Contacts of the helix formed by residues 564 - 571 (chain B) in PDB entry 1UMW
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 LEU 564 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377B MET* 6.1 1.3 - - + -
380B GLN* 3.8 40.4 - - + +
381B LEU* 4.5 12.6 - - + -
384B VAL* 3.6 27.5 - - + +
543B LEU* 4.5 4.9 - - + -
544B CYS 5.5 0.2 - - - +
548B ALA* 2.9 26.1 + - + +
549B ALA* 4.2 9.9 - - - +
550B VAL* 3.8 28.3 - - + -
562B TYR 3.5 0.6 + - - -
563B ARG* 1.3 70.8 - - - +
565B SER* 1.3 62.8 + - - +
567B LEU* 3.1 21.3 + - + +
568B GLU* 3.3 9.7 + - - +
580B LEU* 4.2 16.4 - - + -
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Residues in contact with SER 565 (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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548B ALA* 4.5 8.9 + - - +
563B ARG* 3.3 3.2 - - - +
564B LEU* 1.3 79.3 - - - +
566B LEU* 1.3 62.0 + - - +
568B GLU* 3.2 31.0 + - - +
569B GLU* 3.4 13.5 + - - +
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Residues in contact with LEU 566 (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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399B GLU 3.7 16.8 - - - +
400B ALA* 3.5 19.0 - - + +
401B GLU 5.2 2.7 - - - +
402B ASP* 5.8 1.1 - - + +
563B ARG* 3.0 32.9 + - + +
565B SER* 1.3 79.0 - - - +
567B LEU* 1.3 60.9 + - - +
568B GLU 3.1 1.6 - - - -
569B GLU* 3.3 7.4 + - + +
570B TYR* 2.9 53.4 + - + +
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Residues in contact with LEU 567 (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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384B VAL* 4.1 9.6 - - + -
389B PRO* 3.7 5.0 - - - +
397B GLN* 4.1 3.1 - - + -
400B ALA* 3.5 18.8 - - + -
550B VAL* 4.0 8.5 - - + -
562B TYR* 3.8 27.6 - - + -
563B ARG 3.0 15.7 + - - +
564B LEU* 3.1 15.2 + - + +
566B LEU* 1.3 76.8 - - - +
568B GLU* 1.3 57.5 + - - +
571B GLY* 2.8 36.3 + - - +
572B CYS* 3.8 26.9 - - + -
576B LEU* 3.8 22.4 - - + -
580B LEU* 4.0 18.2 - - + -
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Residues in contact with GLU 568 (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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383B SER* 3.1 43.3 + - - +
384B VAL* 3.8 8.0 + - + +
387B SER* 3.6 27.0 - - - +
392B ARG* 2.7 30.3 + - - -
564B LEU 3.3 6.8 + - - +
565B SER* 3.2 21.6 + - - +
567B LEU* 1.3 80.0 - - - +
569B GLU* 1.3 68.1 + - + +
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Residues in contact with GLU 569 (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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392B ARG* 3.5 10.0 + - - -
396B ARG* 5.3 3.5 + - - -
565B SER 3.4 12.7 + - - +
566B LEU* 3.3 12.4 + - + +
567B LEU 3.3 0.2 - - - -
568B GLU* 1.3 89.4 - - + +
570B TYR* 1.3 75.6 + - + +
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Residues in contact with TYR 570 (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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392B ARG* 4.3 2.9 - - - -
394B LEU 3.9 5.8 - - - +
395B VAL* 3.8 3.5 - - - -
396B ARG* 2.9 78.4 + - + +
399B GLU* 3.6 50.1 + - + -
400B ALA* 4.9 2.5 - - + +
566B LEU* 2.9 41.6 + - + +
569B GLU* 1.3 87.4 - - + +
571B GLY* 1.3 60.3 + - - +
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Residues in contact with GLY 571 (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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389B PRO* 3.2 15.7 - - - -
392B ARG* 3.8 12.4 - - - +
395B VAL* 3.8 6.7 - - - -
397B GLN* 3.6 15.9 - - - -
567B LEU* 2.8 24.6 + - - +
569B GLU 3.6 1.6 - - - -
570B TYR* 1.3 83.0 - - - +
572B CYS* 1.3 64.4 + - - +
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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