Contacts of the helix formed by residues 703 - 711 (chain B) in PDB entry 3UEO
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 SER 703 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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702B GLY* 1.3 70.2 - - - -
704B LYS* 1.3 62.8 + - - +
706B GLU* 3.2 9.6 + - - +
707B ALA* 2.9 27.3 + - - +
4E SEP 4.8 0.4 + - - -
5E ASP* 2.9 27.3 + - - -
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Residues in contact with LYS 704 (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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652B SER* 5.3 1.1 - - - -
653B PHE 3.1 21.8 + - - +
654B SER* 3.8 24.0 + - - +
677B GLU* 3.8 24.5 + - - -
678B TYR* 5.6 0.7 - - - +
679B PHE* 3.7 27.4 - - + +
695B LEU* 3.8 21.5 - - + -
702B GLY 3.3 0.6 - - - -
703B SER* 1.3 79.1 - - - +
705B TYR* 1.3 67.6 + - - +
707B ALA* 3.1 8.7 + - - +
708B ALA* 2.9 24.8 + - - +
6E TPO 3.0 34.7 + - - +
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Residues in contact with TYR 705 (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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654B SER* 5.3 1.0 + - - -
695B LEU* 3.8 10.4 - - - +
697B LEU* 3.8 14.8 - - + +
700B ARG* 3.6 15.3 - - + +
701B GLY* 3.3 39.9 + - - +
702B GLY 3.1 8.3 + - - +
704B LYS* 1.3 80.0 - - - +
706B GLU* 1.3 75.0 + - - +
708B ALA* 3.2 3.3 + - - +
709B LYS* 3.1 50.9 + - + +
715B ALA* 4.8 5.4 - - + -
738B ILE* 3.5 33.2 - - + -
739B GLU* 2.7 34.3 + - - -
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Residues in contact with GLU 706 (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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701B GLY* 5.2 1.2 - - - -
702B GLY 3.0 25.4 + - - +
703B SER* 3.2 8.9 + - - +
705B TYR* 1.3 89.7 - - - +
707B ALA* 1.3 58.3 + - - +
709B LYS* 3.2 24.8 + - - +
710B LYS* 2.9 29.4 + - - +
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Residues in contact with ALA 707 (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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679B PHE* 4.0 6.1 - - + -
703B SER 2.9 13.6 + - - +
704B LYS* 3.1 9.6 + - - +
706B GLU* 1.3 77.2 - - - +
708B ALA* 1.3 50.8 + - - +
710B LYS* 3.1 8.4 + - - +
711B TRP* 2.7 74.1 + - + -
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Residues in contact with ALA 708 (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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679B PHE* 3.6 24.1 - - + -
695B LEU* 4.3 12.6 - - + -
704B LYS 2.9 12.9 + - - +
705B TYR 3.6 8.1 - - - +
707B ALA* 1.3 74.9 - - - +
709B LYS* 1.3 57.9 + - - +
711B TRP* 4.4 1.1 - - - +
712B ASN* 2.8 26.9 + - - -
713B LEU* 3.0 29.5 + - + +
715B ALA* 4.3 10.8 - - + -
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Residues in contact with LYS 709 (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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705B TYR* 3.1 50.2 + - + +
706B GLU* 3.2 27.3 + - - +
708B ALA* 1.3 77.7 - - - +
710B LYS* 1.3 62.6 + - - +
712B ASN* 3.4 9.9 + - - +
713B LEU 5.3 0.2 - - - -
739B GLU* 4.8 9.4 + - - +
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Residues in contact with LYS 710 (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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681B ARG* 4.7 6.4 + - - +
706B GLU 2.9 13.5 + - - +
707B ALA* 3.4 11.0 - - - +
709B LYS* 1.3 78.7 - - - +
711B TRP* 1.3 75.9 + - + +
712B ASN* 3.5 1.4 + - - +
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Residues in contact with TRP 711 (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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679B PHE* 3.4 54.5 - + - -
680B VAL* 3.6 4.0 - - - -
681B ARG* 3.3 86.3 + - + +
707B ALA* 2.7 33.4 + - + +
708B ALA 4.1 0.4 - - - +
710B LYS* 1.3 92.0 - - + +
712B ASN* 1.3 69.6 + - - +
713B LEU* 3.5 22.4 + - + +
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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