Contacts of the strand formed by residues 906 - 914 (chain B) in PDB entry 3QCF
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 TYR 906 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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868B HIS* 4.2 6.3 - - + -
869B SER* 2.8 39.5 + - - -
874B ASN* 3.4 54.5 - - + +
877B LYS* 3.8 25.0 + - + +
878B ASN* 2.5 29.9 + - - -
885B ALA* 4.3 6.1 - - + -
890B ARG* 3.9 18.4 - - - +
893B LEU* 3.9 10.0 - - - +
903B HIS 3.0 5.9 + - - +
904B SER* 5.1 0.5 - - - -
905B ASP* 1.3 84.4 + - - +
907B ILE* 1.3 75.4 + - - +
908B ASN* 3.5 24.1 + - - +
934B ASP* 4.2 5.9 - - - +
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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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877B LYS* 5.8 1.3 - - - -
885B ALA* 4.2 1.6 - - - +
890B ARG* 4.9 1.2 - - - +
891B VAL* 3.4 23.1 + - + +
893B LEU* 4.3 14.6 - - + -
905B ASP 3.7 0.8 + - - -
906B TYR* 1.3 93.3 - - - +
908B ASN* 1.3 66.8 + - - +
909B ALA* 3.0 18.6 + - + +
924B THR* 4.5 5.6 - - - +
925B GLN* 6.2 1.8 - - + +
931B THR* 5.2 6.3 - - - +
934B ASP* 3.9 34.5 - - + +
935B PHE* 3.9 15.0 - - + +
938B MET* 3.9 34.5 - - + -
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Residues in contact with ASN 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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877B LYS 4.2 2.9 + - - +
878B ASN* 3.0 23.6 + - - +
880B TYR 5.9 0.2 - - - +
883B ILE* 3.0 26.6 + - - +
884B LEU* 3.9 7.1 - - - +
885B ALA* 4.2 3.8 - - - -
906B TYR* 3.5 18.4 + - + +
907B ILE* 1.3 74.2 - - - +
909B ALA* 1.3 52.8 + - - +
924B THR* 2.8 22.6 + - - -
925B GLN* 3.4 41.9 + - - +
1099B ARG* 3.1 24.7 + - - -
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Residues in contact with ALA 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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885B ALA* 3.8 2.2 - - - +
890B ARG* 3.2 10.6 - - - +
891B VAL* 2.9 28.6 + - + -
907B ILE* 3.0 11.9 + - + +
908B ASN* 1.3 76.6 + - - +
910B ASN* 1.3 64.2 + - - +
922B ILE* 3.7 15.7 - - + -
923B ALA 3.2 7.6 - - - -
924B THR* 3.4 20.2 - - - +
938B MET* 4.0 11.4 - - - -
1099B ARG* 3.6 1.9 - - - +
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Residues in contact with ASN 910 (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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885B ALA* 3.5 8.4 - - - +
886B TYR 3.2 29.3 + - - +
889B SER* 3.1 22.5 + - - +
890B ARG* 3.4 9.1 - - - +
891B VAL* 4.0 6.5 - - - -
909B ALA* 1.3 74.2 - - - +
911B TYR* 1.3 62.5 + - - +
912B VAL* 3.9 1.7 - - + +
922B ILE* 3.3 4.0 - - - -
923B ALA 3.0 31.1 + - - -
1098B GLN 3.3 21.1 - - - +
1099B ARG* 2.7 45.3 + - + +
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Residues in contact with TYR 911 (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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889B SER* 2.9 35.8 + - - +
890B ARG 3.5 17.0 - - - -
891B VAL* 3.9 20.1 - - + +
892B LYS 4.7 2.7 + - - -
910B ASN* 1.3 74.6 - - - +
912B VAL* 1.3 62.1 + - - +
919B LYS* 3.8 52.0 - - + -
921B TYR 3.4 7.6 - - - -
922B ILE* 4.6 4.7 - - + -
942B GLN* 2.9 39.0 + - - -
1055B PRO* 4.6 9.4 - - + -
1098B GLN* 3.6 22.1 + - - +
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Residues in contact with VAL 912 (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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910B ASN 3.9 4.0 - - - +
911B TYR* 1.3 79.9 - - - +
913B ASP* 1.3 71.8 + - - +
919B LYS* 4.1 0.9 - - - +
920B ALA 2.9 20.3 + - - -
921B TYR* 2.9 19.3 + - + +
923B ALA* 3.9 28.9 - - + +
1071B ILE* 4.3 18.6 - - + -
1095B ILE* 3.6 28.5 - - + -
1098B GLN* 3.4 15.7 - - + +
1099B ARG* 4.6 5.6 - - + -
1102B LEU* 4.1 16.2 - - + -
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Residues in contact with ASP 913 (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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912B VAL* 1.3 83.3 - - - +
914B GLY* 1.3 66.8 + - - +
917B LYS 3.6 7.4 - - - +
918B ALA* 3.1 16.3 - - - +
919B LYS* 2.9 22.4 + - - +
921B TYR* 3.4 11.2 - - - -
1091B PHE* 3.7 12.2 - - + -
1094B HIS* 2.8 34.7 + - + +
1095B ILE* 5.1 0.2 - - + -
1098B GLN* 2.8 31.9 + - - +
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Residues in contact with GLY 914 (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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913B ASP* 1.3 81.3 - - - +
915B TYR* 1.3 65.6 + - - -
916B ASN 3.2 3.8 + - - -
917B LYS* 2.8 16.8 + - - +
920B ALA* 3.3 12.4 - - - +
921B TYR* 3.5 12.6 - - - -
1075B SER* 3.3 14.1 - - - -
1091B PHE* 4.1 9.1 - - - -
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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