Contacts of the strand formed by residues 917 - 924 (chain A) in PDB entry 3QCH
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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913A ASP* 3.4 5.9 - - - +
914A GLY 3.1 25.4 + - - +
915A TYR 2.9 8.7 + - - +
916A ASN* 1.3 79.9 - - - +
918A ALA* 1.3 73.6 + - - +
919A LYS 4.2 2.2 - - - -
920A ALA* 3.8 34.1 - - + +
1049A ARG* 4.0 20.1 - - - +
1053A THR 4.8 10.5 + - - -
1054A GLY 5.6 1.2 + - - -
1055A PRO* 6.1 0.7 - - - -
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Residues in contact with ALA 918 (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* 2.9 12.3 - - - +
917A LYS* 1.3 83.6 - - - +
919A LYS* 1.3 80.8 + - + +
920A ALA 3.2 2.8 + - - -
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Residues in contact with LYS 919 (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* 3.8 60.5 - - + -
912A VAL 3.3 11.4 + - - -
913A ASP* 3.0 12.4 + - - +
917A LYS* 4.2 3.8 - - - -
918A ALA* 1.3 81.3 - - + +
920A ALA* 1.3 63.7 + - - +
921A TYR 3.2 2.7 - - - -
1055A PRO* 3.5 15.7 - - + +
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Residues in contact with ALA 920 (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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912A VAL 3.0 3.8 + - - -
914A GLY* 3.4 30.7 - - - +
917A LYS* 3.8 26.9 - - + +
918A ALA 3.2 1.8 - - - -
919A LYS* 1.3 78.0 - - - +
921A TYR* 1.3 62.0 + - + +
1049A ARG* 3.2 29.3 + - - +
1055A PRO* 3.4 1.3 - - - +
1056A VAL 2.9 20.1 + - - -
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Residues in contact with TYR 921 (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* 3.3 7.3 - - - +
912A VAL* 2.9 30.7 + - + +
913A ASP 3.5 16.4 - - - -
914A GLY* 3.5 24.6 - - - -
919A LYS 3.2 1.3 - - - -
920A ALA* 1.3 83.6 - - + +
922A ILE* 1.3 67.9 + - - +
1049A ARG* 4.0 15.6 + - - -
1055A PRO* 3.8 4.5 - - - +
1056A VAL* 3.3 20.0 - - + +
1058A VAL* 4.1 11.0 - - + -
1070A TYR* 4.4 10.1 - + - -
1071A ILE* 3.8 41.7 - - + -
1074A ASP* 2.5 40.9 + - + +
1075A SER* 3.6 9.4 + - - -
1078A GLN* 5.6 0.7 - - - +
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Residues in contact with ILE 922 (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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891A VAL* 3.8 35.0 - - + -
909A ALA* 4.1 9.2 - - + -
910A ASN 3.4 4.9 - - - +
911A TYR* 4.1 6.5 - - + -
921A TYR* 1.3 77.4 - - - +
923A ALA* 1.3 59.2 + - - +
924A THR* 3.9 3.3 + - + -
938A MET* 4.0 26.7 - - + -
942A GLN* 3.9 22.7 - - + -
944A THR* 4.3 7.6 - - - +
1055A PRO* 3.4 30.2 - - + +
1056A VAL 2.8 11.6 + - - +
1057A LEU* 3.3 8.1 - - + +
1058A VAL* 2.8 33.3 + - - +
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Residues in contact with ALA 923 (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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909A ALA* 3.5 1.0 - - - -
910A ASN 3.0 28.6 + - - -
912A VAL* 4.1 17.9 - - + +
921A TYR 4.0 1.2 - - - -
922A ILE* 1.3 70.5 - - - +
924A THR* 1.3 61.9 + - - +
1058A VAL* 3.2 6.1 - - - -
1063A GLY 4.1 0.4 - - - +
1067A THR* 3.3 25.8 - - + -
1071A ILE* 4.2 6.1 - - + -
1099A ARG* 3.7 24.3 - - - -
1102A LEU* 4.6 2.5 - - + -
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Residues in contact with THR 924 (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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907A ILE* 4.7 8.0 - - - +
908A ASN 2.5 24.8 + - - -
909A ALA* 3.5 13.9 - - - +
922A ILE* 4.4 1.6 - - + -
923A ALA* 1.3 76.7 - - - +
925A GLN* 1.3 73.3 + - - +
935A PHE* 4.2 5.9 - - + -
938A MET* 4.2 7.2 - - + -
1057A LEU* 3.8 38.6 - - + -
1058A VAL 2.9 7.3 + - - -
1059A HIS* 2.9 27.2 - - + +
1063A GLY* 3.4 11.4 + - - -
1099A ARG* 4.2 3.1 - - - +
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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