Contacts of the helix formed by residues 528 - 535 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492B ILE* 3.9 11.4 - - - -
500B LYS 3.6 1.9 - - - +
501B MET* 3.4 17.1 - - - +
527B PHE* 1.3 76.6 - - - +
529B GLU* 1.3 63.8 + - - +
530B ILE 3.4 1.8 - - - -
532B LEU* 3.7 6.8 - - - +
538B ARG* 3.2 22.3 + - - -
646B CMP 2.8 26.6 + - - -
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Residues in contact with GLU 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B MET* 3.8 26.2 - - + -
526B TYR* 3.4 15.3 + - + -
527B PHE* 3.4 2.9 - - - -
528B GLY* 1.3 80.6 + - - +
530B ILE* 1.3 78.2 + - + +
532B LEU* 3.1 17.0 + - - +
533B LEU* 3.2 23.9 + - + +
558B PHE* 4.7 4.8 - - + -
572B PHE* 4.2 18.4 - - + +
576B ALA* 4.3 10.2 + - + -
579B ARG* 2.8 38.9 + - - -
646B CMP 2.5 28.5 + - - -
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Residues in contact with ILE 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B GLU* 1.3 89.6 - - - +
531B CYS* 1.3 71.5 + - - +
533B LEU* 3.1 10.3 + - - +
534B THR* 3.1 30.1 + - + +
539B THR* 3.9 24.2 - - + +
576B ALA* 4.0 13.2 - - + +
579B ARG* 4.3 10.5 - - + -
580B LEU* 4.0 31.9 - - + -
587B ASN* 5.6 0.2 - - - +
646B CMP 3.3 47.4 + - + +
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Residues in contact with CYS 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B GLY* 3.6 36.6 - - - -
530B ILE* 1.3 76.4 - - - +
532B LEU* 1.3 58.2 + - - +
534B THR* 3.0 7.1 + - - -
535B LYS* 2.9 28.6 + - - -
536B GLY 3.5 22.7 - - - -
537B ARG 4.6 4.0 - - - -
538B ARG* 3.5 22.4 - - - +
646B CMP 2.7 31.8 + - - +
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Residues in contact with LEU 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B GLY 3.8 24.0 - - - +
499B LYS 4.3 1.6 - - - -
500B LYS 3.8 22.4 - - - +
501B MET* 3.6 39.0 - - + +
528B GLY 3.7 6.7 - - - +
529B GLU 3.1 7.6 + - - +
531B CYS* 1.3 78.1 - - - +
533B LEU* 1.3 64.0 + - - +
535B LYS* 3.9 13.2 + - - +
538B ARG* 4.3 2.5 - - - +
553B LEU 4.6 2.2 - - - +
555B VAL* 3.9 27.0 - - + +
558B PHE* 3.9 36.4 - - + -
559B ASN* 5.1 4.5 + - - -
569B ARG* 5.0 3.1 + - - -
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Residues in contact with LEU 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B GLU* 3.2 17.3 + - + +
530B ILE* 3.1 7.4 + - - +
532B LEU* 1.3 80.7 - - - +
534B THR* 1.3 67.4 + - + +
535B LYS* 3.3 11.1 + - - +
558B PHE* 4.0 23.3 - - + -
562B LEU* 4.7 0.2 - - + -
569B ARG* 3.8 41.5 + - + +
572B PHE* 4.2 13.9 - - + -
573B GLU* 4.1 38.8 - - + +
576B ALA* 4.1 17.3 - - + -
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Residues in contact with THR 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530B ILE* 3.1 20.2 + - + +
531B CYS* 3.0 15.2 + - - -
533B LEU* 1.3 77.7 - - + +
535B LYS* 1.3 66.5 + - - +
536B GLY* 3.0 18.7 + - - -
537B ARG 4.7 1.7 + - - -
539B THR* 5.6 0.5 - - - +
580B LEU* 5.6 2.7 - - + -
587B ASN* 3.5 37.0 + - + +
588B SER 6.3 0.7 - - - -
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Residues in contact with LYS 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531B CYS* 2.9 12.6 + - - -
532B LEU* 4.0 9.6 + - - +
533B LEU 3.3 11.5 + - - +
534B THR* 1.3 79.4 - - - +
536B GLY* 1.3 62.2 + - - +
559B ASN* 5.4 7.1 + - - +
569B ARG* 5.3 8.7 - - - +
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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