Contacts of the strand formed by residues 846 - 854 (chain K) in PDB entry 6R8Y
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 GLY 846 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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771K PHE* 5.0 1.5 - - - -
811K GLU* 4.4 0.2 - - - -
833K THR* 3.6 10.3 - - - -
834K ALA* 4.2 4.0 - - - -
835K MET* 4.0 6.0 - - - +
845K GLN* 1.3 77.4 - - - +
847K ARG* 1.3 65.6 + - - +
865K GLU* 3.6 8.3 - - - +
866K VAL* 2.9 36.2 + - - +
868K GLY 3.5 11.6 + - - -
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Residues in contact with ARG 847 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766K SER* 3.9 13.1 + - - -
768K SER* 3.1 23.6 + - - -
770K LEU* 4.5 6.3 - - + +
771K PHE* 3.4 35.0 - - + -
807K PHE* 4.2 17.2 - - - -
808K LEU* 3.7 18.2 - - - +
811K GLU* 3.1 29.1 + - - +
831K VAL 3.7 1.2 - - - +
832K GLY* 3.4 2.9 - - - -
833K THR* 2.9 36.8 + - - +
846K GLY* 1.3 74.5 - - - +
848K ILE* 1.3 62.0 + - - +
849K VAL* 3.7 23.1 - - + +
851K PHE* 6.2 0.2 - - - -
863K GLU* 2.7 40.7 + - - -
864K LYS 3.3 9.4 - - - +
865K GLU* 4.9 0.4 - - - -
866K VAL* 4.6 0.6 - - - +
870K VAL* 3.9 3.9 - - - +
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Residues in contact with ILE 848 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830K ILE* 3.7 24.9 - - + -
831K VAL 3.4 4.5 - - - +
847K ARG* 1.3 74.6 - - - +
849K VAL* 1.3 65.7 + - - +
863K GLU* 3.2 4.5 - - - +
864K LYS* 2.8 38.7 + - + +
866K VAL* 5.2 2.2 - - + +
870K VAL* 4.0 22.4 - - + -
873K MET* 4.2 4.3 - - - -
880K LEU* 4.0 5.4 - - + -
882K ALA* 4.1 17.7 - - + -
884K ILE* 4.8 2.5 - - + -
891K TYR* 3.5 41.1 - - + +
899K LEU* 3.5 25.7 - - + +
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Residues in contact with VAL 849 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768K SER* 5.2 0.2 - - - +
807K PHE* 5.3 0.9 - - + -
829K PHE 3.7 1.4 - - - +
830K ILE* 3.3 4.1 - - - -
831K VAL* 2.9 48.6 + - + +
833K THR* 4.9 4.0 - - + -
847K ARG* 3.7 42.6 - - + +
848K ILE* 1.3 79.9 - - - +
850K VAL* 1.3 65.8 + - - +
851K PHE* 3.5 31.1 + - + -
860K THR* 4.6 7.2 - - + -
862K ALA 3.6 9.6 - - - +
863K GLU* 4.0 11.4 - - + -
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Residues in contact with VAL 850 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821K LEU* 5.1 1.8 - - + -
828K TYR* 3.3 49.1 - - + -
829K PHE 3.6 2.5 - - - -
830K ILE* 4.0 24.7 - - + -
849K VAL* 1.3 74.9 - - - +
851K PHE* 1.3 59.0 + - - +
860K THR* 3.9 1.9 - - - -
861K VAL* 2.9 24.6 + - + -
862K ALA* 2.9 25.3 + - + +
893K TRP* 4.6 13.7 - - + -
899K LEU* 4.2 27.4 - - + -
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Residues in contact with PHE 851 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766K SER* 5.4 0.4 - - - -
791K LEU* 4.6 5.8 - - + -
805K HIS* 3.5 39.5 - + - -
807K PHE* 4.1 9.0 - + - -
828K TYR* 3.1 12.9 - - - +
829K PHE* 2.8 39.3 + - + +
831K VAL* 3.5 27.4 - - + -
847K ARG* 6.2 0.4 - - - -
849K VAL* 3.5 20.6 - - + -
850K VAL* 1.3 73.2 - - - +
852K GLN* 1.3 60.5 + - - +
858K LEU* 3.7 43.3 - - + -
859K GLN 3.3 9.4 - - - +
860K THR* 3.4 32.1 - - + -
861K VAL* 4.4 0.2 - - - -
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Residues in contact with GLN 852 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826K ASN* 3.2 42.8 + - - +
827K THR 3.9 14.8 + - - +
828K TYR* 3.7 16.1 + - + +
851K PHE* 1.3 74.1 - - - +
853K TYR* 1.3 70.6 + - - +
854K SER* 3.8 8.5 + - - +
857K LYS 3.6 1.0 - - - +
858K LEU* 3.4 5.8 - - - -
859K GLN* 2.9 44.7 + - - +
861K VAL* 3.8 12.8 - - + +
897K LYS* 5.5 1.9 + - - -
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Residues in contact with TYR 853 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727K GLN* 4.1 15.4 + - - +
730K SER* 3.6 34.2 + - - -
732K CYS* 4.5 7.9 - - - -
793K ILE* 4.1 30.1 - - + -
802K LEU* 4.3 17.3 - - - +
803K HIS* 5.0 1.6 - - + -
827K THR 4.7 3.5 + - - +
829K PHE* 4.3 5.9 - + + +
851K PHE 4.5 0.2 + - - -
852K GLN* 1.3 79.1 + - - +
854K SER* 1.3 68.6 + - - +
856K GLY* 3.3 43.2 + - - -
857K LYS* 3.2 16.4 - - - -
858K LEU* 3.7 16.3 - - + +
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Residues in contact with SER 854 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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852K GLN* 3.8 8.9 + - - +
853K TYR* 1.3 81.9 - - - +
855K ASP* 1.3 73.2 + - - +
856K GLY 3.2 2.7 - - - +
857K LYS* 3.0 20.5 + - - +
859K GLN* 3.2 30.1 + - - +
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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