Contacts of the strand formed by residues 732 - 743 (chain K) in PDB entry 6R90
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 CYS 732 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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726K TYR* 3.4 5.6 - - - -
727K GLN* 3.2 29.1 + - - +
730K SER* 3.0 29.1 - - - -
731K GLN* 1.3 80.3 - - - +
733K PHE* 1.3 66.1 + - - +
793K ILE* 3.9 14.8 - - + -
794K ILE 3.3 13.0 - - - +
795K ASP* 5.3 1.3 - - - -
796K GLN* 4.3 2.7 - - - +
802K LEU* 3.3 24.5 - - - -
829K PHE* 5.5 2.7 - - + -
853K TYR* 3.9 19.3 - - + -
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Residues in contact with PHE 733 (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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363K CYS* 5.9 2.5 - - + -
365K VAL* 3.8 10.3 - - + -
367K LEU* 3.8 18.2 - - + -
376K VAL* 4.0 23.1 - - + -
387K LEU* 6.1 1.3 - - + -
724K ILE* 4.0 24.2 - - + -
725K CYS 3.7 15.5 - - - +
726K TYR* 3.3 31.9 - + + -
732K CYS* 1.3 75.6 - - - +
734K GLY* 1.3 60.6 + - - +
735K VAL* 4.7 1.1 - - + -
792K LEU 3.6 0.7 - - - +
793K ILE* 3.4 8.1 - - - +
794K ILE* 2.9 44.9 + - + +
795K ASP 4.8 1.6 - - - -
796K GLN* 3.4 38.1 - - + -
799K PHE* 4.7 11.9 - + - -
829K PHE* 4.6 3.1 - - - -
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Residues in contact with GLY 734 (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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724K ILE* 3.4 2.1 - - - -
725K CYS 3.2 31.0 + - - +
733K PHE* 1.3 71.8 - - - +
735K VAL* 1.3 67.5 - - - +
791K LEU* 4.1 7.0 - - - -
792K LEU 3.4 6.7 - - - -
793K ILE* 4.9 1.8 - - - -
816K LEU* 3.5 10.0 - - - +
829K PHE* 4.0 24.6 - - - -
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Residues in contact with VAL 735 (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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378K CYS* 4.6 0.9 - - - -
387K LEU* 4.4 15.5 - - + -
717K LEU* 5.1 1.8 - - + -
721K PRO* 4.1 17.0 - - + -
723K LYS 3.4 8.7 - - - +
724K ILE* 3.5 29.2 - - + -
733K PHE* 4.7 1.8 - - + -
734K GLY* 1.3 79.7 - - - +
736K LEU* 1.3 76.3 + - - +
737K SER* 3.7 5.4 + - - -
791K LEU* 3.2 6.3 - - - +
792K LEU* 2.8 41.7 + - + +
794K ILE* 3.6 24.2 - - + -
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Residues in contact with LEU 736 (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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721K PRO* 3.3 4.2 - - - +
722K ARG* 2.9 39.1 + - + -
723K LYS* 3.2 15.6 + - + +
735K VAL* 1.3 75.6 - - - +
737K SER* 1.3 58.2 + - - +
789K HIS* 6.3 0.4 - - - +
790K ASN 3.5 3.6 - - - +
791K LEU* 4.2 9.9 - - + -
807K PHE* 4.2 12.3 - - + -
813K ALA* 3.9 35.0 - - + +
814K LEU 4.0 2.7 - - - -
815K SER 3.6 40.6 - - - +
816K LEU* 3.8 12.9 - - + +
831K VAL* 4.1 21.3 - - + -
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Residues in contact with SER 737 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717K LEU* 5.9 1.6 - - - -
719K GLU* 2.8 35.4 + - - -
720K SER 3.2 12.8 - - - -
721K PRO* 4.4 2.7 - - - -
722K ARG* 4.7 3.1 - - - +
735K VAL* 4.8 2.5 - - - -
736K LEU* 1.3 76.2 - - - +
738K SER* 1.3 62.4 + - - +
789K HIS* 3.3 7.2 + - - +
790K ASN* 2.9 39.3 + - - +
792K LEU* 3.7 20.9 - - - +
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Residues in contact with SER 738 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382K PHE* 5.7 1.7 - - - -
719K GLU* 3.4 4.2 - - - +
720K SER* 2.8 45.1 + - - -
722K ARG* 3.0 30.2 + - - -
737K SER* 1.3 78.1 - - - +
739K ARG* 1.3 61.5 + - - +
787K GLU* 4.6 6.1 + - - -
788K VAL 3.3 10.1 - - - -
789K HIS* 3.9 20.4 - - - -
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Residues in contact with ARG 739 (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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382K PHE* 6.4 0.2 - - - -
718K TYR 5.0 2.2 - - - +
719K GLU* 3.5 20.1 + - + +
738K SER* 1.3 73.2 - - - +
740K ILE* 1.3 67.7 + - - +
741K GLU* 3.2 27.2 + - + -
751K ALA* 4.1 11.2 - - - +
753K ARG 5.5 0.4 - - - -
755K SER* 3.7 11.9 - - - +
757K SER* 2.5 39.5 + - - -
758K THR* 3.5 21.1 - - - +
786K VAL 3.6 0.2 - - - +
787K GLU* 3.4 4.9 - - - -
788K VAL* 2.9 47.5 + - + +
790K ASN* 3.0 24.9 + - - +
806K GLN* 3.3 23.2 - - - +
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Residues in contact with ILE 740 (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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277K GLU* 5.5 2.5 - - - +
382K PHE* 4.0 35.0 - - + -
739K ARG* 1.3 77.7 - - - +
741K GLU* 1.3 69.6 + - - +
751K ALA* 4.0 10.9 - - - +
752K LEU* 4.1 21.4 + - + +
785K GLU* 3.7 44.2 - - + +
786K VAL 3.3 4.9 - - - +
787K GLU* 3.9 28.0 - - + +
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Residues in contact with GLU 741 (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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739K ARG* 3.2 31.2 + - - +
740K ILE* 1.3 78.0 - - - +
742K VAL* 1.3 65.6 + - - +
749K THR* 2.7 39.3 + - - +
750K THR* 3.2 8.5 - - - +
751K ALA* 3.5 24.7 + - + +
752K LEU* 5.2 0.4 - - - +
784K GLU 4.0 0.2 - - - +
785K GLU* 3.2 4.3 - - - +
786K VAL* 2.8 46.1 + - + +
788K VAL* 3.6 21.6 - - + +
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Residues in contact with VAL 742 (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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740K ILE* 4.9 0.7 - - + -
741K GLU* 1.3 78.6 - - - +
743K GLN* 1.3 71.8 + - - +
749K THR* 3.3 6.0 - - - -
750K THR* 2.8 39.2 + - - +
752K LEU* 3.9 29.2 - - + -
783K GLY* 4.5 10.3 - - - +
784K GLU 3.8 6.5 - - - +
785K GLU* 3.7 32.5 - - + +
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Residues in contact with GLN 743 (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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742K VAL* 1.3 84.6 - - - +
744K ASP* 1.3 73.6 + - - +
747K GLY 3.1 19.2 + - - +
748K GLY* 2.5 30.9 + - - -
749K THR* 4.3 8.0 - - - +
750K THR* 4.4 0.2 + - - -
780K THR* 4.0 20.2 + - - +
781K SER 5.4 1.9 - - - +
782K PHE* 4.4 16.1 - - + -
783K GLY* 4.0 22.8 - - - +
784K GLU* 3.9 12.0 + - + +
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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