Contacts of the helix formed by residues 794 - 806 (chain F) in PDB entry 6C3P
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 794 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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792F PRO* 3.2 21.7 + - - +
793F PHE* 1.3 80.2 - - - +
795F LYS* 1.3 56.6 + - - +
796F GLN* 3.1 2.7 - - + +
797F ARG* 3.1 25.0 + - + +
798F TYR* 2.5 41.0 + - - +
844F TYR* 3.1 11.2 + - - +
846F HIS* 6.2 2.0 - - - -
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Residues in contact with LYS 795 (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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793F PHE* 3.6 28.8 + - + -
794F ASN* 1.3 69.8 - - - +
796F GLN* 1.3 63.8 + - - +
798F TYR* 3.6 3.8 - - - +
799F LYS* 2.9 50.1 + - - +
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Residues in contact with GLN 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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794F ASN* 3.1 3.3 - - + -
795F LYS* 1.3 78.9 - - - +
797F ARG* 1.3 58.5 + - - +
799F LYS* 3.6 9.3 - - - +
800F MET* 2.9 34.3 + - - +
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Residues in contact with ARG 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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794F ASN* 3.1 25.4 + - + +
796F GLN* 1.3 78.8 - - - +
798F TYR* 1.3 57.5 + - - +
800F MET* 3.6 20.0 - - + +
801F VAL* 2.9 37.1 + - + +
844F TYR* 3.8 17.5 - - + -
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Residues in contact with TYR 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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783F VAL* 4.9 0.9 - - - +
784F GLU* 3.6 12.0 + - + +
787F ILE* 3.8 33.6 - - + +
788F ILE* 4.7 6.1 - - + -
793F PHE* 3.4 38.1 - + + -
794F ASN 2.5 22.5 + - - +
795F LYS* 3.6 4.9 - - - +
797F ARG* 1.3 74.3 - - - +
799F LYS* 1.3 66.6 + - + +
801F VAL* 3.2 3.6 + - + +
802F ILE* 3.0 48.3 + - + +
811F ILE* 5.6 0.5 - - - +
818F ASP* 2.5 43.9 + - - -
844F TYR* 4.0 12.3 - + + -
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Residues in contact with LYS 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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795F LYS* 2.9 45.8 + - - +
796F GLN* 3.6 7.4 - - - +
798F TYR* 1.3 78.1 - - + +
800F MET* 1.3 61.1 + - + +
802F ILE* 4.3 10.8 - - + -
803F GLU* 2.9 49.4 + - + +
808F GLN* 5.6 4.5 - - - +
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Residues in contact with MET 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 GLN 2.9 20.4 + - - +
797F ARG* 3.6 22.7 - - + +
798F TYR 3.2 0.2 - - - -
799F LYS* 1.3 79.3 - - + +
801F VAL* 1.3 66.2 + - + +
803F GLU* 3.5 6.2 + - - +
804F ALA* 2.9 30.3 + - + +
874F GLU* 3.6 42.4 - - + +
881F ARG* 6.2 0.7 - - - +
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Residues in contact with VAL 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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787F ILE* 5.4 2.9 - - + -
797F ARG* 2.9 23.8 + - + +
798F TYR* 3.2 4.7 + - + +
800F MET* 1.3 85.0 - - + +
802F ILE* 1.3 65.5 + - + +
804F ALA* 3.2 9.4 + - - +
805F CYS* 3.0 21.0 + - - +
840F ALA* 3.7 28.3 - - + +
843F LEU* 3.7 28.9 - - + +
844F TYR* 3.6 31.4 - - + +
874F GLU* 6.0 0.7 - - - +
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Residues in contact with ILE 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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787F ILE* 5.2 11.4 - - + -
798F TYR* 3.0 61.2 + - + +
799F LYS* 3.8 6.7 - - + +
801F VAL* 1.3 81.0 - - + +
803F GLU* 1.3 51.7 + - - +
805F CYS* 3.0 8.0 + - - +
806F SER 2.5 32.1 + - - -
807F LEU* 3.3 10.4 + - + -
808F GLN* 3.1 38.1 - - + +
811F ILE* 3.6 23.6 - - + -
840F ALA* 6.0 2.0 - - + -
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Residues in contact with GLU 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 LYS* 2.9 35.4 + - + +
800F MET* 4.0 5.3 - - - +
802F ILE* 1.3 71.9 - - - +
804F ALA* 1.3 65.0 + - - +
806F SER* 3.3 10.4 + - - +
808F GLN* 4.4 21.2 + - + +
866F HIS* 3.5 21.7 + - - -
870F ALA* 4.7 1.4 - - - +
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Residues in contact with ALA 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 MET* 2.9 15.6 + - + +
801F VAL* 3.2 13.7 - - - +
802F ILE 3.1 0.2 - - - -
803F GLU* 1.3 78.9 - - - +
805F CYS* 1.3 60.5 + - - +
806F SER* 3.4 1.7 + - - -
843F LEU* 4.5 7.9 - - + -
866F HIS 4.0 4.0 - - - +
867F LEU* 3.4 25.9 + - + -
870F ALA* 3.9 13.0 - - + +
871F GLY* 3.8 28.3 - - - +
874F GLU* 6.2 1.1 - - + -
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Residues in contact with CYS 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 VAL 3.0 11.7 + - - +
802F ILE* 3.7 7.2 - - - +
804F ALA* 1.3 74.1 - - - +
806F SER* 1.3 74.8 + - - +
807F LEU* 4.5 8.1 - - + +
836F ARG* 3.3 54.0 - - + +
839F VAL* 4.3 0.7 - - - -
840F ALA* 3.9 10.8 - - + -
843F LEU* 3.7 27.8 - - - -
863F LEU* 5.3 0.5 - - - +
867F LEU* 4.1 21.2 - - - +
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Residues in contact with SER 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 ILE 2.5 14.4 + - - -
803F GLU* 3.3 7.8 + - - +
804F ALA 3.2 3.1 + - - -
805F CYS* 1.3 81.9 + - - +
807F LEU* 1.3 58.5 + - - +
808F GLN* 3.4 3.4 - - - +
809F PRO* 3.6 14.9 - - - +
810F ASP* 5.0 2.6 - - - +
836F ARG* 4.6 4.2 + - - -
863F LEU* 4.1 22.3 + - - +
866F HIS* 3.3 36.3 + - - +
867F LEU 5.6 0.2 + - - -
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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