Contacts of the helix formed by residues 830 - 844 (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 SER 830 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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829F LEU* 1.3 81.8 - - - +
831F GLY* 1.3 65.3 + - - +
832F GLY* 3.0 9.9 + - - -
833F GLN* 3.1 22.5 + - - -
834F ARG 3.1 7.8 + - - -
2001F ADP 5.0 20.6 + - - -
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Residues in contact with GLY 831 (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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776F PRO* 4.2 3.3 - - - +
829F LEU 3.6 2.0 + - - -
830F SER* 1.3 72.4 - - - +
832F GLY* 1.3 56.8 + - - +
834F ARG* 3.4 28.8 - - - +
835F GLN* 2.8 29.1 + - - +
858F ALA* 3.8 8.6 - - - +
1427F ASP* 5.4 9.0 + - - -
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Residues in contact with GLY 832 (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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830F SER* 3.0 7.0 - - - -
831F GLY* 1.3 73.6 - - - +
833F GLN* 1.3 64.9 - - - +
835F GLN* 3.2 3.8 + - - +
836F ARG* 3.0 41.4 + - - +
858F ALA* 4.2 15.3 - - - +
859F LEU* 4.2 4.4 - - - +
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Residues in contact with GLN 833 (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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807F LEU* 4.3 7.4 - - + -
810F ASP* 3.2 38.7 + - + +
813F ILE* 4.6 6.7 - - - +
814F LEU* 4.6 10.0 - - - +
829F LEU* 3.4 42.4 - - + +
830F SER* 3.1 11.8 + - - +
832F GLY* 1.3 73.4 - - - +
834F ARG* 1.3 64.2 + - - +
836F ARG* 3.0 28.0 + - - +
837F ILE* 2.9 36.4 + - + +
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Residues in contact with ARG 834 (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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775F LYS* 5.7 3.2 - - - +
776F PRO* 2.6 62.2 + - + +
777F TRP* 4.6 4.7 - - - +
778F LEU* 4.1 25.7 - - + +
829F LEU* 3.5 27.1 - - + -
830F SER 3.1 9.3 + - - +
831F GLY* 3.4 23.6 - - - +
833F GLN* 1.3 77.3 - - - +
835F GLN* 1.3 57.8 + - - +
837F ILE* 3.7 7.0 - - - +
838F SER* 2.9 24.1 + - - -
841F ARG* 4.5 2.3 + - - -
1427F ASP* 5.3 7.5 + - - -
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Residues in contact with GLN 835 (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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772F ALA* 5.1 1.9 - - - +
773F SER 4.7 5.3 + - - +
774F GLN 4.3 7.7 + - - -
776F PRO* 3.7 26.9 - - + +
831F GLY 2.8 17.6 + - - +
832F GLY 3.7 4.3 - - - +
834F ARG* 1.3 75.5 - - - +
836F ARG* 1.3 64.4 + - - +
838F SER* 3.2 12.2 + - - -
839F VAL* 2.9 33.5 + - + +
853F ASP 4.8 1.7 + - - +
854F ASP 3.5 15.8 + - - -
855F PRO* 3.4 32.2 - - + +
857F SER* 5.2 2.2 - - - -
858F ALA* 4.0 22.3 - - + +
859F LEU* 4.9 6.3 - - + -
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Residues in contact with ARG 836 (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 CYS* 3.3 45.6 + - + +
806F SER 4.6 2.6 + - - -
807F LEU* 3.7 17.0 - - + +
810F ASP* 2.2 32.6 + - - -
832F GLY* 3.0 36.6 + - - +
833F GLN* 3.0 26.4 - - - +
835F GLN* 1.3 75.3 - - - +
837F ILE* 1.3 57.9 + - - +
839F VAL* 3.3 6.2 + - - +
840F ALA* 2.9 24.0 + - - +
859F LEU* 3.3 27.0 - - + +
863F LEU* 3.2 32.5 - - - +
867F LEU* 4.7 4.0 - - + -
1380F THR* 6.0 1.8 + - - +
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Residues in contact with ILE 837 (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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778F LEU* 5.6 3.8 - - + -
783F VAL* 5.2 13.2 - - + -
786F ASN* 3.9 17.9 - - - +
787F ILE* 4.1 11.6 - - + +
807F LEU* 3.9 26.2 - - + -
822F ILE* 5.7 5.4 - - + -
829F LEU* 5.0 11.9 - - + -
833F GLN* 2.9 32.5 + - + +
834F ARG* 3.7 7.0 - - - +
836F ARG* 1.3 75.0 - - - +
838F SER* 1.3 66.1 + - - +
840F ALA* 3.1 7.7 + - - +
841F ARG* 2.9 50.8 + - - +
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Residues in contact with SER 838 (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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772F ALA* 3.2 31.6 - - - +
773F SER* 4.1 5.7 + - - -
776F PRO* 4.2 16.6 - - - +
777F TRP 4.6 2.8 + - - -
834F ARG 2.9 15.7 + - - -
835F GLN* 3.5 16.6 + - - -
837F ILE* 1.3 76.2 - - - +
839F VAL* 1.3 63.6 + - - +
841F ARG* 3.1 35.4 + - - +
842F ALA 3.6 2.8 + - - -
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Residues in contact with VAL 839 (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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772F ALA* 4.6 0.9 - - + -
805F CYS* 4.4 2.0 - - - -
835F GLN* 2.9 27.4 + - - +
836F ARG 3.6 7.0 - - - +
837F ILE 3.2 0.2 - - - -
838F SER* 1.3 75.5 - - - +
840F ALA* 1.3 63.8 + - - +
842F ALA* 3.1 6.4 + - - +
843F LEU* 2.9 46.9 + - + +
852F LEU* 4.2 23.3 - - + -
855F PRO* 3.6 31.6 - - + +
867F LEU* 4.1 27.1 - - + -
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Residues in contact with ALA 840 (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* 4.6 20.1 - - + +
801F VAL* 3.7 24.9 - - + -
802F ILE* 6.0 2.7 - - + -
805F CYS* 3.9 7.6 - - + -
807F LEU* 6.1 2.0 - - + -
836F ARG 2.9 14.6 + - - +
837F ILE* 3.5 12.1 - - - +
839F VAL* 1.3 77.2 - - - +
841F ARG* 1.3 63.1 + - - +
843F LEU* 4.0 3.6 - - - -
844F TYR* 2.9 29.5 + - - +
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Residues in contact with ARG 841 (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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771F TYR 4.8 8.3 - - - +
777F TRP* 2.8 28.1 + - - -
778F LEU* 3.1 24.5 - - - +
779F LEU* 3.6 8.8 - - - +
786F ASN* 2.8 61.2 + - - +
787F ILE* 4.4 11.6 - - - +
789F PHE* 5.5 8.2 - - + +
834F ARG 4.5 0.8 + - - -
837F ILE* 2.9 41.0 + - + +
838F SER* 3.2 26.2 - - - +
839F VAL 3.1 0.4 - - - -
840F ALA* 1.3 78.3 - - - +
842F ALA* 1.3 58.8 + - - +
844F TYR 4.1 0.5 - - - -
845F GLN* 3.2 29.1 + - - +
1216F PHE* 4.9 12.1 - - + -
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Residues in contact with ALA 842 (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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770F ALA* 3.6 22.9 - - + +
771F TYR 4.0 16.4 + - - +
838F SER 3.6 1.7 + - - +
839F VAL 3.1 7.5 + - - +
841F ARG* 1.3 78.2 - - - +
843F LEU* 1.3 54.5 + - + +
845F GLN* 3.1 14.1 - - - +
850F VAL* 4.0 13.6 - - + +
851F PHE 4.0 8.7 - - - +
852F LEU* 4.4 9.0 - - + -
881F ARG* 2.6 28.9 + - - -
1216F PHE* 5.1 0.7 - - - -
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Residues in contact with LEU 843 (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* 3.7 20.0 - - + +
804F ALA* 4.5 14.4 - - + -
805F CYS* 3.7 21.8 - - - -
839F VAL* 2.9 40.6 + - + +
840F ALA* 3.1 5.1 + - - +
842F ALA* 1.3 78.1 - - + +
844F TYR* 1.3 58.0 + - - +
845F GLN 3.0 0.7 + - - -
846F HIS 3.6 0.2 + - - -
850F VAL* 5.6 2.2 - - + -
852F LEU* 5.6 3.4 - - + -
867F LEU* 5.3 3.6 - - + -
871F GLY* 4.8 11.2 - - - +
872F ILE* 5.4 2.7 - - + -
874F GLU* 5.6 1.3 - - - +
875F LEU* 3.8 35.4 - - + -
881F ARG* 2.4 35.0 + - - +
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Residues in contact with TYR 844 (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* 3.5 27.6 - - + +
788F ILE* 3.6 32.5 - - + +
791F SER* 3.7 15.4 + - - -
792F PRO 2.8 27.1 + - - -
793F PHE* 3.1 19.7 - + - -
794F ASN* 3.1 8.4 + - + -
797F ARG* 3.8 40.2 - - + -
798F TYR* 4.0 14.6 - + + -
801F VAL* 3.6 16.5 - - + +
840F ALA 2.9 17.4 + - - +
841F ARG 4.1 0.9 - - - +
843F LEU* 1.3 72.6 - - - +
845F GLN* 1.3 62.5 + - - +
846F HIS* 3.1 7.1 + - - +
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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