Contacts of the helix formed by residues 528 - 535 (chain A) in PDB entry 3U0Z
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 528 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492A ILE* 3.9 13.0 - - - -
500A LYS 3.6 1.7 - - - +
501A MET* 3.4 17.1 - - - +
527A PHE* 1.3 76.5 - - - +
529A GLU* 1.3 62.7 + - - +
530A ILE 3.4 1.6 - - - -
532A LEU* 3.7 6.9 - - - +
538A ARG* 3.2 23.0 + - - -
646A CMP 2.8 27.0 + - - -
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Residues in contact with GLU 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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501A MET* 3.9 24.9 - - + +
526A TYR* 3.5 15.0 + - + -
527A PHE* 3.4 3.1 - - - -
528A GLY* 1.3 81.4 + - - +
530A ILE* 1.3 77.9 + - + +
532A LEU* 3.1 16.3 + - - +
533A LEU* 3.1 24.9 + - + +
558A PHE* 4.7 4.6 - - + -
572A PHE* 4.2 20.1 - - + +
576A ALA* 4.3 9.9 + - + -
579A ARG* 2.8 38.4 + - - -
646A CMP 2.5 27.3 + - - -
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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 GLY 3.4 0.8 - - - -
529A GLU* 1.3 88.6 - - - +
531A CYS* 1.3 72.5 + - - +
533A LEU* 3.1 11.4 + - - +
534A THR* 3.0 31.2 + - + +
539A THR* 3.9 20.2 - - + +
576A ALA* 4.0 14.4 - - + +
579A ARG* 4.2 14.8 - - + -
580A LEU* 4.3 27.1 - - + -
587A ASN* 6.1 0.4 - - - +
646A CMP 3.4 51.8 + - + +
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Residues in contact with CYS 531 (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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498A GLY* 3.5 39.7 - - - -
530A ILE* 1.3 77.7 - - - +
532A LEU* 1.3 58.0 + - - +
534A THR* 3.1 6.5 + - - -
535A LYS* 2.9 27.0 + - - -
536A GLY 3.0 24.4 - - - +
537A ARG 4.5 2.9 - - - -
538A ARG* 3.4 22.0 - - - +
646A CMP 2.6 31.9 + - - +
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Residues in contact with LEU 532 (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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498A GLY 3.8 23.6 - - - +
499A LYS 4.3 1.3 - - - -
500A LYS 3.7 23.8 - - - +
501A MET* 3.6 39.5 - - + +
528A GLY 3.7 7.2 - - - +
529A GLU 3.1 8.3 + - - +
531A CYS* 1.3 78.3 - - - +
533A LEU* 1.3 64.4 + - - +
535A LYS* 3.8 14.1 + - - +
538A ARG* 4.2 2.5 - - - +
553A LEU 4.6 1.8 - - - +
555A VAL* 4.0 26.5 - - + +
558A PHE* 3.9 36.6 - - + -
559A ASN* 5.2 4.0 + - - +
569A ARG* 4.9 2.9 + - - -
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Residues in contact with LEU 533 (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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529A GLU* 3.1 17.4 + - + +
530A ILE* 3.1 6.3 + - - +
532A LEU* 1.3 82.6 - - - +
534A THR* 1.3 67.1 + - + +
535A LYS* 3.3 9.2 + - - +
558A PHE* 4.1 22.2 - - + -
562A LEU* 4.7 0.2 - - + -
569A ARG* 3.8 47.0 + - + +
572A PHE* 4.2 11.4 - - + -
573A GLU* 4.1 38.8 - - + +
576A ALA* 4.2 17.3 - - + -
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Residues in contact with THR 534 (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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530A ILE* 3.0 28.3 + - + +
531A CYS* 3.1 9.2 + - - -
533A LEU* 1.3 81.5 - - + +
535A LYS* 1.3 65.0 + - - +
536A GLY* 2.9 18.0 + - - -
537A ARG 5.2 1.2 + - - -
539A THR* 5.4 1.0 - - - +
580A LEU* 5.6 2.7 - - + -
587A ASN* 3.9 37.6 + - + +
588A SER* 5.8 1.2 + - - -
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Residues in contact with LYS 535 (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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531A CYS* 2.9 10.8 + - - -
532A LEU* 3.8 9.2 + - - +
533A LEU 3.2 10.0 - - - +
534A THR* 1.3 79.3 - - - +
536A GLY* 1.4 60.3 + - - +
559A ASN* 4.8 17.0 + - - +
569A ARG* 5.7 6.0 - - - +
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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