Contacts of the strand formed by residues 900 - 906 (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 THR 900 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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896A LEU* 2.9 35.5 + - + -
897A SER* 3.1 24.8 + - - +
898A HIS 3.6 0.2 - - - -
899A ASP* 1.3 92.5 + - - +
901A ILE* 1.3 65.0 + - - +
947A LEU* 3.7 33.9 - - + -
948A VAL 3.3 6.5 - - - +
949A THR* 3.8 13.8 - - + +
951A LEU* 4.4 1.8 - - - +
980A THR* 4.6 0.2 - - - +
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Residues in contact with ILE 901 (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* 3.6 27.4 - - + -
894A SER 3.5 15.3 - - - +
895A ILE* 3.5 25.8 - - + -
900A THR* 1.3 79.5 - - - +
902A ARG* 1.3 65.1 + - - +
903A ILE* 3.8 10.7 + - + -
947A LEU* 4.2 2.2 - - - -
948A VAL* 2.9 39.7 + - - +
951A LEU* 3.8 16.2 - - + -
957A TYR* 4.9 1.1 - - + -
959A PHE* 3.9 18.6 - - + -
978A GLY 3.7 22.2 - - - +
980A THR* 4.0 13.0 - - + -
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Residues in contact with ARG 902 (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 3.5 1.7 - - - +
893A ALA* 3.4 1.7 - - - -
894A SER* 2.8 45.8 + - - +
896A LEU* 3.2 20.9 - - + +
901A ILE* 1.3 71.4 - - - +
903A ILE* 1.3 66.2 + - - +
904A THR* 4.9 1.6 + - - +
945A SER* 4.2 15.7 - - - +
946A TYR 3.5 6.3 - - - +
947A LEU* 3.1 31.3 - - + +
311B ASN* 3.0 38.2 + - - +
314B ILE 2.8 18.7 + - - -
315B VAL* 2.3 44.7 + - - +
317B PRO 5.5 1.2 + - - -
318B PRO* 6.0 3.8 - - - +
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Residues in contact with ILE 903 (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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891A VAL* 3.9 23.1 - - + -
892A GLN 3.3 5.4 - - - +
893A ALA* 3.7 18.4 - - + +
901A ILE* 3.8 4.0 - - + +
902A ARG* 1.3 77.9 - - - +
904A THR* 1.3 65.5 + - - +
905A TRP* 3.6 16.1 - - + -
924A VAL* 4.8 7.9 - - + -
945A SER* 3.1 5.9 + - - -
946A TYR* 2.8 40.3 + - - +
948A VAL* 4.0 14.8 - - + -
959A PHE* 3.4 54.5 - - + -
961A VAL* 4.6 5.2 - - + -
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Residues in contact with THR 904 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A GLY 3.5 1.7 - - - +
891A VAL* 3.2 5.5 - - - +
892A GLN* 2.8 52.8 + - - +
894A SER* 5.4 1.9 + - - -
902A ARG 4.9 1.8 + - - +
903A ILE* 1.3 77.2 - - - +
905A TRP* 1.3 67.0 + - - +
944A LEU 3.5 12.3 - - - +
945A SER* 3.7 6.1 - - - +
306B SER* 3.3 19.1 - - - +
311B ASN* 3.0 33.0 + - - +
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Residues in contact with TRP 905 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A PRO* 3.7 23.1 - - + -
889A VAL 3.6 11.4 - - - +
890A GLY 3.8 4.9 - - - -
891A VAL* 4.1 14.4 - - + -
903A ILE* 3.6 23.3 - - + -
904A THR* 1.3 86.7 - - - +
906A ALA* 1.3 62.7 + - - +
922A TYR* 3.2 43.6 - + + -
924A VAL* 3.8 25.4 - - + -
941A ALA* 4.7 2.5 - - + -
943A THR 3.1 21.8 - - - -
944A LEU* 3.3 35.4 + - + +
945A SER 3.5 17.3 - - - -
946A TYR* 3.6 10.1 - - + -
961A VAL* 3.8 22.0 - - + -
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Residues in contact with ALA 906 (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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888A PRO* 3.2 7.1 - - - +
889A VAL* 2.7 54.8 + - + +
890A GLY* 5.0 3.8 - - - +
905A TRP* 1.3 75.9 - - - +
907A ASP* 1.3 62.8 + - - +
908A ASN* 4.0 3.1 - - - +
912A LYS* 5.1 12.3 - - - +
944A LEU* 4.1 4.3 - - - -
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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