Contacts of the strand formed by residues 997 - 1009 (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 VAL 997 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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844A GLU* 3.8 17.5 - - - +
847A ARG* 4.0 4.0 + - - +
848A TYR* 4.1 6.4 - - - +
877A LEU* 4.5 7.4 - - + +
895A ILE* 3.9 16.8 - - + -
897A PHE* 3.8 31.4 - - + -
922A GLY* 5.0 2.2 - - - -
923A GLU 3.5 6.3 - - - +
924A VAL* 4.9 1.6 - - + -
991A VAL* 3.9 19.1 - - + -
994A ILE 3.9 13.2 - - - +
995A ALA 3.2 2.7 - - - +
996A GLN* 1.3 84.2 - - - +
998A ASN* 1.3 65.6 + - - +
999A LEU* 3.7 30.3 - - + +
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Residues in contact with ASN 998 (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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840A GLU* 6.0 1.6 - - - +
841A ARG 5.9 0.8 - - - +
844A GLU* 2.9 22.7 + - - +
845A CYS* 3.5 28.9 - - - +
848A TYR* 3.8 36.2 - - + -
923A GLU* 2.9 38.0 + - + +
997A VAL* 1.3 77.6 - - - +
999A LEU* 1.3 71.5 + - - +
1000A LYS* 3.4 27.1 + - - +
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Residues in contact with LEU 999 (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* 3.3 31.8 - - + +
840A GLU* 5.0 1.7 - - - -
841A ARG* 4.4 16.8 + - + +
844A GLU* 2.6 29.3 + - - +
872A ILE* 4.1 28.9 - - + +
873A LEU* 4.8 2.7 - - + -
876A GLY* 4.6 4.5 - - - -
877A LEU* 4.0 19.3 - - + +
897A PHE* 5.4 0.7 - - + -
920A LEU* 4.2 20.6 - - + -
921A LEU 4.2 0.4 - - - +
922A GLY* 4.1 9.9 - - - -
997A VAL* 3.7 22.0 - - + -
998A ASN* 1.3 81.5 + - - +
1000A LYS* 1.3 61.8 + - - +
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Residues in contact with LYS1000 (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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838A LYS* 3.3 32.3 + - - +
839A ILE* 3.2 25.3 + - - -
840A GLU* 6.6 0.2 - - - -
845A CYS* 5.1 4.9 - - - -
859A LEU* 4.4 8.1 - - + -
921A LEU 2.9 12.5 + - - +
923A GLU* 3.4 34.2 + - + +
965A ASP* 6.1 3.2 - - - +
967A VAL* 5.6 1.0 - - - +
998A ASN* 3.4 38.7 + - - +
999A LEU* 1.3 74.1 - - - +
1001A TYR* 1.3 90.2 + - + +
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Residues in contact with TYR1001 (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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804A VAL* 4.2 11.9 - - + -
810A GLU* 2.9 25.0 + - - +
814A ILE* 3.8 29.6 - - + -
836A ILE* 4.3 1.3 - - + -
837A PHE 3.2 15.0 - - - +
838A LYS* 3.4 28.4 - - + +
839A ILE* 3.7 5.3 - - - +
859A LEU* 4.7 7.4 - - + -
920A LEU* 3.3 10.7 - - - +
921A LEU* 2.8 49.4 + - + +
964A LEU* 3.9 25.4 - - + +
965A ASP* 5.5 4.0 + - - -
1000A LYS* 1.3 98.0 - - + +
1002A LEU* 1.3 60.8 + - - +
1003A LEU* 4.3 12.8 - - + -
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Residues in contact with LEU1002 (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* 3.9 37.0 - - + -
836A ILE* 3.7 0.9 - - - -
837A PHE* 2.8 48.7 + - + -
839A ILE* 4.3 17.4 - - + +
869A PHE* 3.4 33.4 - - + -
873A LEU* 4.3 21.5 - - + -
918A LEU* 4.1 7.0 - - + -
919A ILE 3.4 22.4 - - - +
920A LEU* 3.8 7.6 - - + -
1001A TYR* 1.3 74.4 - - - +
1003A LEU* 1.3 65.0 + - - +
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Residues in contact with LEU1003 (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* 3.8 23.6 - - + -
818A VAL* 3.8 29.4 - - + -
833A VAL* 4.1 13.2 - - + -
835A ASP 3.4 4.7 - - - +
836A ILE* 4.2 17.5 - - + -
837A PHE* 5.3 0.2 - - - -
861A TRP* 3.9 11.7 - - + -
917A GLY 3.9 0.2 - - - +
918A LEU* 3.3 9.4 - - - +
919A ILE* 2.8 46.4 + - + +
921A LEU* 4.2 15.9 - - + -
1001A TYR* 4.3 10.3 - - + -
1002A LEU* 1.3 80.8 - - - +
1004A LYS* 1.3 59.9 + - - +
1005A LEU* 3.9 11.1 + - + -
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Residues in contact with LYS1004 (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 5.7 0.6 + - - +
671A ASP* 4.3 23.8 + - - +
672A LEU* 5.6 1.8 - - + +
675A MET* 3.5 25.3 - - + +
833A VAL* 3.9 0.3 - - - -
834A ILE* 2.9 46.3 + - + +
835A ASP* 3.0 41.2 + - + +
837A PHE* 4.6 9.3 - - + -
916A ILE* 3.4 27.0 - - + +
917A GLY 3.5 4.5 - - - +
918A LEU* 4.0 9.0 - - + -
1002A LEU 4.3 0.4 + - - -
1003A LEU* 1.3 72.5 - - - +
1005A LEU* 1.3 62.5 + - - +
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Residues in contact with LEU1005 (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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818A VAL* 5.2 3.1 - - + -
831A LEU* 4.1 32.3 - - + -
832A GLU 3.5 12.6 - - - +
833A VAL* 4.0 18.4 - - + -
834A ILE* 4.4 1.6 - - - -
901A VAL* 5.1 1.8 - - + -
905A ALA* 4.9 1.3 - - + -
908A CYS* 5.3 0.4 - - - -
916A ILE* 3.2 11.1 - - - +
917A GLY 2.8 37.8 + - - +
918A LEU 5.3 0.2 - - - -
919A ILE* 3.6 36.8 - - + +
1003A LEU* 4.1 17.9 - - + +
1004A LYS* 1.3 82.2 - - - +
1006A LYS* 1.3 59.3 + - - +
1007A PHE* 3.9 20.0 - - + -
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Residues in contact with LYS1006 (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 3.5 1.0 - - - +
831A LEU* 3.4 6.6 - - - +
832A GLU* 2.9 59.5 + - + +
834A ILE* 3.9 21.2 - - + +
915A PRO* 4.0 7.4 - - + +
916A ILE* 3.5 28.7 - - + -
1005A LEU* 1.3 71.5 - - - +
1007A PHE* 1.3 69.5 + - - +
1008A ASN 3.8 0.3 + - - -
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Residues in contact with PHE1007 (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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829A TYR* 3.6 35.9 - + + -
830A ASP 3.4 5.4 - - - +
831A LEU* 3.7 20.2 - - + -
905A ALA* 3.6 32.3 - - + -
906A ASN* 5.5 0.2 - - - -
908A CYS* 4.0 8.3 - - + -
910A THR* 3.1 32.3 - - + -
915A PRO* 3.2 24.7 + - - +
917A GLY* 3.9 13.5 - - - -
1005A LEU* 3.9 14.1 - - + -
1006A LYS* 1.3 81.4 - - - +
1008A ASN* 1.3 60.0 + - - +
1009A PHE* 3.5 31.1 + + + -
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Residues in contact with ASN1008 (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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829A TYR* 3.1 4.8 - - - -
830A ASP* 2.8 54.0 + - - +
832A GLU* 6.2 3.8 - - + +
1006A LYS* 3.8 1.6 + - + -
1007A PHE* 1.3 68.6 - - - +
1009A PHE* 1.3 72.4 + - - +
1010A LYS* 3.4 8.1 + - - +
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Residues in contact with PHE1009 (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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828A ALA* 3.7 7.6 - - + +
829A TYR* 3.9 25.4 - + + -
910A THR* 3.4 18.8 - - - -
911A SER* 3.2 49.8 - - - -
912A GLN* 3.6 30.3 - - + +
915A PRO* 5.1 1.6 - - + -
1007A PHE* 3.5 31.2 + + + -
1008A ASN* 1.3 77.8 + - - +
1010A LYS* 1.3 62.9 + - - +
1011A THR* 3.4 10.2 + - - +
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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