Contacts of the strand formed by residues 889 - 897 (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 VAL 889 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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887A PRO* 3.6 12.1 - - + +
888A PRO* 1.3 80.6 - - - +
890A GLY* 1.3 65.1 + - - +
891A VAL* 3.3 6.6 + - - -
905A TRP* 3.6 3.6 - - - +
906A ALA* 2.7 46.3 + - + +
908A ASN* 3.7 36.1 - - - +
974A MET* 5.9 3.6 - - - -
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Residues in contact with GLY 890 (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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889A VAL* 1.3 79.9 - - - +
891A VAL* 1.3 60.7 + - - +
892A GLN* 3.1 26.9 + - - +
904A THR 3.5 5.0 - - - +
905A TRP* 3.8 4.2 - - - -
906A ALA* 4.5 4.6 + - - +
974A MET* 5.9 2.8 - - - +
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Residues in contact with VAL 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A PRO 4.6 0.4 - - - +
889A VAL* 4.0 13.5 - - - +
890A GLY* 1.3 72.9 - - - +
892A GLN* 1.3 64.8 + - - +
903A ILE* 3.9 20.2 - - + -
904A THR 3.2 10.3 - - - +
905A TRP* 4.1 7.9 - - + -
959A PHE* 4.5 10.5 - - + +
961A VAL* 4.1 13.2 - - + -
973A SER* 3.4 32.8 - - - +
974A MET* 3.7 14.6 - - + +
976A ALA* 3.3 26.5 - - + +
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Residues in contact with GLN 892 (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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890A GLY* 3.1 18.8 - - - +
891A VAL* 1.3 80.3 - - - +
893A ALA* 1.3 63.6 + - - +
894A SER* 5.2 4.1 + - - +
902A ARG 3.5 1.7 - - - +
903A ILE* 3.3 8.8 - - - +
904A THR* 2.8 51.2 + - - +
976A ALA* 4.7 3.1 - - - -
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Residues in contact with ALA 893 (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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892A GLN* 1.3 76.5 - - - +
894A SER* 1.3 63.0 + - - +
895A ILE* 4.1 1.7 + - + -
901A ILE* 3.6 19.3 - - + -
902A ARG 3.4 4.7 - - - -
903A ILE* 3.7 11.0 - - + -
959A PHE* 4.2 6.1 - - + -
976A ALA* 5.0 4.1 - - - +
977A HIS 4.1 9.1 + - - +
978A GLY* 4.1 23.1 - - - -
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Residues in contact with SER 894 (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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892A GLN* 5.2 5.9 + - - +
893A ALA* 1.3 75.3 + - - +
895A ILE* 1.3 65.4 + - - +
896A LEU* 3.4 5.6 + - - +
901A ILE* 3.5 1.7 - - - +
902A ARG* 2.8 42.6 + - - -
904A THR* 5.4 1.7 + - - -
311B ASN* 5.0 6.4 + - - -
312B ASP* 3.6 40.4 + - - +
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Residues in contact with ILE 895 (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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893A ALA* 4.1 1.5 + - + -
894A SER* 1.3 74.7 - - - +
896A LEU* 1.3 64.3 + - - +
897A SER 5.0 0.4 - - - +
900A THR 4.1 3.1 - - - +
901A ILE* 3.5 31.0 - - + -
978A GLY* 4.3 3.4 - - - -
979A ALA 3.3 37.2 - - - +
980A THR* 4.4 2.5 - - - +
981A PHE* 3.5 43.9 - - + +
312B ASP* 4.6 3.8 - - - +
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Residues in contact with LEU 896 (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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894A SER 3.7 12.3 - - - +
895A ILE* 1.3 75.8 - - - +
897A SER* 1.3 61.3 + - - +
900A THR* 2.9 18.5 + - + +
902A ARG* 3.2 51.8 - - + +
947A LEU* 3.6 11.7 - - + -
981A PHE* 3.8 7.9 - - - -
311B ASN 4.2 3.1 - - - +
312B ASP* 3.2 33.4 - - - +
313B TRP* 5.1 3.1 - - - -
315B VAL* 5.3 11.7 - - + -
374B LEU* 3.3 32.7 - - + +
378B GLU* 4.8 3.8 - - - +
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Residues in contact with SER 897 (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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895A ILE* 5.0 1.0 - - - +
896A LEU* 1.3 79.3 + - - +
898A HIS* 1.3 63.6 + - - +
899A ASP* 2.7 26.1 + - - -
900A THR* 3.1 26.8 + - - +
980A THR* 4.0 5.2 - - - -
981A PHE* 3.5 23.9 + - - -
374B LEU* 4.8 4.7 - - - -
378B GLU* 3.6 25.1 - - - -
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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