Contacts of the helix formed by residues 794 - 806 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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792H PRO* 3.2 22.3 + - - +
793H PHE* 1.3 80.3 - - - +
795H LYS* 1.3 56.9 + - - +
796H GLN* 3.1 3.4 - - + +
797H ARG* 3.7 24.8 - - + +
798H TYR* 2.5 40.7 + - - +
844H TYR* 3.1 10.1 + - - +
846H HIS* 6.2 1.8 - - - -
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Residues in contact with LYS 795 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793H PHE* 3.6 28.8 + - + -
794H ASN* 1.3 70.2 - - - +
796H GLN* 1.3 64.1 + - - +
798H TYR* 3.6 3.9 - - - +
799H LYS* 2.9 50.8 + - - +
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Residues in contact with GLN 796 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794H ASN* 3.1 2.6 - - + +
795H LYS* 1.3 79.5 - - - +
797H ARG* 1.3 58.6 + - - +
799H LYS* 3.6 8.4 - - - +
800H MET* 2.9 34.4 + - - +
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Residues in contact with ARG 797 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794H ASN* 3.1 26.2 + - + +
796H GLN* 1.3 78.1 - - - +
798H TYR* 1.3 57.2 + - - +
800H MET* 3.6 18.8 - - + +
801H VAL* 2.9 36.0 + - + +
844H TYR* 3.8 16.6 - - + -
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Residues in contact with TYR 798 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783H VAL* 4.9 0.5 - - - +
784H GLU* 3.6 12.4 + - + +
787H ILE* 3.8 35.2 - - + +
788H ILE* 4.7 6.1 - - + -
793H PHE* 3.4 38.6 - + + -
794H ASN 2.5 22.6 + - - +
795H LYS* 3.6 4.9 - - - +
797H ARG* 1.3 76.5 - - - +
799H LYS* 1.3 66.5 + - + +
801H VAL* 3.2 3.4 + - - +
802H ILE* 3.0 49.6 + - + +
811H ILE* 5.6 0.5 - - - +
818H ASP* 2.5 44.0 + - - -
844H TYR* 4.0 12.7 - + + -
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Residues in contact with LYS 799 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795H LYS* 2.9 46.6 + - - +
796H GLN* 3.6 8.5 - - - +
798H TYR* 1.3 78.5 - - + +
800H MET* 1.3 60.7 + - - +
802H ILE* 3.8 10.9 - - + +
803H GLU* 2.9 50.8 + - + +
808H GLN* 5.6 4.5 - - - +
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Residues in contact with MET 800 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796H GLN 2.9 19.7 + - - +
797H ARG* 3.6 22.7 - - + +
799H LYS* 1.3 79.0 - - + +
801H VAL* 1.3 63.5 + - + +
803H GLU* 3.5 6.3 + - - +
804H ALA* 2.9 30.1 + - + +
874H GLU* 3.6 41.7 - - + +
881H ARG* 6.2 0.9 - - - +
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Residues in contact with VAL 801 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787H ILE* 5.4 2.9 - - + -
797H ARG* 2.9 23.1 + - + +
798H TYR 3.6 4.3 - - - +
800H MET* 1.3 85.4 - - + +
802H ILE* 1.3 64.5 + - + +
804H ALA* 3.2 8.6 + - - +
805H CYS* 3.0 21.5 + - - +
840H ALA* 3.7 28.9 - - + +
843H LEU* 3.7 27.1 - - + +
844H TYR* 3.6 33.0 - - + +
874H GLU* 6.0 1.1 - - - +
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Residues in contact with ILE 802 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787H ILE* 5.2 11.2 - - + -
798H TYR* 3.0 61.0 + - + +
799H LYS* 3.8 6.7 - - + +
800H MET 3.2 0.4 - - - -
801H VAL* 1.3 80.2 - - + +
803H GLU* 1.3 51.6 + - - +
805H CYS* 3.0 8.3 + - - +
806H SER 2.5 32.1 + - - -
807H LEU* 3.3 9.4 + - + -
808H GLN* 3.1 40.2 - - + +
811H ILE* 3.6 23.1 - - + -
840H ALA* 6.0 2.2 - - + -
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Residues in contact with GLU 803 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799H LYS* 2.9 35.3 + - + +
800H MET* 4.0 5.3 - - - +
802H ILE* 1.3 71.7 - - - +
804H ALA* 1.3 66.1 + - - +
806H SER* 3.3 10.3 + - - +
808H GLN* 4.4 21.3 + - + +
866H HIS* 3.5 22.2 + - - -
870H ALA* 4.7 0.8 - - - +
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Residues in contact with ALA 804 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800H MET* 2.9 16.7 + - + +
801H VAL* 3.2 13.7 - - - +
802H ILE 3.1 0.2 - - - -
803H GLU* 1.3 78.8 - - - +
805H CYS* 1.3 60.7 + - - +
806H SER* 3.4 1.7 + - - -
843H LEU* 4.5 8.1 - - + -
866H HIS* 4.0 4.3 - - - +
867H LEU* 3.4 26.0 + - - -
870H ALA* 3.9 13.0 - - + +
871H GLY* 3.8 27.4 - - - +
874H GLU* 6.2 0.9 - - + -
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Residues in contact with CYS 805 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801H VAL 3.0 12.2 + - - +
802H ILE* 3.7 7.2 - - - +
804H ALA* 1.3 74.9 - - - +
806H SER* 1.3 76.1 + - - +
807H LEU* 4.5 8.1 - - + +
836H ARG* 3.3 52.1 - - + +
839H VAL* 4.3 0.7 - - - -
840H ALA* 3.9 11.0 - - + -
843H LEU* 3.7 27.4 - - - -
863H LEU* 4.8 0.5 - - - +
867H LEU* 4.1 21.3 - - - +
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Residues in contact with SER 806 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802H ILE 2.5 14.0 + - - -
803H GLU* 3.3 8.0 + - - +
804H ALA 3.2 2.7 + - - -
805H CYS* 1.3 82.3 + - - +
807H LEU* 1.3 59.0 - - - +
808H GLN* 3.4 3.6 - - - +
809H PRO* 3.6 14.1 - - - +
810H ASP* 5.0 2.6 - - - +
836H ARG* 4.6 4.3 + - - -
863H LEU* 4.1 22.9 + - - +
866H HIS* 3.3 37.1 + - - +
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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