Contacts of the helix formed by residues 578 - 585 (chain A) in PDB entry 1UUR
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 HIS 578 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576A GLN 3.4 1.0 + - - -
577A ARG* 1.3 113.5 + - + +
579A ILE* 1.3 53.1 + - - +
580A SER 3.3 2.9 - - - +
581A THR* 3.4 12.9 + - - +
582A LEU* 2.7 52.6 + - + +
650A THR* 3.6 23.3 + - - +
652A PRO* 3.7 11.2 - - + -
689A PHE* 3.6 32.1 - + + -
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Residues in contact with ILE 579 (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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572A THR* 3.6 18.2 - - + +
573A LEU* 3.9 13.5 - - + -
576A GLN* 3.1 42.8 + - + +
577A ARG 3.1 3.7 - - - +
578A HIS* 1.3 78.7 - - - +
580A SER* 1.3 56.1 + - - +
582A LEU* 3.2 3.7 + - + +
583A TRP* 2.8 37.4 + - - +
588A ILE* 4.2 3.8 - - + -
621A PHE* 3.5 34.1 - - + -
651A PHE* 3.7 42.2 - - + -
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Residues in contact with SER 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A THR* 4.2 16.6 + - - +
573A LEU* 2.9 33.2 + - - -
574A ARG* 5.1 1.3 - - - -
576A GLN 4.2 1.0 + - - -
578A HIS* 3.3 0.6 - - - +
579A ILE* 1.3 79.4 - - - +
581A THR* 1.3 59.2 + - - +
583A TRP* 3.3 2.5 + - - +
584A GLN* 2.8 59.2 + - - +
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Residues in contact with THR 581 (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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578A HIS* 3.4 14.6 + - - -
579A ILE 3.3 0.4 - - - -
580A SER* 1.3 79.3 - - - +
582A LEU* 1.3 60.2 + - - +
584A GLN* 3.3 10.3 + - - +
585A GLU* 2.9 45.7 + - + +
689A PHE* 3.9 24.2 - - + -
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Residues in contact with LEU 582 (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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578A HIS* 2.7 45.5 + - + +
579A ILE* 4.4 0.9 - - + +
581A THR* 1.3 73.7 - - - +
583A TRP* 1.3 57.5 + - - +
585A GLU 3.5 0.3 + - - -
586A GLY 3.5 2.1 + - - -
587A ILE* 3.0 69.6 + - + +
588A ILE* 3.1 19.2 + - + -
651A PHE* 4.1 19.1 - - + -
652A PRO* 4.1 21.3 - - + -
655A LEU* 5.6 0.9 - - + -
686A LEU* 4.0 8.3 - - + -
689A PHE* 3.5 25.4 - - + -
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Residues in contact with TRP 583 (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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520A PHE* 3.5 35.4 - + - -
524A THR* 4.9 3.4 - - + -
526A GLN* 4.1 5.2 - - - -
533A ARG* 2.5 83.8 + - + +
534A PRO 4.4 5.2 - - - -
535A LEU* 4.7 0.9 - - + -
539A ASP* 4.4 11.2 - - - -
573A LEU* 3.7 28.0 - - + -
579A ILE* 2.8 20.4 + - + +
580A SER* 3.8 1.8 - - - +
582A LEU* 1.3 70.0 - - - +
584A GLN* 1.3 70.7 + - + +
585A GLU 3.0 5.6 + - - -
586A GLY 3.4 1.9 + - - -
588A ILE* 3.2 35.8 - - + +
589A TYR 2.9 23.3 + - - -
590A GLY* 4.1 8.3 - - - -
591A TYR* 4.6 16.0 - + - -
613A PHE* 5.3 2.9 - + - -
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Residues in contact with GLN 584 (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 THR* 3.9 14.3 + - - -
526A GLN* 3.7 26.4 - - - +
532A LYS* 3.6 48.7 - - + +
533A ARG* 3.9 17.5 - - - +
580A SER* 2.8 48.8 + - - +
581A THR* 3.7 9.0 + - - +
583A TRP* 1.3 86.9 - - + +
585A GLU* 1.3 62.8 + - - +
586A GLY 3.6 0.2 - - - -
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Residues in contact with GLU 585 (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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532A LYS* 2.6 39.7 + - - +
581A THR* 2.9 37.7 + - + +
582A LEU 3.7 6.3 - - - +
583A TRP 3.0 0.6 - - - -
584A GLN* 1.3 80.3 - - - +
586A GLY* 1.3 56.6 + - - +
587A ILE* 3.3 24.0 - - + -
666A GLN* 4.0 11.5 + - - +
667A TRP 3.7 8.4 - - - +
668A THR* 5.5 0.3 - - - -
689A PHE* 5.7 1.6 - - + -
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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