Contacts of the strand formed by residues 720 - 727 (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 SER 720 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380K GLY 5.4 0.2 - - - -
381K ALA* 3.6 9.0 - - - +
382K PHE* 3.3 39.8 + - - -
719K GLU* 1.3 70.7 - - - +
721K PRO* 1.3 68.4 - - - +
722K ARG* 4.1 8.6 - - - +
737K SER* 3.2 3.8 - - - -
738K SER* 2.8 52.4 + - - -
74L HIS* 5.0 5.4 - - - -
78L LEU* 5.3 2.1 - - - +
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Residues in contact with PRO 721 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360K VAL* 3.4 13.9 - - + +
378K CYS* 3.6 31.6 - - + -
379K SER 3.4 27.4 - - - +
380K GLY 4.2 7.8 - - - +
385K GLY* 4.6 0.4 - - - -
386K SER 3.7 9.4 - - - +
387K LEU* 4.7 0.4 - - + -
717K LEU* 4.4 9.6 - - + -
719K GLU 3.3 10.8 - - - +
720K SER* 1.3 86.8 - - - +
722K ARG* 1.3 66.8 + - - +
735K VAL* 4.1 10.1 - - + -
736K LEU 3.3 9.9 - - - +
737K SER* 4.2 2.4 - - - -
74L HIS* 4.3 4.2 + - - -
78L LEU* 5.7 0.3 - - - +
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Residues in contact with ARG 722 (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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360K VAL* 3.5 20.3 - - - +
361K ASP* 3.6 4.0 - - - +
378K CYS* 4.4 0.7 - - - -
382K PHE* 6.3 0.6 - - - -
720K SER* 4.1 9.2 + - - +
721K PRO* 1.3 77.7 + - - +
723K LYS* 1.3 76.3 + - + +
736K LEU* 2.9 25.4 + - + +
737K SER* 4.8 2.7 - - - +
738K SER* 3.0 25.7 + - - +
787K GLU* 3.2 27.3 + - - -
789K HIS* 3.3 24.6 - - + +
812K TYR* 4.7 5.3 - - - -
813K ALA 4.5 13.6 + - - +
814K LEU* 4.8 10.3 - - - +
71L ARG* 6.3 0.4 - - - +
74L HIS* 3.0 55.2 + - - +
77L LYS* 5.6 0.9 + - - -
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Residues in contact with LYS 723 (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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361K ASP* 3.1 32.9 + - - +
378K CYS* 3.7 7.0 - - - -
722K ARG* 1.3 86.8 - - + +
724K ILE* 1.3 62.3 + - - +
734K GLY 4.7 0.2 - - - -
735K VAL* 3.4 5.0 - - - +
736K LEU* 3.2 28.1 + - + +
814K LEU 3.8 24.5 - - - +
815K SER* 4.5 9.0 - - - +
816K LEU* 4.4 24.5 - - + +
871K TYR 6.1 0.9 - - - -
1006K VAL* 4.3 13.7 - - - +
77L LYS* 4.7 12.9 - - - +
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Residues in contact with ILE 724 (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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361K ASP* 2.9 16.1 + - - +
362K MET* 4.1 25.6 - - - -
363K CYS* 3.2 18.8 - - + -
376K VAL* 3.6 35.0 - - + +
378K CYS* 3.7 16.8 - - - -
387K LEU* 4.7 8.5 - - + -
723K LYS* 1.3 77.4 - - - +
725K CYS* 1.3 73.4 + - - +
733K PHE* 4.0 17.0 - - + -
734K GLY 3.4 14.1 - - - +
735K VAL* 3.5 18.2 - - + -
816K LEU* 4.8 2.5 - - - +
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Residues in contact with CYS 725 (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* 4.3 9.4 - - - -
724K ILE* 1.3 76.0 - - - +
726K TYR* 1.3 60.2 + - - +
727K GLN 4.2 0.2 + - - -
733K PHE* 3.7 9.4 - - - -
734K GLY 3.2 26.5 + - - +
816K LEU* 4.0 23.1 - - - +
817K VAL* 3.9 10.1 - - + -
818K SER* 3.5 41.1 - - - +
829K PHE* 4.0 10.1 - - - -
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Residues in contact with TYR 726 (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* 5.3 3.8 - - + -
365K VAL* 3.5 44.8 - - + +
366K ASP* 5.6 1.3 - - - -
725K CYS* 1.3 75.3 - - - +
727K GLN* 1.3 60.1 + - - +
728K GLU* 3.5 32.9 + - + +
731K GLN* 3.2 16.8 + - - -
732K CYS 3.4 23.3 - - - -
733K PHE* 3.3 30.3 - + + -
796K GLN* 2.3 37.9 + - - -
818K SER* 4.0 12.1 + - - +
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Residues in contact with GLN 727 (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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725K CYS 4.2 0.4 + - - -
726K TYR* 1.3 72.5 - - - +
728K GLU* 1.3 66.2 + - - +
729K VAL* 4.2 11.3 - - + +
730K SER* 3.3 22.6 + - - +
731K GLN* 3.1 15.4 + - - -
732K CYS 3.2 18.6 + - - +
818K SER* 2.6 28.3 + - - +
827K THR* 3.7 24.0 - - + +
828K TYR 3.5 13.7 + - - -
829K PHE* 3.1 53.1 - - + -
853K TYR* 4.0 6.6 + - - +
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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