Contacts of the strand formed by residues 906 - 914 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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868A HIS* 3.7 21.3 - - + -
869A SER* 2.7 40.7 + - - -
874A ASN* 3.5 26.9 - - + +
877A LYS* 3.6 38.2 - - + +
878A ASN* 2.5 30.1 + - - -
885A ALA* 4.9 2.2 - - + -
890A ARG* 3.7 16.4 - - - +
893A LEU* 3.8 9.9 - - - +
903A HIS 2.9 10.1 + - - +
904A SER 3.4 1.2 - - - -
905A ASP* 1.3 83.8 + - - +
907A ILE* 1.3 70.6 + - - +
908A ASN* 3.7 26.1 + - - -
934A ASP* 4.2 5.4 - - - +
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Residues in contact with ILE 907 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877A LYS* 5.7 1.6 - - - +
885A ALA* 4.5 1.4 - - - +
890A ARG* 4.8 2.6 - - - +
891A VAL 3.4 22.5 + - - +
893A LEU* 4.3 16.2 - - + -
905A ASP 3.8 1.8 + - - -
906A TYR* 1.3 86.6 - - - +
908A ASN* 1.3 63.9 + - + +
909A ALA* 2.6 34.1 + - + +
924A THR* 4.5 5.4 - - - +
925A GLN* 6.0 2.5 - - + +
931A THR* 5.3 8.7 - - + +
934A ASP* 4.1 12.1 - - + +
935A PHE* 4.1 26.2 - - + +
938A MET* 3.7 34.5 - - + -
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Residues in contact with ASN 908 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877A LYS 4.4 3.3 + - - +
878A ASN* 2.7 30.1 + - - +
879A ARG 4.5 0.2 - - - +
883A ILE* 3.1 23.1 + - - +
884A LEU* 3.9 4.8 - - - +
885A ALA* 3.8 9.1 - - - +
906A TYR* 3.7 14.6 + - - -
907A ILE* 1.3 72.4 - - - +
909A ALA* 1.3 52.0 + - - +
924A THR* 2.8 25.1 + - - -
925A GLN* 3.1 42.5 + - - +
1099A ARG* 3.3 23.4 + - - -
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Residues in contact with ALA 909 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885A ALA* 3.8 3.5 - - - +
890A ARG* 3.3 10.4 - - - +
891A VAL* 3.1 21.4 + - + -
907A ILE* 2.6 16.1 + - + +
908A ASN* 1.3 76.3 - - - +
910A ASN* 1.3 66.4 + - - +
922A ILE* 3.9 4.9 - - + -
923A ALA 3.3 7.2 - - - -
924A THR* 3.7 14.4 - - - +
938A MET* 3.7 30.7 - - - -
1099A ARG* 4.0 0.7 - - - +
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Residues in contact with ASN 910 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885A ALA* 3.1 15.9 - - - +
886A TYR 3.3 24.6 + - - +
889A SER* 2.7 31.2 + - - +
890A ARG* 3.5 2.2 - - - +
891A VAL* 3.9 6.1 - - - -
909A ALA* 1.3 74.4 - - - +
911A TYR* 1.3 65.2 + - - +
912A VAL* 3.5 1.4 + - + +
922A ILE* 3.3 1.4 - - - -
923A ALA 2.8 35.9 + - - +
1098A GLN 3.2 19.0 + - - +
1099A ARG* 2.9 41.5 + - + +
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Residues in contact with TYR 911 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889A SER* 2.9 34.5 + - - +
890A ARG 3.7 15.0 - - - -
891A VAL* 3.6 21.5 - - + +
892A LYS* 4.9 2.5 + - + -
910A ASN* 1.3 73.6 - - - +
912A VAL* 1.3 61.7 + - - +
913A ASP* 5.4 0.7 - - - -
919A LYS* 3.4 57.2 - - + +
921A TYR 3.4 4.5 - - - -
922A ILE* 4.1 14.1 - - + -
942A GLN* 2.7 37.3 + - - -
1055A PRO* 4.4 6.7 - - + -
1098A GLN* 3.5 18.4 - - - +
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Residues in contact with VAL 912 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910A ASN 3.8 10.1 - - - +
911A TYR* 1.3 80.5 - - - +
913A ASP* 1.3 78.1 + - - +
919A LYS* 4.2 1.6 - - - -
920A ALA 3.2 3.8 + - - -
921A TYR* 2.8 35.3 + - + +
923A ALA* 3.8 20.6 - - + -
1071A ILE* 4.0 24.9 - - + -
1095A ILE* 3.8 19.7 - - + -
1098A GLN* 3.1 15.0 - - + +
1099A ARG* 4.5 5.2 - - + -
1102A LEU* 4.1 16.2 - - + -
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Residues in contact with ASP 913 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911A TYR 5.4 0.2 - - - -
912A VAL* 1.3 83.4 - - - +
914A GLY* 1.3 66.7 + - - +
917A LYS 4.3 3.1 - - - +
918A ALA* 3.5 14.8 - - - +
919A LYS* 3.1 24.6 + - - +
921A TYR* 4.1 4.4 - - - -
1071A ILE* 4.1 0.2 - - - +
1091A PHE* 3.3 19.1 - - + -
1094A HIS* 2.9 23.9 + - + +
1095A ILE* 4.0 1.0 - - + +
1098A GLN* 2.5 42.6 + - - +
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Residues in contact with GLY 914 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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913A ASP* 1.3 79.1 - - - +
915A TYR* 1.3 64.0 + - - -
916A ASN 3.4 2.9 + - - -
917A LYS 3.2 16.3 + - - +
920A ALA* 3.5 13.2 - - - +
921A TYR* 3.6 14.8 - - - -
1075A SER* 3.5 15.5 - - - -
1091A PHE* 3.8 11.0 - - - -
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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