLN* 3.0 29.5 + - - +
893F TYR* 4.1 7.6 - - - +
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Residues in contact with HIS 867 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804F GLU 3.1 22.2 + - - -
805F ALA 3.1 28.6 + - - -
806F CYS 4.4 0.4 - - - -
807F SER* 3.3 31.3 - - - -
863F HIS 2.9 12.9 + - - +
864F LEU* 3.3 13.7 - - - +
866F ASP* 1.3 77.5 - - - +
868F LEU* 1.3 56.0 + - - +
870F GLN* 3.3 3.1 + - - +
871F ALA* 2.8 46.6 + - + +
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Residues in contact with LEU 868 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805F ALA 5.9 0.2 - - - -
856F PRO* 6.1 3.6 - - + +
857F PHE* 4.9 12.6 - - + -
864F LEU 2.8 18.7 + - - +
865F SER* 3.3 8.7 + - - +
867F HIS* 1.3 73.0 + - - +
869F MET* 1.3 58.1 + - - +
871F ALA* 4.9 1.6 - - - -
872F GLY* 2.8 30.3 + - - +
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Residues in contact with MET 869 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865F SER 2.8 14.5 + - - +
866F ASP* 3.3 12.6 - - - +
868F LEU* 1.3 75.2 - - - +
870F GLN* 1.3 58.6 + - + +
872F GLY 3.8 0.2 - - - -
873F ILE* 2.9 30.5 + - - +
893F TYR* 3.8 32.3 - - + -
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Residues in contact with GLN 870 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866F ASP 3.0 18.8 + - - +
867F HIS* 4.1 2.9 - - - +
869F MET* 1.3 72.9 - - - +
871F ALA* 1.3 58.2 + - - +
873F ILE* 3.2 7.7 + - - +
874F LEU* 3.0 26.5 + - - +
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Residues in contact with ALA 871 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805F ALA* 3.3 37.8 - - + +
867F HIS* 2.8 29.1 + - + +
868F LEU* 4.9 1.3 - - - -
870F GLN* 1.3 71.0 - - - +
872F GLY* 1.3 61.1 + - - +
874F LEU* 3.3 8.2 - - - +
875F GLU* 2.9 28.3 + - - +
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Residues in contact with GLY 872 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868F LEU* 2.8 25.2 + - - +
869F MET 3.8 0.2 - - - -
871F ALA* 1.3 79.5 - - - +
873F ILE* 1.3 54.3 + - - +
874F LEU 3.0 1.3 - - - -
875F GLU* 3.0 7.6 + - - +
876F LEU* 2.8 36.5 + - - +
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Residues in contact with ILE 873 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869F MET 2.9 18.6 + - - +
870F GLN* 3.6 7.4 - - - +
872F GLY* 1.3 75.2 - - - +
874F LEU* 1.3 49.4 + - - +
875F GLU 3.3 0.7 - - - -
876F LEU* 3.6 18.8 - - + +
877F LEU* 2.8 33.7 + - - +
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Residues in contact with LEU 874 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870F GLN 3.0 15.3 + - - +
871F ALA* 3.3 9.8 + - - +
872F GLY 3.0 0.2 - - - -
873F ILE* 1.3 75.7 - - - +
875F GLU* 1.3 51.6 + - - +
877F LEU* 3.7 9.0 - - + -
878F ARG* 2.8 30.4 + - - +
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Residues in contact with GLU 875 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805F ALA* 6.3 1.6 - - + -
844F LEU* 5.9 6.5 - - + -
871F ALA 3.0 15.9 - - - +
872F GLY* 3.3 11.2 - - - +
874F LEU* 1.3 78.8 - - - +
876F LEU* 1.3 56.2 + - - +
877F LEU 3.2 0.4 - - - -
878F ARG* 3.4 6.3 - - - +
879F ASP* 2.5 32.4 + - - +
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Residues in contact with LEU 876 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708F LEU* 5.3 14.1 - - + -
872F GLY 2.8 21.5 + - - +
873F ILE* 3.6 19.3 - - + +
875F GLU* 1.3 75.3 - - - +
877F LEU* 1.3 72.8 + - + +
879F ASP* 2.9 31.8 - - - +
882F ARG 5.4 2.0 - - - +
884F VAL* 4.8 19.5 - - + -
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Residues in contact with LEU 877 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873F ILE 2.8 24.2 + - - +
874F LEU* 3.7 8.3 - - + -
876F LEU* 1.3 82.4 - - + +
878F ARG* 1.3 61.4 + - - +
879F ASP 3.5 7.1 + - - +
880F ASP* 5.1 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