Contacts of the strand formed by residues 916 - 925 (chain A) in PDB entry 5WRZ
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 ILE 916 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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675A MET* 4.3 14.6 - - - +
834A ILE* 5.6 1.6 - - + -
866A THR* 3.9 13.0 - - - +
910A THR* 3.7 8.2 - - - +
914A ASP* 4.1 8.2 - - - +
915A PRO* 1.3 101.9 - - + +
917A GLY* 1.3 59.6 + - - +
1004A LYS* 3.4 42.6 - - + +
1005A LEU 3.2 10.8 - - - +
1006A LYS* 3.5 36.1 - - + -
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Residues in contact with GLY 917 (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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675A MET* 5.5 0.2 - - - -
866A THR* 4.2 6.3 - - - -
908A CYS* 4.4 5.6 - - - -
910A THR* 3.9 13.5 - - - -
916A ILE* 1.3 76.8 - - - +
918A LEU* 1.3 64.9 + - - +
1004A LYS* 3.5 4.7 - - - -
1005A LEU* 2.8 38.1 + - - -
1007A PHE* 3.9 11.9 - - - -
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Residues in contact with LEU 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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672A LEU* 3.8 24.5 - - + -
675A MET* 3.8 23.1 - - + -
676A ILE* 3.8 29.8 - - + -
864A SER 3.5 11.4 + - - +
866A THR* 4.3 17.9 - - + +
869A PHE* 3.7 38.2 - - + -
908A CYS* 3.2 19.2 - - - -
917A GLY* 1.3 82.9 - - - +
919A ILE* 1.3 61.0 + - - +
1002A LEU* 4.1 6.5 - - + -
1003A LEU 3.3 10.8 - - - +
1004A LYS* 4.0 10.1 - - + +
1005A LEU* 5.3 0.4 - - - -
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Residues in contact with ILE 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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861A TRP* 3.6 33.0 - - + -
862A HIS 3.5 16.2 - - - +
863A GLY* 3.9 2.7 - - - -
869A PHE* 4.4 0.7 - - - -
901A VAL* 4.0 17.9 - - + +
904A SER* 3.5 27.6 - - - -
905A ALA* 4.0 10.3 - - + +
908A CYS* 4.7 2.2 - - - -
918A LEU* 1.3 76.6 - - - +
920A LEU* 1.3 63.2 + - - +
1002A LEU* 3.4 6.7 - - - +
1003A LEU* 2.8 51.3 + - + +
1005A LEU* 3.6 23.8 - - + -
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Residues in contact with LEU 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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839A ILE* 4.0 19.3 - - + -
861A TRP* 3.4 13.6 - - - -
862A HIS* 2.8 48.7 + - + +
869A PHE* 3.6 25.6 - - + -
872A ILE* 3.7 27.1 - - + -
873A LEU* 4.7 4.0 - - + -
877A LEU* 4.2 12.8 - - + -
897A PHE* 6.3 0.2 - - + -
919A ILE* 1.3 73.2 - - - +
921A LEU* 1.4 64.6 + - - +
922A GLY 5.0 0.4 - - - +
999A LEU* 4.2 22.2 - - + -
1001A TYR 3.3 12.8 - - - +
1002A LEU* 3.8 9.0 - - + -
1003A LEU* 5.6 0.2 - - - -
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Residues in contact with LEU 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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814A ILE* 4.0 31.4 - - + -
817A TYR* 3.5 30.7 - - + -
859A LEU* 4.1 19.3 - - + -
860A LEU 3.3 11.2 - - - +
861A TRP* 3.4 44.4 - - + -
920A LEU* 1.4 71.7 - - - +
922A GLY* 1.3 58.7 + - - +
999A LEU* 4.2 0.8 - - - -
1000A LYS* 2.9 23.6 + - - +
1001A TYR* 2.8 32.9 + - + +
1003A LEU* 4.2 7.6 - - + -
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Residues in contact with GLY 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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858A ARG 3.3 3.6 - - - +
859A LEU* 3.4 5.0 - - - -
860A LEU 2.9 32.8 + - - +
897A PHE* 5.0 5.1 - - - -
920A LEU* 4.1 2.6 - - - +
921A LEU* 1.3 73.5 - - - +
923A GLU* 1.4 62.0 + - - -
924A VAL* 3.5 9.5 + - - +
997A VAL* 5.0 0.9 - - - -
998A ASN 3.4 11.7 - - - -
999A LEU* 4.1 12.8 - - - -
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Residues in contact with GLU 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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848A TYR* 2.7 38.9 + - - +
852A LYS 4.3 0.3 - - - +
857A ARG* 3.1 29.0 + - + -
858A ARG 3.5 3.8 - - - -
859A LEU* 3.9 7.3 - - + +
922A GLY* 1.4 69.7 - - - -
924A VAL* 1.3 60.0 + - - +
967A VAL* 3.4 36.8 - - + +
996A GLN 3.7 1.6 - - - +
997A VAL* 3.5 3.6 - - - -
998A ASN* 2.9 43.8 + - + +
1000A LYS* 3.4 29.7 + - + +
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Residues in contact with VAL 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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848A TYR* 4.4 0.9 - - - -
856A ASN 3.6 0.5 - - - +
857A ARG* 3.3 4.6 - - - -
858A ARG 2.9 34.4 + - - +
860A LEU* 4.2 11.7 - - + -
897A PHE* 3.6 49.1 - - + -
922A GLY* 3.5 13.2 - - - +
923A GLU* 1.3 79.2 - - - +
925A ALA* 1.3 62.0 + - - +
926A LEU* 3.5 27.0 + - + +
989A TYR* 5.7 0.2 - - + -
991A VAL* 3.9 19.3 - - + -
996A GLN 3.5 5.6 - - - +
997A VAL* 4.9 2.2 - - + -
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Residues in contact with ALA 925 (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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848A TYR* 3.8 9.4 + - - +
851A PHE* 3.7 32.5 - - + +
854A LEU* 4.0 13.4 - - + +
857A ARG* 4.1 10.3 - - + -
924A VAL* 1.3 69.0 - - - +
926A LEU* 1.3 60.2 + - - +
927A GLY 3.6 1.8 - - - -
991A VAL* 4.1 1.6 - - - +
996A GLN* 2.7 53.3 + - + +
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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