Contacts of the strand formed by residues 944 - 954 (chain A) in PDB entry 1WXR
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 944 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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911A PHE* 3.5 8.3 - - - -
919A THR 3.2 7.7 + - - -
920A THR* 3.5 15.5 - - - +
921A LEU 3.1 24.1 + - - +
935A MET* 3.7 1.1 - - - +
942A ALA 4.5 4.7 - - - +
943A ASP* 1.3 76.7 - - - +
945A LEU* 1.3 62.4 + - - +
946A VAL* 3.5 18.6 - - + +
975A PRO* 3.4 43.3 - - - +
976A LEU 3.6 8.5 - - - +
978A SER* 3.3 30.9 - - - +
1014A GLU* 4.8 2.7 + - - -
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Residues in contact with LEU 945 (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 PHE* 4.4 10.8 - - + -
921A LEU* 3.3 36.1 - - + +
923A THR* 4.7 1.1 - - + -
926A LEU* 4.3 5.6 - - + -
933A PHE* 3.6 40.2 - - + -
935A MET* 3.8 3.6 - - + +
944A LYS* 1.3 75.8 - - - +
946A VAL* 1.3 69.0 + - - +
947A ILE* 3.6 26.9 - - + -
976A LEU 3.1 12.3 + - - +
977A VAL* 3.3 14.0 - - + -
978A SER 3.0 23.6 + - - +
988A PHE* 4.1 13.2 - - + -
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Residues in contact with VAL 946 (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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920A THR* 4.7 12.6 - - + -
921A LEU 2.8 10.3 + - - +
922A THR* 3.1 19.3 - - - -
923A THR 2.9 25.3 + - - -
944A LYS* 3.5 33.4 - - + +
945A LEU* 1.3 77.5 - - - +
947A ILE* 1.3 68.4 + - - +
948A ASN* 3.6 20.9 - - + +
978A SER* 3.7 13.5 - - - +
1012A LYS* 5.8 4.3 - - - -
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Residues in contact with ILE 947 (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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923A THR* 3.2 7.6 - - - +
924A ASP 3.4 13.9 - - - +
926A LEU* 3.9 28.9 - - + +
945A LEU* 3.6 31.6 - - + -
946A VAL* 1.3 78.5 - - - +
948A ASN* 1.3 63.3 + - - +
949A LYS 3.9 0.2 - - - -
950A SER 2.7 36.6 - - - +
951A ALA* 3.9 7.0 - - + -
977A VAL* 4.1 11.0 - - + -
978A SER* 2.8 29.0 + - - +
979A ALA* 3.3 20.6 - - + -
980A PRO* 3.6 3.6 - - + +
988A PHE* 4.5 4.9 - - + -
1012A LYS* 5.9 1.6 - - - +
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Residues in contact with ASN 948 (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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922A THR* 4.0 11.9 + - - -
923A THR 3.1 9.9 + - - +
924A ASP* 2.8 25.2 + - - +
946A VAL* 3.6 21.7 - - + +
947A ILE* 1.3 75.1 - - - +
949A LYS* 1.3 75.7 + - - +
980A PRO* 4.6 1.6 - - - -
1012A LYS* 6.1 5.4 - - - -
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Residues in contact with LYS 949 (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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924A ASP* 3.1 38.2 + - + +
925A ASN* 3.6 12.6 - - - +
948A ASN* 1.3 79.3 - - - +
950A SER* 1.3 61.2 + - - +
980A PRO* 3.5 20.7 - - - +
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Residues in contact with SER 950 (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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924A ASP 3.0 4.9 + - - +
925A ASN* 3.3 21.8 - - - -
926A LEU 3.1 15.1 + - - -
947A ILE* 2.7 26.9 - - - +
949A LYS* 1.3 78.3 - - - +
951A ALA* 1.3 59.2 + - - +
952A THR* 3.9 18.0 + - - +
980A PRO* 3.6 5.1 - - - +
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Residues in contact with ALA 951 (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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926A LEU* 3.3 8.5 - - + +
947A ILE* 3.9 19.1 - - + -
950A SER* 1.3 78.4 + - - +
952A THR* 1.3 63.3 + - - +
979A ALA* 4.2 9.0 - - + -
980A PRO* 4.5 0.4 - - + +
983A THR* 3.5 31.6 + - + +
984A ALA 5.2 0.5 + - - -
987A LEU* 3.4 26.1 - - + +
988A PHE* 5.2 0.7 - - + -
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Residues in contact with THR 952 (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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926A LEU* 3.0 7.5 + - - +
927A ASP* 4.0 18.4 - - - +
928A ALA* 3.1 19.3 + - - +
950A SER* 3.9 16.3 + - - +
951A ALA* 1.3 77.2 - - - +
953A GLY* 1.3 63.5 + - - +
987A LEU* 3.4 14.0 - - - +
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Residues in contact with GLY 953 (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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927A ASP* 3.7 13.5 + - - -
928A ALA 3.0 10.3 - - - -
929A VAL* 4.1 6.5 - - - -
952A THR* 1.3 78.9 + - - +
954A HIS* 1.3 74.2 + - - +
987A LEU* 3.3 9.7 - - - +
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Residues in contact with HIS 954 (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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928A ALA 2.8 9.7 + - - -
929A VAL* 3.3 35.4 - - + +
930A GLN* 2.9 28.5 + - + -
953A GLY* 1.3 79.8 - - - +
955A ASP* 1.3 89.8 + - + +
956A ASN* 3.5 5.8 - - - +
986A ASN* 5.6 4.0 - - - +
987A LEU* 3.4 11.4 - - - +
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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