Contacts of the strand formed by residues 525 - 530 (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 THR 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483A ASP* 4.1 6.9 + - - +
484A ILE* 5.2 1.6 - - - +
487A SER* 2.9 30.9 + - - +
523A THR 3.7 1.8 + - - -
524A GLU* 1.3 73.1 - - - +
526A GLU* 1.3 63.8 + - - +
871A LEU* 6.3 0.4 - - + -
878A LEU* 3.7 35.1 + - + +
880A LEU* 3.9 28.7 - - + -
948A ARG 3.5 9.2 + - - -
949A PHE* 3.2 18.4 - - + +
950A ALA 2.9 23.9 + - - -
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Residues in contact with GLU 526 (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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524A GLU* 3.9 6.4 - - + +
525A THR* 1.3 79.8 - - - +
527A LEU* 1.3 58.0 + - - +
528A LEU* 4.2 5.3 - - + +
558A GLU* 4.0 9.6 - - - +
877A LYS* 3.2 29.5 + - - +
878A LEU 3.1 11.2 + - - +
879A PHE* 2.9 26.0 - - + -
880A LEU* 2.6 37.1 + - - +
949A PHE* 6.1 0.4 - - - -
950A ALA* 3.3 21.4 - - + +
952A GLN* 3.9 20.5 + - - +
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Residues in contact with LEU 527 (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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525A THR 4.3 0.2 + - - -
526A GLU* 1.3 74.6 - - - +
528A LEU* 1.3 65.3 + - - +
529A LEU* 3.7 32.0 + - + +
809A LEU* 6.4 0.4 - - + -
880A LEU* 3.0 18.6 - - + +
882A GLY 5.3 4.5 - - - +
894A TRP* 5.7 5.4 - - + -
917A LEU* 5.2 13.0 - - + -
920A ILE* 4.2 15.5 - - + -
921A GLY* 5.6 3.8 - - - +
924A LEU* 3.3 33.2 - - + -
949A PHE* 6.1 2.9 - - + -
950A ALA 2.9 11.3 + - - +
951A VAL* 3.6 14.9 - - + -
952A GLN* 2.9 26.7 + - - +
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Residues in contact with LEU 528 (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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526A GLU* 4.3 10.1 - - + +
527A LEU* 1.3 74.6 - - - +
529A LEU* 1.3 61.2 + - - +
530A ILE* 3.8 2.2 + - + +
554A ALA* 4.1 11.2 - - + +
558A GLU* 3.4 36.8 - - + +
805A PHE* 5.4 0.2 - - + -
879A PHE* 4.8 7.9 - - + -
880A LEU 2.9 9.5 + - - +
881A ILE* 3.5 39.2 - - + +
882A GLY 3.3 24.6 + - - +
952A GLN* 3.2 46.2 - - + +
954A ILE* 4.3 12.3 - - + -
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Residues in contact with LEU 529 (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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527A LEU* 3.7 18.5 - - + +
528A LEU* 1.3 70.1 - - - +
530A ILE* 1.3 61.8 + - - +
882A GLY 4.2 6.7 - - - +
883A SER 5.4 0.4 - - - +
884A CYS* 3.4 23.3 - - - +
887A HIS* 3.2 27.1 - - + +
890A GLN* 3.0 22.4 - - - +
891A LEU* 4.3 10.1 - - + -
894A TRP* 4.3 12.6 - - + -
917A LEU* 5.7 7.0 - - + -
951A VAL* 6.1 0.4 - - + -
952A GLN 2.9 14.5 + - - +
953A MET* 4.2 20.9 - - + -
954A ILE* 2.7 34.5 + - - +
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Residues in contact with ILE 530 (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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528A LEU 4.1 5.6 - - - +
529A LEU* 1.3 82.0 - - - +
531A ASP* 1.3 68.1 + - - +
547A THR 5.9 0.4 - - - +
550A PHE* 3.2 38.4 - - + +
551A GLU* 4.1 8.3 - - - +
554A ALA* 3.3 24.7 - - + -
881A ILE* 4.6 8.7 - - + -
882A GLY 3.5 11.0 + - - +
883A SER* 3.2 9.5 - - - -
884A CYS 3.0 25.1 + - - -
954A ILE* 3.5 20.2 - - + -
956A SER* 3.3 27.4 - - - -
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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