Contacts of the helix formed by residues 824 - 838 (chain O) in PDB entry 5X0X
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 PRO 824 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15J T 4.4 6.7 - - - +
823O VAL* 1.3 90.3 - - + +
825O LEU* 1.3 67.4 + - - +
826O SER* 3.5 3.1 - - - +
827O THR* 2.4 46.5 + - + +
828O LEU 3.2 4.0 + - - -
831O TRP* 5.4 0.4 - - - +
873O PHE* 3.3 23.6 - - + -
894O ASP* 4.7 5.6 - - + -
895O GLU* 3.8 33.7 - - + +
1168O LEU* 5.1 7.9 - - + -
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Residues in contact with LEU 825 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J T 3.1 60.4 + - - +
16J C 4.7 8.5 - - - +
824O PRO* 1.3 68.5 - - - +
826O SER* 1.3 69.0 + - - +
828O LEU* 2.7 28.2 + - + +
829O SER* 4.0 1.9 + - - -
847O PHE 5.5 6.1 - - - +
848O LYS* 5.9 6.1 - - + -
872O THR* 3.6 28.8 - - + +
873O PHE* 5.1 0.8 - - - -
875O TYR* 5.7 2.5 - - + -
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Residues in contact with SER 826 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J T 3.9 5.7 + - - -
825O LEU* 1.3 80.8 + - - +
827O THR* 1.3 76.5 + - - +
828O LEU 3.2 0.7 + - - -
829O SER* 3.2 21.5 + - - -
830O ASN 4.2 0.5 + - - -
1139O SER* 5.9 3.6 - - - -
1168O LEU* 3.2 45.2 - - - +
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Residues in contact with THR 827 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823O VAL* 3.5 5.0 - - - +
824O PRO* 2.4 52.7 + - + +
826O SER* 1.3 88.8 + - - +
828O LEU* 1.3 53.9 + - - +
830O ASN* 2.7 35.2 + - - +
831O TRP* 2.9 25.5 + - - -
1168O LEU* 5.5 3.6 - - + -
1169O GLY* 6.0 3.4 - - - +
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Residues in contact with LEU 828 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823O VAL* 3.5 11.2 - - + -
824O PRO 4.0 0.2 - - - +
825O LEU* 2.7 26.9 + - + +
827O THR* 1.3 74.7 + - - +
829O SER* 1.3 58.1 + - - +
831O TRP* 3.6 11.3 - - - +
832O SER* 2.9 30.3 + - - -
846O SER* 3.6 22.9 - - - +
847O PHE 4.8 6.7 - - - +
848O LYS* 4.7 17.3 - - - +
870O LEU* 3.7 30.7 - - + +
871O THR* 4.0 9.9 - - - -
872O THR* 3.8 23.6 - - + -
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Residues in contact with SER 829 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825O LEU 4.0 1.2 + - - -
826O SER* 3.2 13.6 + - - -
827O THR 3.0 0.6 - - - -
828O LEU* 1.3 79.3 - - - +
830O ASN* 1.3 66.2 + - - +
832O SER* 3.1 8.7 + - - -
833O SER* 2.9 22.1 + - - -
848O LYS* 5.4 5.4 + - - -
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Residues in contact with ASN 830 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799O THR* 4.3 17.0 + - - +
826O SER 4.2 0.2 + - - -
827O THR* 2.7 22.4 + - - +
829O SER* 1.3 74.8 - - - +
831O TRP* 1.3 68.5 + - + +
833O SER* 3.2 8.1 + - - -
834O GLU* 2.9 40.0 + - - +
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Residues in contact with TRP 831 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798O LYS* 6.1 0.2 - - + -
799O THR* 3.4 56.3 - - + -
802O THR* 4.8 12.1 - - + -
803O ILE* 5.2 3.1 - - + -
821O VAL* 6.5 0.9 - - + -
823O VAL* 3.3 23.7 - - + +
824O PRO* 5.4 0.6 - - - +
827O THR* 2.9 48.8 + - - -
828O LEU* 3.6 7.4 - - - +
830O ASN* 1.3 79.1 - - + +
832O SER* 1.3 65.5 + - - +
834O GLU* 2.8 15.4 + - - +
835O PHE* 2.9 38.4 + + + -
870O LEU* 4.2 13.7 - - + -
892O ILE* 6.2 0.4 - - + -
894O ASP* 2.9 35.8 - - + +
922O LEU* 4.8 8.1 - - + -
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Residues in contact with SER 832 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828O LEU* 2.9 20.9 + - - -
829O SER* 3.5 10.1 - - - -
831O TRP* 1.3 71.5 - - - +
833O SER* 1.3 64.3 + - - +
835O PHE* 3.1 13.5 + - - +
836O ALA* 2.9 20.3 + - - +
844O THR* 5.6 3.8 + - - -
846O SER* 6.1 3.4 - - - -
870O LEU* 4.3 9.1 - - - +
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Residues in contact with SER 833 (chain O).
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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829O SER 2.9 12.2 + - - -
830O ASN* 3.3 14.1 - - - -
832O SER* 1.3 75.3 - - - +
834O GLU* 1.3 63.5 + - - +
836O ALA* 2.7 29.2 + - - +
837O LYS* 2.9 28.8 + - - +
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Residues in contact with GLU 834 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799O THR* 3.5 24.2 - - + -
800O ILE* 3.7 12.9 - - - +
803O ILE* 3.5 19.4 - - + +
830O ASN* 2.9 33.6 + - - +
831O TRP* 2.8 11.5 + - + +
833O SER* 1.3 77.8 + - - +
835O PHE* 1.3 59.1 + - + +
837O LYS* 5.0 8.1 - - - +
838O TRP* 3.0 63.1 + - - +
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Residues in contact with PHE 835 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803O ILE* 4.7 18.6 - - + -
806O LEU* 4.7 14.8 - - + -
821O VAL* 5.3 6.1 - - + -
831O TRP* 2.9 58.9 + + + -
832O SER* 3.6 8.5 - - - +
834O GLU* 1.3 76.1 - - + +
836O ALA* 1.3 60.9 + - - +
839O ALA* 2.8 46.7 - - + +
840O PRO* 3.4 2.8 - - - +
842O LEU* 5.9 3.1 - - + -
844O THR* 3.6 38.1 - - + +
868O VAL* 4.3 27.1 - - + -
870O LEU* 4.7 12.1 - - + -
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Residues in contact with ALA 836 (chain O).
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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832O SER 2.9 11.1 + - - +
833O SER* 2.7 20.9 + - - +
835O PHE* 1.3 69.8 - - - +
837O LYS* 1.3 69.3 + - + +
840O PRO* 3.1 19.4 - - - +
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Residues in contact with LYS 837 (chain O).
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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763O VAL* 4.3 7.4 - - - +
764O GLY* 5.2 4.9 + - - -
833O SER* 2.9 25.5 + - - +
834O GLU* 5.0 7.6 - - - +
836O ALA* 1.3 82.4 - - + +
838O TRP* 1.3 89.0 + - + +
840O PRO* 3.3 7.6 - - - +
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Residues in contact with TRP 838 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758O GLN* 4.6 2.0 - - - -
761O ILE 4.1 2.1 - - - +
762O LEU* 3.5 31.0 - - + -
763O VAL* 3.1 50.0 + - - +
764O GLY 3.1 23.6 - - - -
765O GLY* 3.7 22.4 - - - -
766O THR* 4.5 6.3 - - - -
767O LEU* 5.2 2.5 - - + -
800O ILE* 3.5 41.0 - - + +
803O ILE* 4.2 12.1 - - + -
834O GLU* 3.0 42.8 + - - +
837O LYS* 1.3 98.8 - - + +
839O ALA* 1.3 61.1 + - - +
840O PRO* 3.1 8.2 - - - +
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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