Contacts of the strand formed by residues 829 - 841 (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 TYR 829 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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822A HIS* 3.2 42.0 + + - -
826A HIS* 3.5 13.2 - - + +
827A ASN* 3.1 5.1 - - - +
828A ALA* 1.3 83.6 - - + +
830A ASP* 1.3 69.9 + - - +
831A LEU* 3.9 9.6 - - + -
902A SER* 3.0 20.4 + - - -
905A ALA* 3.5 8.8 - - - +
906A ASN* 2.6 30.7 + - - -
1007A PHE* 3.6 34.5 - + + -
1008A ASN 3.1 16.4 - - - +
1009A PHE* 3.9 26.7 - + + -
1010A LYS* 4.1 8.0 + - - +
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Residues in contact with ASP 830 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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822A HIS* 3.8 11.4 - - + +
829A TYR* 1.3 75.7 - - - +
831A LEU* 1.3 67.8 + - - +
832A GLU* 6.0 0.9 - - - +
1006A LYS 3.5 0.5 - - - +
1007A PHE* 3.4 5.2 - - - -
1008A ASN* 2.8 62.1 + - - +
1010A LYS* 3.6 24.2 - - - +
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Residues in contact with LEU 831 (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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818A VAL* 4.5 19.8 - - + +
822A HIS* 4.2 13.4 + - + +
829A TYR* 3.9 7.2 - - + -
830A ASP* 1.3 80.8 - - - +
832A GLU* 1.3 63.3 + - - +
901A VAL* 3.9 37.2 - - + -
905A ALA* 4.1 13.0 - - + -
1005A LEU* 4.1 15.0 - - + -
1006A LYS 3.4 3.4 - - - +
1007A PHE* 3.7 49.8 - - + -
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Residues in contact with GLU 832 (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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830A ASP* 5.9 1.1 - - - +
831A LEU* 1.3 75.2 - - - +
833A VAL* 1.3 67.7 + - - +
834A ILE* 3.4 22.2 + - - +
1005A LEU* 3.5 5.8 - - - -
1006A LYS* 2.9 57.3 + - + +
1008A ASN* 6.2 3.1 - - + -
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Residues in contact with VAL 833 (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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815A ARG* 4.4 23.2 - - + -
818A VAL* 3.9 36.8 - - + -
832A GLU* 1.3 76.5 - - - +
834A ILE* 1.3 65.3 + - - +
835A ASP 4.1 9.0 - - - +
836A ILE* 3.4 38.4 - - + -
1003A LEU* 4.1 12.6 - - + -
1004A LYS 3.9 3.8 - - - +
1005A LEU* 4.0 4.0 - - + -
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Residues in contact with ILE 834 (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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806A ARG* 3.9 18.4 + - - +
832A GLU* 3.5 31.6 - - - +
833A VAL* 1.3 75.8 - - - +
835A ASP* 1.3 73.7 + - - +
916A ILE* 5.6 1.6 - - + -
1004A LYS* 2.9 43.3 + - - +
1005A LEU 4.4 1.3 - - - -
1006A LYS* 3.9 34.3 - - + +
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Residues in contact with ASP 835 (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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668A PRO* 3.7 32.5 - - - +
803A VAL* 5.8 3.6 - - + +
806A ARG* 4.0 12.2 + - - +
833A VAL* 4.1 0.7 - - - +
834A ILE* 1.3 92.3 - - - +
836A ILE* 1.3 65.7 + - - +
837A PHE* 3.8 25.3 - - + -
1002A LEU 4.0 0.4 - - - +
1003A LEU* 3.4 5.0 - - - +
1004A LYS* 3.0 53.9 + - + +
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Residues in contact with ILE 836 (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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803A VAL* 3.8 7.0 - - - +
804A VAL* 2.9 52.4 + - + +
806A ARG* 6.2 2.0 - - + -
811A ALA* 4.1 28.5 - - + +
814A ILE* 3.9 34.8 - - + -
815A ARG* 4.3 10.3 - - + +
833A VAL* 3.4 28.9 - - + -
835A ASP* 1.3 73.1 - - - +
837A PHE* 1.3 63.7 + - - +
1001A TYR* 4.3 5.6 - - + -
1002A LEU 3.7 2.7 - - - -
1003A LEU* 4.2 14.6 - - + +
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Residues in contact with PHE 837 (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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668A PRO* 3.5 32.5 - - + -
669A VAL* 3.8 24.0 - - + -
672A LEU* 4.0 29.6 - - + -
801A ILE* 3.8 25.4 - - + -
802A LYS 3.2 12.8 - - - +
803A VAL* 4.0 5.6 - - + -
804A VAL* 3.9 4.3 - - - -
835A ASP* 3.8 28.0 - - + -
836A ILE* 1.3 77.2 - - - +
838A LYS* 1.3 59.3 + - - +
839A ILE* 4.5 1.3 - - + -
1001A TYR* 3.2 9.2 - - - +
1002A LEU* 2.8 57.9 + - + +
1004A LYS* 4.6 10.8 - - + -
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Residues in contact with LYS 838 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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800A ASP* 3.6 1.7 - - - +
801A ILE* 3.6 3.1 - - - -
802A LYS* 2.8 49.7 + - + +
804A VAL* 3.5 17.3 - - + +
810A GLU* 4.3 7.4 - - - +
837A PHE* 1.3 72.6 - - - +
839A ILE* 1.3 72.4 + - - +
840A GLU* 5.4 5.8 - - + +
1000A LYS* 3.3 44.2 + - - +
1001A TYR* 3.4 29.6 - - + +
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Residues in contact with ILE 839 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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799A THR* 4.1 7.9 - - + -
800A ASP 3.2 3.6 - - - +
801A ILE* 4.0 29.4 - - + -
837A PHE* 4.5 1.3 - - + -
838A LYS* 1.3 93.7 + - - +
840A GLU* 1.3 61.9 + - - +
841A ARG* 4.1 2.2 - - + -
873A LEU* 4.3 13.9 - - + -
920A LEU* 4.0 22.0 - - + -
999A LEU* 3.3 41.0 - - + +
1000A LYS 3.2 18.7 + - - +
1001A TYR* 3.7 10.5 - - - +
1002A LEU* 4.3 19.3 - - + -
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Residues in contact with GLU 840 (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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799A THR* 3.4 3.4 - - - -
800A ASP* 2.9 51.9 + - + +
838A LYS* 5.4 5.4 - - + +
839A ILE* 1.3 77.9 - - - +
841A ARG* 1.3 67.5 + - - +
842A GLU* 3.4 3.4 + - - -
843A GLY 5.9 0.3 + - - -
845A CYS* 4.1 30.7 - - - +
998A ASN* 6.0 1.6 - - - +
999A LEU 5.0 0.9 - - - -
1000A LYS* 6.6 0.2 - - - -
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Residues in contact with ARG 841 (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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798A LYS 3.9 5.1 + - - +
799A THR* 3.8 11.2 - - + +
839A ILE* 4.1 1.7 + - + -
840A GLU* 1.3 78.3 - - - +
842A GLU* 1.3 73.9 + - - +
843A GLY 3.3 0.7 + - - -
844A GLU* 3.0 62.0 + - + +
845A CYS 4.5 1.2 + - - -
847A ARG* 3.5 28.1 - - - +
872A ILE 3.6 7.2 - - - -
873A LEU* 2.7 38.6 - - + +
874A SER 3.0 23.4 + - - -
875A GLN* 3.3 8.1 + - - +
876A GLY* 3.2 15.4 - - - -
998A ASN* 5.9 0.6 - - - +
999A LEU* 4.4 15.0 + - + +
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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