Contacts of the helix formed by residues 795 - 806 (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 ASN 795 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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793F PRO 4.7 2.0 - - - +
794F PHE* 1.3 74.8 - - - +
796F LYS* 1.3 60.1 + - - +
797F GLN 3.6 1.1 - - - +
798F ARG* 3.7 30.3 - - + +
799F TYR* 3.2 21.9 + - - +
845F TYR* 3.3 13.2 + - + +
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Residues in contact with LYS 796 (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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795F ASN* 1.3 72.1 - - - +
797F GLN* 1.3 60.7 + - - +
798F ARG 3.4 0.2 - - - -
799F TYR* 3.7 13.8 - - + +
800F LYS* 3.0 23.6 + - - +
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Residues in contact with GLN 797 (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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795F ASN* 3.6 0.8 - - - +
796F LYS* 1.3 75.7 - - - +
798F ARG* 1.3 64.9 + - + +
799F TYR 3.2 0.2 - - - -
800F LYS* 3.2 6.3 + - - +
801F MET* 2.9 29.3 + - - +
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Residues in contact with ARG 798 (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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795F ASN* 3.7 25.3 + - + -
797F GLN* 1.3 80.4 - - + +
799F TYR* 1.3 55.8 + - - +
801F MET* 3.4 11.7 + - - +
802F VAL* 2.8 30.9 + - - +
844F LEU 4.4 14.6 + - - -
845F TYR* 4.0 23.9 + - + +
847F GLN* 4.8 12.9 - - - +
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Residues in contact with TYR 799 (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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784F VAL* 5.8 1.8 - - - +
785F GLU* 5.0 10.8 + - + -
788F ILE* 4.7 21.3 - - + -
794F PHE* 6.5 1.6 - + - -
795F ASN 3.2 19.0 + - - +
796F LYS* 3.7 14.1 - - + -
797F GLN 3.2 0.4 - - - -
798F ARG* 1.3 77.9 - - - +
800F LYS* 1.3 64.7 + - - +
802F VAL* 3.7 8.0 - - + +
803F ILE* 2.8 39.4 + - + +
819F ASP* 3.5 26.9 + - + +
845F TYR* 4.2 10.0 - + + -
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Residues in contact with LYS 800 (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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796F LYS 3.0 20.4 + - - +
797F GLN* 3.2 7.4 + - - +
799F TYR* 1.3 79.5 - - + +
801F MET* 1.3 57.3 + - - +
803F ILE* 3.3 6.3 + - - +
804F GLU* 3.0 29.8 + - - +
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Residues in contact with MET 801 (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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797F GLN 2.9 16.1 + - - +
798F ARG* 3.8 15.5 - - - +
800F LYS* 1.3 75.0 - - - +
802F VAL* 1.3 58.3 + - - +
804F GLU* 4.0 4.8 - - - +
805F ALA* 2.9 32.3 + - - +
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Residues in contact with VAL 802 (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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798F ARG 2.8 21.3 + - - +
799F TYR* 3.8 10.1 - - + +
801F MET* 1.3 72.7 - - - +
803F ILE* 1.3 57.7 + - - +
805F ALA* 3.9 4.2 - - - +
806F CYS* 2.7 39.7 + - + +
841F ALA* 5.2 10.5 - - + +
844F LEU* 5.7 6.5 - - + -
845F TYR* 4.5 22.0 - - + +
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Residues in contact with ILE 803 (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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799F TYR* 2.8 38.5 + - + +
800F LYS* 3.6 7.2 - - - +
802F VAL* 1.3 74.6 - - - +
804F GLU* 1.3 62.2 + - - +
807F SER* 3.6 0.5 + - - -
808F LEU* 3.2 39.6 + - + +
809F GLN* 3.9 8.8 + - + +
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Residues in contact with GLU 804 (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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800F LYS 3.0 16.7 + - - +
801F MET* 4.0 4.9 - - - +
803F ILE* 1.3 78.9 - - - +
805F ALA* 1.3 59.4 + - - +
807F SER* 3.5 1.7 + - - -
809F GLN* 6.0 2.9 - - - -
867F HIS* 3.1 24.9 + - - -
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Residues in contact with ALA 805 (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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801F MET 2.9 23.6 + - - +
802F VAL* 3.9 4.5 - - - +
804F GLU* 1.3 74.8 - - - +
806F CYS* 1.3 58.0 + - + +
807F SER 3.4 0.2 - - - -
844F LEU* 6.2 4.3 - - + -
867F HIS* 3.1 16.1 + - - -
868F LEU* 5.9 0.3 - - - -
871F ALA* 3.3 24.4 - - + +
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Residues in contact with CYS 806 (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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802F VAL 2.7 21.4 + - - +
805F ALA* 1.3 73.4 - - - +
807F SER* 1.3 69.8 + - - +
808F LEU* 3.2 10.2 + - + +
837F ARG* 4.1 21.5 - - - +
840F VAL* 5.1 4.7 - - + +
841F ALA* 3.7 34.1 - - + +
844F LEU* 6.0 2.5 - - + -
867F HIS* 4.0 0.4 - - - -
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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