Contacts of the helix formed by residues 628 - 636 (chain B) in PDB entry 4UN5
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 ASP 628 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451B TYR* 3.1 36.7 + - + +
484B LYS* 4.8 1.8 + - - -
626B PHE* 4.4 2.1 - - + +
627B GLU* 1.3 80.8 - - + +
629B ARG* 1.3 59.2 + - - +
630B GLU* 3.0 42.2 + - - +
631B MET* 3.1 25.7 + - + +
632B ILE* 2.9 30.4 + - - +
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Residues in contact with ARG 629 (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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171B GLU* 6.1 1.6 - - - +
627B GLU 3.4 0.6 + - - +
628B ASP* 1.3 73.4 + - - +
630B GLU* 1.3 58.0 + - + +
632B ILE* 3.6 5.9 - - - +
633B GLU* 2.9 28.6 + - - +
652B LYS* 3.3 38.2 + - - +
653B ARG* 3.3 50.3 + - - +
655B ARG* 3.2 52.8 - - - +
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Residues in contact with GLU 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B LYS* 4.5 11.5 + - - +
628B ASP* 3.0 17.9 + - - +
629B ARG* 1.3 76.8 - - + +
631B MET* 1.3 62.5 + - + +
633B GLU* 3.2 10.8 + - - +
634B GLU* 2.9 27.9 + - - +
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Residues in contact with MET 631 (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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451B TYR* 3.2 35.2 - - - -
484B LYS* 3.6 50.9 - - + +
485B GLY* 3.7 5.6 - - - +
488B ALA* 3.8 2.5 - - + -
626B PHE* 3.6 35.9 - - + -
628B ASP* 3.1 19.7 + - + +
630B GLU* 1.3 74.0 - - + +
632B ILE* 1.3 60.0 + - - +
634B GLU* 3.4 7.3 + - - +
635B ARG* 2.9 31.4 + - - +
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Residues in contact with ILE 632 (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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622B THR* 4.3 16.2 - - + +
623B LEU* 4.2 16.2 - - + -
626B PHE* 3.9 32.8 - - + +
627B GLU 4.2 0.4 - - - -
628B ASP 2.9 25.7 + - - +
629B ARG* 3.6 9.0 - - - +
631B MET* 1.3 76.3 - - - +
633B GLU* 1.3 62.0 + - - +
635B ARG* 3.3 2.4 + - - +
636B LEU* 3.1 44.0 + - + +
652B LYS* 4.3 18.8 - - - +
654B ARG 4.9 0.9 - - - +
655B ARG* 4.1 28.3 - - + -
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Residues in contact with GLU 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B ARG 2.9 18.1 + - - +
630B GLU* 3.2 9.3 + - - +
632B ILE* 1.3 77.6 - - - +
634B GLU* 1.3 64.4 + - - +
636B LEU* 3.2 14.1 + - - +
637B LYS* 3.5 16.9 + - + +
648B MET* 5.0 6.9 - - + +
652B LYS* 2.8 46.9 + - + +
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Residues in contact with GLU 634 (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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630B GLU 2.9 16.7 + - - +
631B MET* 3.4 7.1 + - - +
633B GLU* 1.3 78.5 - - - +
635B ARG* 1.3 68.5 + - - +
636B LEU 3.4 0.5 + - - -
637B LYS* 3.5 44.3 + - - +
638B THR 5.2 0.2 + - - -
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Residues in contact with ARG 635 (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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485B GLY 5.7 0.4 + - - -
489B GLN* 4.6 11.1 + - - +
618B ASP* 4.5 13.7 + - - +
621B LEU* 5.3 8.1 - - - +
622B THR* 3.1 45.6 + - + +
625B LEU* 4.2 9.5 - - - +
626B PHE* 3.1 39.3 - - + -
631B MET 2.9 19.0 + - - +
632B ILE 3.5 5.4 - - - +
633B GLU 3.2 0.2 - - - -
634B GLU* 1.3 86.0 + - - +
636B LEU* 1.3 58.3 + - - +
637B LYS 3.3 1.4 + - - -
638B THR* 3.9 12.0 + - - -
639B TYR* 5.1 4.2 - - - -
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Residues in contact with LEU 636 (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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619B ILE* 4.1 34.8 - - + -
622B THR* 4.1 20.4 - - + +
623B LEU* 4.1 10.3 - - + -
632B ILE* 3.1 36.8 + - + +
633B GLU 3.2 5.7 + - - +
635B ARG* 1.3 76.9 - - - +
637B LYS* 1.3 62.6 + - - +
638B THR* 3.3 3.8 - - - -
639B TYR* 3.2 24.5 + - + +
640B ALA 3.8 4.9 + - - -
648B MET* 4.0 24.4 - - + +
651B LEU* 4.6 25.4 - - + +
652B LYS* 4.8 4.5 - - + +
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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