Contacts of the helix formed by residues 830 - 844 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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829E LEU* 1.3 82.9 - - - +
831E GLY* 1.3 63.0 + - - +
832E GLY* 3.0 9.9 + - - -
833E GLN* 3.1 23.3 + - - +
834E ARG* 3.1 8.4 + - - -
2001E ADP 5.0 20.8 + - - -
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Residues in contact with GLY 831 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776E PRO* 4.2 3.2 - - - +
829E LEU 3.6 2.0 + - - -
830E SER* 1.3 72.4 - - - +
832E GLY* 1.3 56.4 + - - +
834E ARG* 3.4 29.0 - - - +
835E GLN* 2.8 28.4 + - - +
858E ALA* 3.8 9.1 - - - +
1427E ASP* 5.4 8.4 + - - -
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Residues in contact with GLY 832 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830E SER* 3.0 7.0 - - - -
831E GLY* 1.3 75.1 - - - +
833E GLN* 1.3 65.2 + - - +
835E GLN* 3.2 3.9 + - - +
836E ARG* 3.0 42.8 + - - +
858E ALA* 4.2 15.3 - - - +
859E LEU* 4.2 4.1 - - - +
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Residues in contact with GLN 833 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807E LEU* 4.3 7.4 - - + -
810E ASP* 3.2 39.6 + - + +
813E ILE* 4.6 7.3 - - - +
814E LEU* 4.6 9.2 - - - +
829E LEU* 3.4 42.6 - - + +
830E SER* 3.1 12.1 + - - +
832E GLY* 1.3 74.3 - - - +
834E ARG* 1.3 62.7 + - - +
836E ARG* 3.0 28.0 + - - +
837E ILE* 2.9 35.4 + - + +
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Residues in contact with ARG 834 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775E LYS* 5.7 3.2 - - - +
776E PRO* 2.6 62.1 + - + +
777E TRP* 4.6 4.3 - - - +
778E LEU* 4.1 25.5 - - + +
829E LEU* 3.5 27.3 - - + +
830E SER 3.1 10.0 + - - +
831E GLY* 3.4 24.0 - - - +
832E GLY 3.1 0.2 - - - -
833E GLN* 1.3 77.0 - - - +
835E GLN* 1.3 57.4 + - - +
837E ILE* 3.3 6.7 + - - +
838E SER* 2.9 23.9 + - - -
841E ARG* 4.5 2.3 + - - -
1427E ASP* 5.3 6.5 + - - -
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Residues in contact with GLN 835 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772E ALA* 5.1 1.7 - - - +
773E SER 4.7 5.3 + - - +
774E GLN 4.3 7.9 + - - -
776E PRO* 3.8 27.6 - - + +
831E GLY 2.8 17.2 + - - +
832E GLY 3.2 4.2 + - - +
834E ARG* 1.3 75.7 - - - +
836E ARG* 1.3 63.9 + - - +
838E SER* 3.2 10.7 + - - -
839E VAL* 2.9 33.5 + - + +
853E ASP 4.8 2.0 + - - +
854E ASP 3.5 16.0 + - - -
855E PRO* 3.4 32.1 - - + +
857E SER* 5.2 2.0 - - - -
858E ALA* 4.0 22.3 - - + +
859E LEU* 4.9 5.8 - - + -
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Residues in contact with ARG 836 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805E CYS* 3.3 44.7 + - + +
806E SER 4.6 2.6 + - - -
807E LEU* 3.7 17.0 - - + +
810E ASP* 2.2 32.7 + - - -
832E GLY* 3.0 36.6 + - - +
833E GLN* 3.0 27.6 - - - +
835E GLN* 1.3 76.0 - - - +
837E ILE* 1.3 57.2 + - - +
839E VAL* 3.3 6.5 + - - +
840E ALA* 2.9 23.6 + - - +
859E LEU* 3.3 26.6 - - + +
863E LEU* 3.2 32.8 - - - +
867E LEU* 4.7 4.0 - - + -
1380E THR* 6.0 1.6 + - - +
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Residues in contact with ILE 837 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778E LEU* 5.6 4.3 - - + -
783E VAL* 5.2 13.0 - - + -
786E ASN* 3.9 19.1 - - - +
787E ILE* 4.1 10.8 - - + -
807E LEU* 3.9 25.8 - - + -
822E ILE* 5.7 5.2 - - + -
829E LEU* 5.0 12.1 - - + -
833E GLN* 2.9 32.3 + - + +
834E ARG* 3.7 7.4 - - - +
836E ARG* 1.3 75.2 - - - +
838E SER* 1.3 65.5 + - - +
840E ALA* 3.1 8.3 + - - +
841E ARG* 2.9 50.3 + - - +
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Residues in contact with SER 838 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772E ALA* 3.2 31.5 - - - +
773E SER* 4.1 5.2 + - - -
776E PRO* 4.2 16.6 - - - +
777E TRP 4.6 2.4 + - - -
834E ARG 2.9 14.0 + - - -
835E GLN* 3.5 17.2 + - - -
837E ILE* 1.3 76.3 - - - +
839E VAL* 1.3 63.0 + - - +
841E ARG* 3.1 35.2 + - - +
842E ALA 3.6 3.1 + - - -
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Residues in contact with VAL 839 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772E ALA* 5.2 1.1 - - + -
805E CYS* 4.3 2.2 - - - -
835E GLN* 2.9 27.4 + - + +
836E ARG 3.6 7.2 - - - +
838E SER* 1.3 74.4 - - - +
840E ALA* 1.3 63.4 + - - +
842E ALA* 3.1 6.6 + - - +
843E LEU* 2.9 46.7 + - + +
852E LEU* 4.2 23.3 - - + -
855E PRO* 3.6 31.9 - - + +
867E LEU* 4.1 26.9 - - + -
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Residues in contact with ALA 840 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787E ILE* 4.6 19.7 - - + -
801E VAL* 3.7 25.7 - - + +
802E ILE* 6.0 2.0 - - + -
805E CYS* 3.9 8.0 - - + -
807E LEU* 6.1 2.0 - - + -
836E ARG 2.9 13.8 + - - +
837E ILE* 3.1 12.8 + - - +
839E VAL* 1.3 76.8 - - - +
841E ARG* 1.3 63.4 + - - +
843E LEU* 4.0 3.8 - - - -
844E TYR* 2.9 28.6 + - - +
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Residues in contact with ARG 841 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771E TYR 4.8 8.1 - - - +
777E TRP* 2.8 28.5 + - - -
778E LEU* 3.1 23.1 - - - +
779E LEU* 3.6 9.6 - - - +
786E ASN* 2.8 59.2 + - - +
787E ILE* 4.4 11.8 - - - +
789E PHE* 5.5 8.5 - - + +
834E ARG 4.5 0.8 + - - -
837E ILE* 2.9 38.5 + - + +
838E SER* 3.2 26.4 - - - +
839E VAL 3.1 0.2 - - - -
840E ALA* 1.3 78.0 - - - +
842E ALA* 1.3 58.9 + - - +
844E TYR 4.1 0.3 - - - -
845E GLN* 3.2 30.0 + - - +
1216E PHE* 4.9 11.7 - - + -
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Residues in contact with ALA 842 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770E ALA* 3.6 22.4 - - + +
771E TYR 4.0 17.5 + - - +
838E SER 3.6 1.5 + - - +
839E VAL 3.1 7.1 + - - +
841E ARG* 1.3 77.3 - - - +
843E LEU* 1.3 55.1 + - + +
845E GLN* 3.1 13.9 - - - +
850E VAL* 4.0 14.4 - - + +
851E PHE 4.0 9.0 - - - +
852E LEU* 4.4 8.3 - - + -
881E ARG* 2.6 28.6 + - - -
1216E PHE* 5.1 0.2 - - - -
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Residues in contact with LEU 843 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801E VAL* 3.7 21.0 - - + +
804E ALA* 4.5 14.6 - - + -
805E CYS* 3.7 21.3 - - - -
839E VAL* 2.9 41.4 + - + +
840E ALA* 3.1 4.5 + - - +
842E ALA* 1.3 77.7 - - + +
844E TYR* 1.3 58.7 + - - +
845E GLN 3.0 0.3 + - - -
850E VAL* 5.6 2.0 - - + -
852E LEU* 5.6 3.8 - - + -
867E LEU* 5.3 4.0 - - + -
871E GLY* 4.8 10.5 - - - +
872E ILE* 5.4 2.7 - - + -
874E GLU* 5.6 1.6 - - - +
875E LEU* 3.8 35.7 - - + -
881E ARG* 2.4 35.6 + - - +
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Residues in contact with TYR 844 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787E ILE* 3.5 28.3 - - + +
788E ILE* 3.6 32.9 - - + +
791E SER* 3.7 16.3 + - - -
792E PRO 2.8 27.0 + - - -
793E PHE* 3.1 19.7 - + - -
794E ASN* 3.1 8.3 + - + -
797E ARG* 3.8 38.1 - - + -
798E TYR* 4.0 15.3 - + + -
801E VAL* 3.6 16.5 - - + +
840E ALA 2.9 17.9 + - - +
841E ARG 4.1 0.2 - - - -
843E LEU* 1.3 72.0 - - - +
845E GLN* 1.3 63.1 + - - +
846E HIS* 3.1 7.5 + - - +
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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