Contacts of the helix formed by residues 804 - 822 (chain K) in PDB entry 6R1U
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 THR 804 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440K ASN* 3.8 16.8 - - + +
795K GLU* 4.0 1.0 - - - +
801K PHE* 3.9 5.4 + - - +
802K PRO 2.9 12.2 + - - +
803K GLN* 1.3 79.4 - - - +
805K VAL* 1.3 60.5 + - - +
806K THR* 3.7 10.2 + - - -
807K GLY* 2.9 24.4 + - - -
808K ALA* 2.8 29.6 + - - +
901K FAD 3.4 18.4 + - - +
3M THR* 5.8 3.4 - - - +
4M MET* 3.7 23.8 - - + -
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Residues in contact with VAL 805 (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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392K PRO* 4.0 17.8 - - + +
421K VAL* 3.9 13.5 - - + -
436K ALA* 3.5 32.1 - - + -
447K VAL* 4.8 4.0 - - + -
450K MET* 6.6 0.2 - - + -
579K TYR* 3.6 35.2 - - + -
582K ILE* 6.5 0.9 - - + -
583K ILE* 5.7 2.5 - - + -
804K THR* 1.3 71.4 - - - +
806K THR* 1.3 54.4 + - - +
808K ALA* 3.2 2.5 + - - +
809K TYR* 2.7 37.4 + - + +
901K FAD 3.0 27.8 + - - +
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Residues in contact with THR 806 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439K VAL* 4.9 1.6 - - - +
440K ASN 5.9 0.2 + - - -
445K ASN* 2.6 38.5 + - - +
446K PRO* 3.8 10.3 - - + -
447K VAL* 3.2 14.2 - - - +
568K PHE* 3.7 35.2 - - + -
579K TYR* 5.0 1.9 + - - -
801K PHE* 5.4 0.2 - - + -
804K THR* 3.2 9.8 - - - +
805K VAL* 1.3 79.6 - - - +
807K GLY* 1.3 57.9 + - - +
809K TYR* 3.3 6.8 + - - +
810K LEU* 2.8 33.5 + - + +
901K FAD 4.7 0.4 + - - -
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Residues in contact with GLY 807 (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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795K GLU* 4.7 1.6 - - - -
798K ASN* 2.9 28.8 + - - +
801K PHE* 3.1 33.7 - - - -
804K THR* 2.9 14.0 + - - -
806K THR* 1.3 76.6 - - - +
808K ALA* 1.3 57.6 + - - +
810K LEU* 4.6 0.9 - - - -
811K SER* 3.0 17.3 + - - -
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Residues in contact with ALA 808 (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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392K PRO* 3.9 6.5 - - + -
393K ALA* 3.3 10.2 - - + +
795K GLU* 3.8 11.5 - - - +
804K THR 2.8 16.8 + - - +
805K VAL 3.6 3.8 - - - +
807K GLY* 1.3 73.4 - - - +
809K TYR* 1.3 65.3 + - - +
811K SER* 2.7 24.3 + - - -
812K GLY 3.2 5.2 + - - -
901K FAD 3.2 41.3 - - - +
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Residues in contact with TYR 809 (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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364K THR* 3.1 10.9 + - + +
365K GLY* 3.0 30.9 + - - -
392K PRO* 3.9 9.9 - - + +
396K ALA* 3.3 39.2 - - + +
400K GLN* 4.3 2.5 + - + -
446K PRO* 3.6 35.0 - - + -
447K VAL* 6.1 0.4 - - + -
449K LEU* 5.6 0.6 - - + +
450K MET* 3.8 30.3 - - + -
586K LEU* 4.3 17.9 - - + -
805K VAL* 2.7 24.2 + - + +
806K THR* 3.4 6.1 - - - +
808K ALA* 1.3 74.1 - - - +
810K LEU* 1.3 66.9 + - + +
812K GLY 3.1 2.8 + - - -
813K VAL* 3.1 37.5 + - + +
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Residues in contact with LEU 810 (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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282K LEU* 4.1 14.8 - - + -
446K PRO* 3.5 23.3 - - + -
568K PHE* 3.7 30.5 - - + -
798K ASN* 3.9 12.8 - - - +
801K PHE* 3.8 20.4 - - + -
806K THR* 2.8 26.9 + - + +
808K ALA 3.2 0.2 - - - -
809K TYR* 1.3 79.2 - - + +
811K SER* 1.3 61.5 + - - +
813K VAL* 3.3 5.2 + - + +
814K ARG* 2.9 28.8 + - - +
220L PHE* 4.1 8.2 - - + -
221L LEU* 4.2 25.8 - - + +
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Residues in contact with SER 811 (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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793K ALA* 3.5 1.7 - - - +
794K GLY 2.8 27.5 + - - -
797K THR* 3.5 22.0 - - - -
798K ASN* 3.9 5.1 - - - +
807K GLY 3.0 14.0 + - - -
808K ALA 2.7 19.4 + - - -
810K LEU* 1.3 76.5 - - - +
812K GLY* 1.3 57.0 + - - +
814K ARG* 3.4 22.0 + - - +
815K GLU* 3.1 34.5 + - - +
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Residues in contact with GLY 812 (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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393K ALA 3.5 24.5 - - - -
397K ALA* 3.4 22.6 - - - +
793K ALA* 4.2 6.3 - - - -
808K ALA 3.2 2.4 + - - -
809K TYR 3.1 7.7 + - - -
811K SER* 1.3 80.8 + - - +
813K VAL* 1.3 58.5 + - - +
815K GLU* 3.3 1.0 + - - -
816K ALA* 2.9 26.0 + - - +
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Residues in contact with VAL 813 (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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358K ARG 4.7 0.9 - - - +
359K LYS 3.7 7.2 - - - +
360K GLY* 3.6 32.3 - - - +
364K THR* 4.6 0.9 - - - +
396K ALA* 4.5 0.9 - - + -
400K GLN* 4.0 25.1 - - + +
809K TYR* 3.1 48.7 + - + +
810K LEU* 3.6 9.4 - - + +
812K GLY* 1.3 75.4 - - - +
814K ARG* 1.3 63.9 + - - +
816K ALA* 3.3 2.3 + - - +
817K SER* 3.0 22.9 + - - -
221L LEU* 4.1 13.7 - - + -
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Residues in contact with ARG 814 (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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783K ALA* 3.8 10.8 - - - +
792K PHE 3.0 23.0 + - - -
797K THR* 2.9 48.8 + - - -
798K ASN* 4.1 5.5 - - - +
810K LEU 2.9 17.5 + - - +
811K SER* 3.4 22.0 - - - +
813K VAL* 1.3 77.6 - - - +
815K GLU* 1.3 79.6 + - - +
817K SER* 3.3 8.5 + - - -
818K LYS* 3.1 29.4 + - - +
220L PHE* 4.3 11.5 - - + -
221L LEU* 4.4 12.1 - - + +
224L GLN* 3.4 45.0 - - + +
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Residues in contact with GLU 815 (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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624K LEU* 3.9 21.5 - - + -
783K ALA 4.0 2.8 - - - +
791K PHE* 3.4 29.6 - - - +
792K PHE 3.3 24.5 + - - +
793K ALA* 3.7 7.0 - - + -
811K SER 3.1 16.6 + - - +
812K GLY 3.9 3.4 - - - +
813K VAL 3.3 0.2 - - - -
814K ARG* 1.3 101.0 + - - +
816K ALA* 1.3 60.6 + - - +
818K LYS* 2.8 26.9 + - - +
819K ILE* 2.8 41.2 + - + +
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Residues in contact with ALA 816 (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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397K ALA* 4.0 12.6 - - - +
400K GLN* 3.5 31.2 - - + -
401K LEU* 3.7 19.4 - - + +
404K PHE* 4.5 5.4 - - + -
812K GLY 2.9 18.1 + - - +
813K VAL 3.6 4.3 - - - +
815K GLU* 1.3 77.2 - - - +
817K SER* 1.3 55.7 + - - +
819K ILE* 4.5 0.7 - - - -
820K ALA* 2.9 32.8 + - - +
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Residues in contact with SER 817 (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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358K ARG* 3.2 45.6 + - - +
359K LYS* 3.6 33.7 + - - +
813K VAL 3.0 12.0 + - - -
814K ARG* 3.4 12.1 - - - -
816K ALA* 1.3 76.0 - - - +
818K LYS* 1.3 63.0 + - - +
820K ALA* 3.3 0.7 + - - -
821K ALA* 3.1 20.4 + - - +
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Residues in contact with LYS 818 (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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783K ALA* 3.7 17.8 + - - +
784K GLU* 5.1 1.4 - - - +
785K ASP* 4.7 15.2 + - - +
791K PHE* 4.2 14.8 - - + -
814K ARG* 3.1 28.0 + - - +
815K GLU* 2.8 42.9 + - - +
817K SER* 1.3 79.5 - - - +
819K ILE* 1.3 62.6 + - - +
821K ALA* 3.5 12.6 + - - +
822K PHE* 3.1 22.7 - - + -
224L GLN* 4.3 18.7 + - + -
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Residues in contact with ILE 819 (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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383K LYS* 3.3 25.3 - - + -
385K VAL* 3.9 41.1 - - + -
401K LEU* 4.0 19.5 - - + -
622K LYS* 4.5 8.1 - - + -
624K LEU* 4.3 13.0 - - + -
791K PHE* 3.8 42.4 - - + -
815K GLU* 2.8 29.2 + - + +
816K ALA 3.9 3.4 - - - +
818K LYS* 1.3 72.9 - - - +
820K ALA* 1.3 63.2 + - - +
822K PHE* 3.4 15.8 + - - +
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Residues in contact with ALA 820 (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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358K ARG* 4.0 12.1 - - + -
376K LEU* 4.5 4.9 - - + -
380K TYR* 3.2 21.2 - - + +
383K LYS* 4.4 4.0 + - - +
404K PHE* 3.7 27.6 - - + -
406K ILE* 3.9 18.6 - - + -
816K ALA 2.9 19.1 + - - +
817K SER 3.9 3.4 - - - +
819K ILE* 1.3 74.9 - - - +
821K ALA* 1.3 66.0 + - - +
822K PHE 3.4 4.5 + - - -
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Residues in contact with ALA 821 (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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358K ARG* 3.5 32.3 - - - +
380K TYR* 5.0 4.0 - - - -
817K SER 3.1 12.6 + - - +
818K LYS* 3.6 9.0 - - - +
819K ILE 3.3 0.4 - - - -
820K ALA* 1.3 77.6 - - - +
822K PHE* 1.3 62.4 + - + +
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Residues in contact with PHE 822 (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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383K LYS* 3.6 21.9 + - - -
622K LYS* 3.8 23.3 - - - -
785K ASP* 5.2 3.4 - - - -
788K GLY* 3.6 24.2 - - - -
791K PHE* 3.4 32.5 - + - -
818K LYS* 3.1 26.0 - - + -
819K ILE 3.4 11.1 + - - +
820K ALA 3.2 3.0 - - - -
821K ALA* 1.3 85.6 - - + +
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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