Contacts of the helix formed by residues 830 - 844 (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 SER 830 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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829H LEU* 1.3 82.5 - - - +
831H GLY* 1.3 64.5 + - - +
832H GLY* 3.0 9.7 + - - -
833H GLN* 3.1 22.4 + - - -
834H ARG* 3.1 7.8 + - - -
2001H ADP 5.0 21.0 + - - -
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Residues in contact with GLY 831 (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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776H PRO* 4.2 2.8 - - - +
829H LEU 3.6 1.4 + - - -
830H SER* 1.3 71.9 - - - +
832H GLY* 1.3 57.6 + - - +
834H ARG* 3.4 28.2 - - - +
835H GLN* 2.9 28.9 + - - +
858H ALA* 3.8 9.1 - - - +
1427H ASP* 5.4 9.4 + - - -
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Residues in contact with GLY 832 (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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830H SER* 3.0 6.6 - - - -
831H GLY* 1.3 74.3 - - - +
833H GLN* 1.3 63.6 + - - +
835H GLN* 3.2 3.3 + - - +
836H ARG* 3.0 43.3 + - - +
858H ALA* 4.2 16.0 - - - +
859H LEU* 4.2 3.7 - - - +
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Residues in contact with GLN 833 (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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807H LEU* 4.3 7.6 - - + -
810H ASP* 3.2 39.4 + - + +
813H ILE* 4.6 7.1 - - - +
814H LEU* 4.6 8.8 - - - +
829H LEU* 3.4 43.7 - - + +
830H SER* 3.1 12.0 + - - +
832H GLY* 1.3 74.0 - - - +
834H ARG* 1.3 63.3 + - - +
836H ARG* 3.0 27.8 + - - +
837H ILE* 2.9 35.8 + - + +
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Residues in contact with ARG 834 (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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775H LYS* 5.7 3.0 - - - +
776H PRO* 2.6 61.7 + - + +
777H TRP* 4.6 3.7 - - - +
778H LEU* 4.1 25.5 - - + +
829H LEU* 3.5 27.4 - - + +
830H SER 3.1 9.5 + - - +
831H GLY* 3.4 23.6 - - - +
832H GLY 3.1 0.2 - - - -
833H GLN* 1.3 76.5 - - - +
835H GLN* 1.3 57.1 + - - +
837H ILE* 3.3 6.4 + - - +
838H SER* 2.9 24.4 + - - -
841H ARG* 4.5 2.3 + - - -
1427H ASP* 5.3 7.7 + - - -
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Residues in contact with GLN 835 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772H ALA* 5.1 2.1 - - - +
773H SER 4.8 4.8 + - - +
774H GLN 4.3 7.7 + - - -
776H PRO* 3.7 28.0 - - + +
831H GLY 2.9 17.2 + - - +
832H GLY* 3.2 4.0 + - - +
834H ARG* 1.3 76.0 - - - +
836H ARG* 1.3 64.4 + - - +
838H SER* 3.2 11.4 + - - -
839H VAL* 2.9 33.4 + - + +
853H ASP 4.8 1.7 + - - +
854H ASP 3.5 16.4 + - - -
855H PRO* 3.4 31.4 - - - +
857H SER* 5.2 2.0 - - - -
858H ALA* 4.0 21.4 - - + +
859H LEU* 4.9 6.1 - - + -
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Residues in contact with ARG 836 (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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805H CYS* 3.3 46.3 + - + +
806H SER 4.6 2.2 + - - -
807H LEU* 3.7 16.7 - - + +
810H ASP* 2.2 33.4 + - - -
832H GLY* 3.0 36.4 + - - +
833H GLN* 3.0 26.0 - - - +
835H GLN* 1.3 75.8 - - - +
837H ILE* 1.3 58.6 + - - +
839H VAL* 3.3 6.2 + - - -
840H ALA* 2.9 24.0 + - - +
859H LEU* 3.3 26.4 - - + +
863H LEU* 3.2 31.9 - - - +
867H LEU* 4.7 3.6 - - + -
1380H THR* 6.0 1.2 + - - +
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Residues in contact with ILE 837 (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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778H LEU* 5.6 4.9 - - + -
783H VAL* 5.2 12.8 - - + -
786H ASN* 3.9 18.6 - - - +
787H ILE* 4.1 11.6 - - + +
807H LEU* 3.9 25.4 - - + -
822H ILE* 5.7 5.4 - - + -
829H LEU* 5.0 11.9 - - + -
833H GLN* 2.9 33.9 + - + +
834H ARG* 3.7 6.5 - - - +
836H ARG* 1.3 73.8 - - - +
838H SER* 1.3 64.9 + - - +
840H ALA* 3.1 8.0 + - - +
841H ARG* 2.9 51.0 + - - +
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Residues in contact with SER 838 (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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772H ALA* 3.2 31.1 - - - +
773H SER* 4.1 5.9 + - - -
776H PRO* 4.2 16.2 - - - +
777H TRP 4.6 2.8 + - - -
834H ARG 2.9 14.4 + - - -
835H GLN* 3.2 17.7 + - - -
837H ILE* 1.3 76.3 - - - +
839H VAL* 1.3 61.7 + - - +
841H ARG* 3.1 35.3 + - - +
842H ALA 3.6 2.9 + - - -
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Residues in contact with VAL 839 (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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772H ALA* 5.2 0.9 - - + -
805H CYS* 4.4 2.2 - - - -
835H GLN* 2.9 27.8 + - - +
836H ARG 3.6 7.0 - - - +
838H SER* 1.3 74.3 - - - +
840H ALA* 1.3 64.2 + - - +
842H ALA* 3.1 7.1 + - - +
843H LEU* 2.9 46.9 + - + +
852H LEU* 4.2 22.9 - - + -
855H PRO* 3.6 31.2 - - + +
867H LEU* 4.1 27.4 - - + -
872H ILE* 6.5 0.2 - - + -
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Residues in contact with ALA 840 (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* 4.6 20.1 - - + +
801H VAL* 3.7 24.5 - - + +
802H ILE* 6.0 2.7 - - + -
805H CYS* 3.9 8.0 - - + -
807H LEU* 6.1 2.5 - - + -
836H ARG 2.9 14.5 + - - +
837H ILE* 3.1 12.3 + - - +
839H VAL* 1.3 76.0 - - - +
841H ARG* 1.3 63.1 + - - +
843H LEU* 3.9 4.3 - - - -
844H TYR* 2.9 28.6 + - - +
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Residues in contact with ARG 841 (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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771H TYR 4.8 6.3 - - - +
777H TRP* 2.8 29.2 + - - -
778H LEU* 3.1 22.5 - - - +
779H LEU* 3.6 10.1 - - - +
786H ASN* 2.8 60.5 + - - +
787H ILE* 4.4 11.1 - - - +
789H PHE* 5.5 8.1 - - + +
834H ARG 4.5 0.6 + - - -
837H ILE* 2.9 38.9 + - + +
838H SER* 3.2 26.1 - - - +
839H VAL 3.1 0.4 - - - -
840H ALA* 1.3 78.0 - - - +
842H ALA* 1.3 58.7 + - - +
844H TYR 4.1 0.5 - - - -
845H GLN* 3.2 29.8 + - - +
1216H PHE* 4.9 11.4 - - + -
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Residues in contact with ALA 842 (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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770H ALA* 3.6 22.2 - - + +
771H TYR 4.0 17.0 + - - +
838H SER 3.6 2.6 + - - +
839H VAL 3.1 7.6 + - - +
841H ARG* 1.3 77.4 - - - +
843H LEU* 1.3 54.7 + - + +
845H GLN* 3.1 15.0 - - - +
850H VAL* 4.0 14.0 - - + +
851H PHE 4.0 9.0 - - - +
852H LEU* 4.4 8.5 - - + -
881H ARG* 2.6 28.8 + - - -
1216H PHE* 5.1 0.2 - - - -
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Residues in contact with LEU 843 (chain H).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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801H VAL* 3.7 20.0 - - + +
804H ALA* 4.5 14.6 - - + -
805H CYS* 3.7 21.3 - - - -
839H VAL* 2.9 39.7 + - + +
840H ALA* 3.7 4.5 - - - +
842H ALA* 1.3 76.4 - - + +
844H TYR* 1.3 59.0 + - - +
845H GLN 3.0 0.9 + - - -
846H HIS* 3.6 0.3 + - - -
850H VAL* 5.6 2.0 - - + -
852H LEU* 5.6 4.0 - - + -
867H LEU* 5.3 4.0 - - + -
871H GLY* 4.8 11.4 - - - +
872H ILE* 5.4 2.9 - - + -
874H GLU* 5.6 1.6 - - - +
875H LEU* 3.8 35.0 - - + -
881H ARG* 2.4 34.7 + - - +
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Residues in contact with TYR 844 (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* 3.5 27.6 - - + +
788H ILE* 3.6 33.2 - - + -
791H SER* 3.7 15.8 + - - -
792H PRO 2.8 27.0 + - - -
793H PHE* 3.1 20.0 - + - -
794H ASN* 3.1 7.6 + - + -
797H ARG* 3.8 39.9 - - + -
798H TYR* 4.0 14.6 - + - -
801H VAL* 3.6 15.8 - - + +
840H ALA 2.9 18.1 + - - +
841H ARG 4.1 0.4 - - - -
843H LEU* 1.3 72.0 - - - +
845H GLN* 1.3 62.8 + - - +
846H HIS* 3.1 7.0 + - - +
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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