Contacts of the strand formed by residues 99 - 103 (chain 3) in PDB entry 1ZUD
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 GLN 99 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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533 GLY 2.8 18.1 + - - +
543 THR* 3.4 24.2 - - + +
553 LEU 3.0 27.4 + - - +
983 ILE* 1.3 69.3 - - - +
1003 LEU* 1.3 76.6 + - - +
1013 THR* 3.1 22.0 + - - +
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Residues in contact with LEU 100 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483 ALA* 5.1 0.2 - - + -
553 LEU* 3.7 38.8 - - + -
573 LEU* 4.5 5.6 - - + -
883 GLN* 2.7 42.1 + - + +
913 LEU* 3.5 23.8 - - + +
923 THR* 3.3 47.1 - - + +
953 ASN 4.3 5.8 - - - +
983 ILE* 3.6 21.7 + - + +
993 GLN* 1.3 84.2 + - - +
1013 THR* 1.3 55.3 + - - +
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Residues in contact with THR 101 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543 THR* 4.6 3.8 - - - +
553 LEU 2.9 14.0 + - - -
563 VAL* 3.4 18.7 - - + +
573 LEU* 2.8 36.6 + - - +
883 GLN* 4.0 1.6 - - - +
993 GLN* 3.1 25.5 + - - +
1003 LEU* 1.3 70.6 - - - +
1023 ALA* 1.3 60.0 + - - +
1033 LEU* 4.0 21.3 + - + -
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Residues in contact with ALA 102 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573 LEU* 3.7 5.2 - - - -
843 SER* 3.6 29.8 - - - +
853 GLN* 4.3 2.9 - - + +
883 GLN* 3.5 30.9 - - + +
1013 THR* 1.3 75.1 - - - +
1033 LEU* 1.3 69.1 + - - +
1043 GLN 4.0 1.4 + - - -
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Residues in contact with LEU 103 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563 VAL* 3.5 29.4 - - + -
573 LEU 2.9 14.0 + - - +
583 ALA* 3.2 12.6 - - + +
593 ASP 3.1 20.8 + - - -
843 SER* 3.5 2.6 + - - -
1013 THR* 4.2 12.6 - - + -
1023 ALA* 1.3 81.6 - - - +
1043 GLN* 1.3 60.9 + - - +
1053 GLN* 3.0 26.8 + - + +
1073 LEU* 4.2 25.1 - - + -
1153 ALA* 4.6 9.2 - - + -
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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