Contacts of the strand formed by residues 829 - 836 (chain A) in PDB entry 3U44
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 GLY 829 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A TRP* 4.1 5.8 - - - -
201A PHE* 3.9 21.3 - - - -
824A LEU* 4.8 0.9 - - - -
825A ASP* 2.8 41.1 + - - -
826A LYS 4.5 0.2 - - - -
827A GLU 3.3 3.2 - - - -
828A LEU* 1.3 79.5 - - - +
830A PHE* 1.3 61.2 + - - -
851A MET* 3.7 7.0 - - - +
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Residues in contact with PHE 830 (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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168A TYR* 3.6 23.1 - + - -
180A LEU* 3.9 17.7 - - + -
184A VAL* 4.6 2.9 - - + -
201A PHE* 3.5 37.9 - + + +
204A LEU* 3.5 12.1 - - - +
205A TYR* 3.2 22.3 + - + -
342A ILE* 3.8 26.2 - - + -
345A LEU* 3.6 26.9 - - + -
822A TYR* 3.6 36.1 - + + -
823A LEU 3.7 3.8 - - - -
824A LEU* 3.6 19.7 - - + -
828A LEU 3.9 0.6 + - - -
829A GLY* 1.3 72.5 - - - -
831A GLY* 1.3 62.9 + - - +
832A THR* 3.8 7.0 - - - -
851A MET* 4.2 1.8 - - - -
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Residues in contact with GLY 831 (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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205A TYR* 3.2 6.5 - - - -
822A TYR* 3.2 4.7 - - - +
823A LEU 2.8 35.1 + - - +
830A PHE* 1.3 77.5 - - - +
832A THR* 1.3 62.1 + - - -
847A PRO* 5.1 3.4 - - - -
848A LEU* 4.6 11.9 - - - -
851A MET* 3.7 17.6 - - - -
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Residues in contact with THR 832 (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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168A TYR* 2.6 36.7 + - - +
205A TYR* 3.3 20.6 + - + +
338A MET* 4.2 8.3 - - + -
342A ILE* 4.2 8.5 - - + -
821A SER 2.9 14.3 + - - -
830A PHE* 3.8 11.7 - - + -
831A GLY* 1.3 75.7 - - - -
833A LYS* 1.3 77.9 + - - +
845A THR* 2.9 28.5 + - - +
847A PRO* 5.8 0.2 - - - +
848A LEU* 3.3 15.4 - - - +
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Residues in contact with LYS 833 (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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338A MET* 3.5 12.9 - - - +
819A ASN 4.8 4.5 + - - -
820A LYS 4.6 5.8 - - - -
821A SER* 2.8 31.2 + - - +
832A THR* 1.3 88.4 + - - +
834A TYR* 1.3 62.8 + - - +
835A ILE* 3.4 20.4 + - + +
842A SER* 4.7 6.5 - - - +
843A TYR* 3.5 17.7 - - - +
844A PRO* 3.8 25.5 - - + +
845A THR* 3.6 1.8 - - - -
848A LEU* 3.4 17.7 - - + -
852A LYS* 6.0 1.1 - - - +
1017B GLN* 4.1 30.5 + - - +
2X C 4.7 9.5 + - - -
3X T 4.8 11.8 + - - -
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Residues in contact with TYR 834 (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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167A ARG* 6.2 0.4 - - - -
334A SER* 3.3 35.7 - - - +
337A GLU* 2.7 38.7 + - + -
338A MET* 4.1 15.7 - - + -
833A LYS* 1.3 70.0 - - - +
835A ILE* 1.3 61.5 + - - +
836A HIS* 3.6 34.9 + - + -
839A LEU* 6.0 0.7 - - - +
841A ILE* 4.6 8.1 - - + -
842A SER* 2.9 26.7 - - - -
843A TYR* 2.8 62.7 + + + +
845A THR* 3.2 11.8 + - - +
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Residues in contact with ILE 835 (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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167A ARG* 2.7 76.2 + - + +
168A TYR* 4.4 15.7 - - + -
338A MET* 3.9 5.8 - - - +
821A SER* 4.3 24.9 - - - +
833A LYS* 3.4 17.5 + - + +
834A TYR* 1.3 84.2 - - - +
836A HIS* 1.3 57.0 + - - +
837A PRO 4.7 0.2 - - - -
841A ILE 3.7 1.8 - - - -
842A SER* 3.9 9.9 - - - -
1015B MET* 3.8 30.3 - - + -
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Residues in contact with HIS 836 (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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167A ARG* 5.4 3.3 + - - -
337A GLU* 4.9 3.7 + - - -
834A TYR* 3.6 23.6 + - + -
835A ILE* 1.3 75.9 - - - +
837A PRO* 1.3 55.8 - - + +
838A GLN* 3.2 29.4 + - - +
839A LEU* 3.2 52.9 - - + +
840A ARG* 2.8 30.1 + - - -
841A ILE* 2.8 35.2 + - + +
1015B MET* 4.3 1.0 - - - +
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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