Contacts of the strand formed by residues 900 - 909 (chain B) in PDB entry 6RQT
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 900 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B LEU* 6.1 0.9 - - + -
808B LYS* 4.4 25.8 - - + -
809B VAL 4.1 6.6 + - - +
810B ASP* 4.9 9.9 + - + -
825B PHE* 4.1 0.6 - - - -
887B LEU* 3.6 1.9 - - - -
888B ILE* 2.6 66.3 + - + +
898B LEU* 3.8 1.5 - - - +
899B GLN* 1.3 90.1 + - - +
901B VAL* 1.3 64.4 + - - +
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Residues in contact with VAL 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808B LYS* 3.3 6.1 - - - +
809B VAL* 3.1 43.4 + - + +
825B PHE* 4.0 25.5 - - + -
845B LEU* 4.0 26.5 - - + -
859B CYS* 6.2 0.2 - - - -
885B VAL* 4.2 9.4 - - + -
886B ASN 3.3 13.9 - - - +
887B LEU* 3.7 20.2 - - + -
900B THR* 1.3 77.3 - - - +
902B SER* 1.3 60.4 + - - +
903B ILE* 3.9 17.2 + - + +
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Residues in contact with SER 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 3.3 35.8 - - - +
737B SER* 4.9 1.7 - - - -
806B THR* 4.5 7.8 - - - +
807B GLU 3.7 8.5 - - - -
808B LYS* 4.1 12.6 - - - -
884B GLU 4.5 0.2 - - - +
886B ASN* 3.3 48.0 + - - +
888B ILE* 3.4 6.3 - - - +
901B VAL* 1.3 71.7 - - - +
903B ILE* 1.3 61.8 + - - +
904B LYS 3.9 1.2 + - - -
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Residues in contact with ILE 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806B THR* 3.3 2.4 - - - -
807B GLU* 2.7 58.3 + - + +
808B LYS* 4.3 7.0 - - - +
809B VAL* 5.6 2.9 - - + -
846B PRO* 3.9 28.9 - - + -
858B ILE* 4.3 17.9 - - + -
882B ILE* 5.0 7.2 - - + -
883B GLU 5.4 0.7 - - - +
884B GLU 3.2 19.3 - - - +
885B VAL* 4.5 8.1 - - + +
901B VAL* 4.5 14.8 - - + +
902B SER* 1.3 73.4 - - - +
904B LYS* 1.3 56.4 + - - +
905B TYR* 4.0 23.7 - - + -
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Residues in contact with LYS 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733B LEU 4.5 6.7 + - - -
734B CYS 5.9 1.1 - - - -
736B ARG 3.2 27.5 + - - -
737B SER* 3.3 24.9 - - - +
738B ASP* 3.9 7.5 + - - +
741B LEU* 5.2 2.2 - - - +
804B TYR* 4.0 29.8 - - + -
806B THR* 3.4 23.7 + - + +
883B GLU* 3.2 26.5 + - + +
884B GLU* 3.3 42.1 + - + +
902B SER 3.9 1.8 + - - +
903B ILE* 1.3 73.1 - - - +
905B TYR* 1.3 78.6 + - - +
906B ARG* 5.5 4.0 - - - +
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Residues in contact with TYR 905 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804B TYR* 3.3 19.8 - - - +
805B LYS* 3.2 37.5 + - + +
807B GLU* 3.4 33.6 + - + -
852B VAL* 4.5 6.2 - - + +
858B ILE* 3.3 33.6 - - - +
874B TYR* 3.4 25.2 - + - -
880B ALA* 5.2 3.6 - - + -
881B TYR 3.9 16.2 - - - +
882B ILE* 3.5 25.2 - - + +
883B GLU* 4.3 1.8 - - - -
903B ILE* 4.0 21.1 - - + -
904B LYS* 1.3 94.5 - - - +
906B ARG* 1.3 64.5 + - - +
907B ILE* 4.7 5.2 - - + -
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Residues in contact with ARG 906 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733B LEU* 5.3 1.2 - - - +
743B ARG* 4.4 15.2 - - - +
802B THR* 4.4 13.8 + - - -
803B MET 3.3 6.1 - - - +
804B TYR* 2.5 44.8 + - + -
881B TYR 3.8 10.5 + - - +
883B GLU* 3.0 43.7 + - + +
884B GLU* 5.5 3.6 + - - -
904B LYS* 5.5 4.7 - - + +
905B TYR* 1.3 76.1 - - - +
907B ILE* 1.3 61.3 + - - +
908B ARG* 2.4 39.5 + - - +
93C GLN* 3.4 45.4 - - - +
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Residues in contact with ILE 907 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802B THR* 3.6 2.9 - - - -
803B MET* 2.4 72.7 + - + +
805B LYS* 3.7 39.5 - - + -
874B TYR* 4.9 2.7 - - - +
878B GLU* 3.9 23.8 - - + +
879B PRO 5.2 2.2 - - - +
880B ALA* 3.7 24.2 - - + -
905B TYR* 4.7 6.3 - - + -
906B ARG* 1.3 79.9 - - - +
908B ARG* 1.3 64.8 - - - +
909B ARG* 3.3 6.0 + - - -
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Residues in contact with ARG 908 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800B TYR* 3.2 18.2 - - - +
802B THR* 4.5 6.3 - - + -
879B PRO 5.9 0.2 + - - -
880B ALA* 5.3 2.7 - - - +
881B TYR* 3.3 39.3 - - + +
883B GLU* 2.4 31.9 + - - +
906B ARG* 2.4 47.6 + - - +
907B ILE* 1.3 76.5 - - - +
909B ARG* 1.3 59.2 + - - +
910B THR* 3.5 8.9 + - - -
93C GLN* 2.4 32.6 + - - -
94C ASP* 3.3 8.9 + - - -
95C GLU* 3.3 28.8 - - + +
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Residues in contact with ARG 909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726B MET* 4.0 25.0 - - - +
742B TYR* 4.9 8.7 + - - -
800B TYR* 3.8 5.3 + - - -
801B GLY 2.9 34.1 + - - +
802B THR* 4.5 2.2 - - - -
803B MET* 2.7 49.6 - - + +
907B ILE* 3.3 9.4 + - + +
908B ARG* 1.3 68.9 - - - +
910B THR* 1.3 66.4 + - - +
911B PRO* 3.7 4.0 - - - +
1035B ARG* 4.2 4.7 + - - +
1037B ARG 5.2 3.8 + - - -
1038B HIS 4.4 6.9 + - - -
1040B VAL* 3.5 51.0 - - + +
1041B ASN 4.4 4.2 - - - +
1042B ASP* 4.4 22.6 + - - +
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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