Contacts of the strand formed by residues 917 - 924 (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 LYS 917 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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913B ASP* 3.6 1.6 - - - -
914B GLY 2.8 33.0 + - - +
915B TYR 3.4 6.7 - - - +
916B ASN* 1.3 80.8 - - - +
918B ALA* 1.3 68.3 + - - +
919B LYS 5.0 1.7 + - - -
920B ALA* 3.8 11.6 - - + +
1049B ARG* 3.2 41.1 - - - +
1052B GLU* 4.1 18.0 + - - -
1053B THR 4.9 10.3 + - - -
1054B GLY 6.3 0.6 - - - -
1055B PRO* 6.1 0.2 - - - -
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Residues in contact with ALA 918 (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* 3.1 18.6 - - - +
917B LYS* 1.3 80.3 + - - +
919B LYS* 1.3 81.4 + - + +
920B ALA 3.2 0.7 + - - -
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Residues in contact with LYS 919 (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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911B TYR* 3.8 51.8 - - + -
912B VAL 3.6 9.2 - - - -
913B ASP* 2.9 15.0 + - - +
917B LYS* 5.0 2.4 + - - -
918B ALA* 1.3 81.8 - - + +
920B ALA* 1.3 63.4 + - - +
921B TYR 3.2 3.6 - - - +
1049B ARG* 4.8 0.2 + - - -
1055B PRO* 3.5 16.9 - - + +
1098B GLN* 6.2 0.4 - - - +
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Residues in contact with ALA 920 (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 2.9 3.6 + - - -
914B GLY* 3.3 31.9 - - - +
917B LYS* 3.8 16.4 - - + +
918B ALA 3.2 2.2 - - - -
919B LYS* 1.3 78.8 - - - +
921B TYR* 1.3 66.6 + - + +
1049B ARG* 2.4 43.0 + - - +
1055B PRO* 3.8 1.6 - - - -
1056B VAL 3.0 12.8 + - - -
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Residues in contact with TYR 921 (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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911B TYR* 3.4 6.2 - - - +
912B VAL* 2.9 38.0 + - + +
913B ASP 3.4 18.4 - - - -
914B GLY* 3.5 13.4 - - - -
915B TYR 5.2 0.2 + - - -
919B LYS 3.2 1.8 - - - -
920B ALA* 1.3 90.1 - - + +
922B ILE* 1.3 63.9 + - - +
923B ALA 3.9 0.2 - - - -
1049B ARG* 4.0 12.0 + - - -
1055B PRO* 3.7 7.4 - - - +
1056B VAL* 3.1 15.3 - - + +
1058B VAL* 4.0 17.5 - - + -
1070B TYR* 4.3 10.1 - + - -
1071B ILE* 3.6 43.8 + - + -
1074B ASP* 2.6 33.7 + - - +
1075B SER* 3.4 13.9 + - - -
1078B GLN* 4.5 3.5 + - - -
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Residues in contact with ILE 922 (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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891B VAL* 3.8 16.8 - - + -
909B ALA* 3.7 27.4 - - + -
910B ASN 3.3 3.4 - - - +
911B TYR* 4.6 4.0 - - + -
921B TYR* 1.3 75.3 - - - +
923B ALA* 1.3 59.1 + - - +
924B THR* 4.0 1.7 + - - -
938B MET* 3.8 26.5 - - + -
942B GLN* 4.0 24.7 - - + +
944B THR* 4.1 10.5 - - - +
1055B PRO* 3.5 29.1 - - + +
1056B VAL 2.9 6.5 + - - +
1057B LEU* 3.4 12.0 - - + +
1058B VAL* 2.8 32.7 + - - +
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Residues in contact with ALA 923 (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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909B ALA* 3.2 1.9 - - - -
910B ASN 3.0 31.5 + - - +
912B VAL* 3.9 18.6 - - + -
921B TYR 3.9 1.4 - - - -
922B ILE* 1.3 70.3 - - - +
924B THR* 1.3 60.4 + - - +
1058B VAL* 3.4 7.0 - - - -
1063B GLY 4.2 0.2 - - - +
1067B THR* 3.6 23.6 - - + -
1071B ILE* 4.4 5.6 - - + -
1099B ARG* 3.6 26.2 + - - -
1102B LEU* 4.5 2.2 - - + -
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Residues in contact with THR 924 (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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907B ILE* 4.5 6.4 - - - +
908B ASN 2.8 21.3 + - - -
909B ALA* 3.4 15.4 - - - +
922B ILE* 4.3 2.0 - - - -
923B ALA* 1.3 77.0 - - - +
925B GLN* 1.3 71.6 + - - +
935B PHE* 4.4 9.2 - - + -
938B MET* 4.4 6.6 - - + +
1057B LEU* 3.6 35.7 - - + -
1058B VAL 3.2 3.2 + - - -
1059B HIS* 3.0 24.7 - - + +
1063B GLY* 3.3 15.4 + - - -
1099B ARG* 4.1 2.5 - - - +
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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