Contacts of the strand formed by residues 921 - 927 (chain A) in PDB entry 4UI2
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 921 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919A SER 4.8 6.3 - - - -
920A ARG* 1.3 77.4 - - - +
922A TYR* 1.3 68.3 + - - +
923A THR* 3.3 23.6 - - - -
940A ASN* 3.3 21.5 - - + -
941A ALA 3.9 13.5 - - - +
942A THR* 4.7 8.5 - - + +
963A VAL* 3.4 3.0 - - - +
964A THR* 2.7 68.1 + - + +
966A GLY 6.2 1.6 - - - -
1E NAG 1.5 54.4 + - - -
2E NAG 4.3 3.1 - - - +
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Residues in contact with TYR 922 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A PRO* 4.3 5.8 - - + -
905A TRP* 3.2 45.1 - + + -
907A ASP* 2.6 41.3 + - + +
910A LEU* 3.7 14.9 - - - +
916A ILE* 5.4 4.7 - - + -
920A ARG* 3.9 15.3 - - + -
921A TYR* 1.3 76.0 - - - +
923A THR* 1.3 64.0 + - - +
924A VAL* 5.1 0.4 - - - -
939A ALA 3.7 0.3 - - - +
940A ASN* 3.3 4.0 - - - -
941A ALA* 2.8 46.2 + - + +
942A THR* 4.5 7.9 - - - -
943A THR 3.6 18.6 - - - -
944A LEU* 4.1 12.1 - - + +
961A VAL* 4.1 3.1 - - + -
962A MET 3.3 5.4 - - - +
963A VAL* 3.8 22.9 - - + -
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Residues in contact with THR 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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921A TYR* 3.3 17.2 - - - -
922A TYR* 1.3 73.7 - - - +
924A VAL* 1.3 63.5 + - - +
938A ASN* 4.8 11.4 - - + +
939A ALA 3.2 11.2 - - - +
940A ASN* 3.1 24.7 + - - +
961A VAL* 3.4 2.4 - - - -
962A MET* 2.7 66.4 + - + +
964A THR* 4.3 2.1 - - - +
972A TRP* 3.2 11.8 - - + -
1E NAG 4.9 5.6 - - - -
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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
----------------------------------------------------------
903A ILE* 4.8 19.7 - - + -
905A TRP* 3.8 31.9 - - + -
923A THR* 1.3 77.6 - - - +
925A ARG* 1.3 69.7 + - - +
926A TRP* 3.4 16.7 - - + -
938A ASN* 3.2 7.1 + - - -
939A ALA* 2.8 38.5 + - + +
941A ALA* 5.1 4.0 - - + -
946A TYR* 4.1 17.7 - - + -
948A VAL* 5.1 1.1 - - + -
959A PHE* 5.2 1.8 - - + -
960A SER 3.6 11.2 - - - +
961A VAL* 4.4 11.2 - - + -
972A TRP* 4.5 0.2 - - - -
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Residues in contact with ARG 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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924A VAL* 1.3 77.2 - - - +
926A TRP* 1.3 67.1 + - - +
936A TYR* 3.7 44.6 + - + -
937A LYS 3.0 5.8 - - - +
938A ASN* 3.4 18.6 - - - +
959A PHE* 3.5 2.3 - - - -
960A SER* 2.6 56.0 + - - +
972A TRP* 3.3 62.5 - - + +
975A THR* 4.5 8.7 - - - +
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Residues in contact with TRP 926 (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 VAL* 3.4 30.7 - - + -
925A ARG* 1.3 78.7 - - - +
927A LYS* 1.3 63.0 + - - +
935A LYS 4.8 0.2 - - - +
936A TYR* 3.6 5.4 - - - -
937A LYS* 3.0 72.6 + - + +
938A ASN 3.5 25.4 - - - -
939A ALA* 3.6 15.3 - - + -
946A TYR* 4.4 12.8 - + - -
948A VAL* 3.2 33.7 - - + +
949A THR 4.9 4.5 + - - -
951A LEU* 3.9 17.9 - - + +
957A TYR* 4.5 7.4 - + + -
958A GLU 3.3 6.3 - - - +
959A PHE* 3.4 24.7 - + + -
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Residues in contact with LYS 927 (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 TRP* 1.3 78.7 - - - +
928A THR* 1.3 75.8 + - - +
929A ASN* 3.9 12.3 + - - +
934A THR* 4.0 25.1 + - - +
935A LYS* 4.3 2.7 - - - +
936A TYR* 3.7 45.7 - - + +
957A TYR* 3.5 11.5 - - - -
958A GLU* 2.9 52.4 + - - +
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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
------------------------------------------------------------
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