Contacts of the strand formed by residues 899 - 905 (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 LEU 899 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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821K LEU* 5.1 5.2 - - + -
848K ILE* 3.3 52.7 - - + -
850K VAL* 5.2 5.6 - - + -
862K ALA* 5.6 0.8 - - + +
863K GLU 5.7 0.8 + - - -
864K LYS* 3.9 36.2 + - + +
880K LEU* 3.5 21.5 - - + -
891K TYR* 3.4 34.5 - - + -
892K GLU 3.3 6.3 - - - +
893K TRP* 4.1 19.2 - - + +
898K GLU* 1.3 78.6 + - - +
900K ARG* 1.3 61.5 + - - +
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Residues in contact with ARG 900 (chain K).
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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891K TYR* 3.3 4.1 - - - -
892K GLU* 2.4 69.6 + - - +
894K THR* 4.0 23.1 - - + +
899K LEU* 1.3 76.0 - - - +
901K THR* 1.3 96.9 + - + +
902K GLU* 3.5 1.9 + - - +
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Residues in contact with THR 901 (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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889K ARG* 4.9 4.0 - - - +
890K LEU 3.4 7.7 + - - -
891K TYR* 3.7 19.5 - - - -
900K ARG* 1.3 90.7 + - - +
902K GLU* 1.3 62.1 + - - +
903K CYS 3.9 6.1 + - - -
904K ASN* 3.7 24.3 + - - -
425L THR* 5.1 9.4 - - - +
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Residues in contact with GLU 902 (chain K).
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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879K LYS* 3.2 26.2 + - - +
890K LEU* 2.7 31.6 + - + +
892K GLU* 4.3 19.6 - - + +
900K ARG* 3.5 2.6 + - - +
901K THR* 1.3 76.3 - - - +
903K CYS* 1.3 62.2 + - - +
935K TYR* 2.5 30.5 + - - -
940K GLY* 3.4 23.6 - - - +
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Residues in contact with CYS 903 (chain K).
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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888K VAL 4.0 0.3 - - - +
889K ARG* 3.5 0.3 - - - -
890K LEU* 3.0 47.1 + - - +
901K THR* 3.9 1.1 + - - -
902K GLU* 1.3 84.5 - - - +
904K ASN* 1.3 75.6 + - - +
935K TYR* 4.2 3.1 - - - -
940K GLY 3.1 30.7 - - - +
941K ASN* 3.7 22.0 - - + -
942K PHE* 4.2 12.6 - - - +
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Residues in contact with ASN 904 (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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887K THR* 6.0 0.9 - - - -
888K VAL 3.2 6.5 - - - +
889K ARG* 3.2 34.3 - - + +
901K THR* 3.7 12.0 + - - -
903K CYS* 1.3 85.6 - - - +
905K HIS* 1.3 60.9 + - - +
906K TYR* 3.2 39.0 + - + +
941K ASN* 5.9 1.4 - - - +
942K PHE* 4.2 8.6 + - - +
425L THR* 2.9 31.8 + - - +
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Residues in contact with HIS 905 (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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887K THR* 3.4 5.0 - - - -
888K VAL* 2.9 40.1 + - + +
904K ASN* 1.3 73.0 - - - +
906K TYR* 1.3 67.2 + - - +
907K ASN* 3.4 33.8 - - - +
908K ASN* 3.4 14.8 + - - -
931K LEU* 4.3 2.0 - - + -
933K LEU* 3.8 27.3 - - + +
942K PHE* 3.6 28.0 - - + -
944K GLU* 2.7 38.4 + - + +
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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