Contacts of the strand formed by residues 917 - 924 (chain A) in PDB entry 6N8Q
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 GLU 917 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A GLU* 3.5 10.5 - - + +
29A HIS 3.2 17.7 - - - +
30A GLY 4.4 4.3 - - - +
31A PHE 3.6 4.9 - - - +
32A PRO* 3.4 27.8 - - - +
33A HIS* 4.0 4.2 + - - +
57A LYS* 2.8 29.5 + - - -
59A TYR* 5.2 0.2 + - - -
382A LEU* 4.1 1.0 - - - +
912A LEU* 3.4 10.7 - - - +
913A ILE* 3.2 46.1 + - + +
914A SER* 3.4 14.7 + - - +
915A PRO 3.7 0.4 - - - -
916A SER* 1.3 81.4 - - - +
918A PHE* 1.3 66.7 + - - +
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Residues in contact with PHE 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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28A GLU* 3.3 9.0 - - - +
29A HIS* 2.6 43.3 + - + +
382A LEU* 3.5 26.9 - - + -
387A ILE* 4.2 12.3 - - + -
390A SER* 3.8 24.0 - - - -
438A LEU* 4.1 24.0 - - + -
440A THR* 4.3 7.6 - - + -
457A LEU* 4.6 6.7 - - + -
900A SER* 4.5 8.3 - - - -
902A VAL* 5.4 1.1 - - + -
910A PHE* 3.8 22.9 - + + -
911A TYR* 3.4 28.0 - - - -
912A LEU* 3.5 28.5 - - + -
913A ILE* 4.7 1.6 - - - -
917A GLU* 1.3 75.9 - - - +
919A GLU* 1.3 61.2 + - - +
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Residues in contact with GLU 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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25A LYS* 3.9 24.9 - - + +
26A THR 4.2 0.2 + - - -
27A VAL 3.3 22.4 + - - +
28A GLU* 3.7 24.4 - - - +
909A GLY 3.9 0.2 - - - +
910A PHE* 3.3 6.3 - - - -
911A TYR* 2.7 59.8 + - + +
913A ILE* 3.7 25.9 - - + +
917A GLU 4.2 0.2 + - - -
918A PHE* 1.3 74.8 - - - +
920A ARG* 1.3 71.5 + - - +
921A PHE 4.1 0.2 + - - -
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Residues in contact with ARG 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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25A LYS* 3.6 3.5 - - - -
26A THR* 2.9 44.0 + - + -
27A VAL* 2.9 21.9 + - + +
28A GLU* 4.8 0.2 - - - +
29A HIS* 3.0 30.8 + - - +
392A HIS* 5.9 0.6 + - - -
436A ASP* 5.3 1.0 + - - -
452A ALA* 2.8 32.5 + - - +
453A SER 4.5 1.8 + - - -
454A GLY 3.1 21.7 + - - -
457A LEU* 5.6 0.2 - - - +
908A GLN* 3.3 35.8 + - - +
909A GLY 3.4 7.9 - - - +
910A PHE* 3.4 32.9 - - + -
918A PHE 4.2 0.2 - - - -
919A GLU* 1.3 78.0 - - - +
921A PHE* 1.3 66.6 + - - +
929A VAL* 3.8 14.8 - - - +
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Residues in contact with PHE 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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23A PHE* 3.9 21.5 - + + -
24A ASN 3.2 13.7 - - - +
25A LYS* 4.1 11.7 - - + -
26A THR* 4.5 2.9 - - - +
873A ILE* 3.4 27.6 - - + -
889A CYS* 4.0 4.7 - - - -
901A CYS* 4.0 17.5 - - - -
903A PHE* 4.1 5.8 - + - -
908A GLN* 3.4 6.9 - - - +
909A GLY* 3.0 56.9 + - - +
910A PHE 3.7 2.9 - - - -
911A TYR* 3.8 31.4 - + + -
919A GLU 4.4 0.4 - - - -
920A ARG* 1.3 78.6 - - - +
922A SER* 1.3 61.9 + - - +
923A LEU* 3.5 25.8 - - + -
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Residues in contact with SER 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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22A GLN 3.1 14.8 - - - +
23A PHE* 3.4 5.0 - - - -
24A ASN* 2.8 24.6 + - - -
26A THR* 5.5 3.4 - - - -
907A GLY 3.6 5.5 + - - -
908A GLN* 4.2 10.5 - - - +
921A PHE* 1.3 77.3 - - - +
923A LEU* 1.3 60.6 + - - +
924A SER 2.9 27.5 + - - -
927A TRP* 3.0 25.5 + - - +
928A LEU* 5.1 8.3 - - - -
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Residues in contact with LEU 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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20A LEU 3.8 0.2 - - - +
21A PHE* 3.3 10.7 - - - +
22A GLN 3.0 28.0 + - - -
23A PHE* 4.8 7.6 - - + +
851A PHE* 3.9 18.9 - - + -
865A ALA* 4.3 13.7 - - + -
873A ILE* 3.6 25.4 - - + -
875A VAL* 3.8 26.0 - - + -
887A TYR* 5.0 8.4 - - + -
903A PHE* 4.2 11.9 - - + -
907A GLY* 2.6 32.7 + - - +
921A PHE* 3.5 31.6 - - + -
922A SER* 1.3 72.5 - - - +
924A SER* 1.3 54.8 + - - +
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Residues in contact with SER 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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20A LEU 3.5 8.0 + - - -
22A GLN 4.3 5.2 - - - +
851A PHE* 4.1 8.5 - - - -
852A GLY 4.3 9.2 + - - -
906A TYR 3.6 23.4 + - - -
907A GLY* 4.0 7.2 - - - -
922A SER* 2.9 16.1 + - - -
923A LEU* 1.3 80.4 - - - +
925A THR* 1.3 61.3 + - - +
926A LYS* 3.1 24.7 + - - +
927A TRP* 3.1 18.7 - - - +
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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