Contacts of the helix formed by residues 683 - 690 (chain D) in PDB entry 5UHO
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 683 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A ASP* 3.0 12.5 + - - -
289A LYS* 3.8 41.4 - - - +
290A ARG* 4.1 4.3 - - - -
690B GLN* 4.6 2.5 - - - -
289C LYS* 5.5 4.5 + - - -
682D ARG* 1.3 73.4 - - - +
684D GLY* 1.3 56.7 + - - +
686D ALA* 4.3 4.5 + - - +
687D GLY* 3.2 20.6 + - - -
691D ARG* 4.4 4.7 - - - -
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Residues in contact with GLY 684 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A LYS 4.9 2.7 - - - -
290A ARG* 3.4 26.7 - - - +
565B PHE* 6.5 0.9 - - - -
571B HIS* 5.0 1.1 - - - -
682D ARG 3.1 6.4 - - - +
683D GLY* 1.3 76.4 - - - +
685D LEU* 1.3 60.3 + - - -
686D ALA 3.3 1.8 - - - -
687D GLY* 3.1 12.1 + - - -
688D GLU* 3.2 22.2 + - - +
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Residues in contact with LEU 685 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564B LEU* 3.7 49.0 + - + +
565B PHE* 6.2 3.0 - - + -
571B HIS* 3.6 28.5 - - + +
575B GLY* 4.1 20.4 - - - +
578B MET* 5.8 0.2 - - + -
579B LEU* 3.9 29.6 - - + -
647B ILE* 4.1 12.1 - - + -
651B MET* 4.5 0.4 - - + -
684D GLY* 1.3 68.9 - - - -
686D ALA* 1.3 66.3 + - - +
688D GLU* 3.3 9.9 + - - +
689D PHE* 3.1 43.7 + - + -
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Residues in contact with ALA 686 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565B PHE* 6.2 0.9 - - + -
646B ASP* 3.9 16.4 - - + +
647B ILE* 3.7 25.0 - - + +
650B ILE* 3.6 32.5 - - + +
289C LYS* 4.7 4.0 - - - +
683D GLY 4.6 4.3 - - - +
684D GLY 3.3 0.4 - - - -
685D LEU* 1.3 77.5 - - - +
687D GLY* 1.3 62.3 + - - +
689D PHE* 3.5 0.9 + - - -
690D GLN* 3.0 26.7 + - - +
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Residues in contact with GLY 687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690B GLN* 5.5 0.7 - - - -
289C LYS* 5.1 6.2 - - - +
683D GLY* 3.2 14.7 + - - -
684D GLY 3.1 10.0 + - - -
686D ALA* 1.3 79.5 - - - +
688D GLU* 1.4 53.1 + - - +
690D GLN* 3.5 6.9 + - - +
691D ARG* 3.2 47.5 + - - -
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Residues in contact with GLU 688 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571B HIS* 2.9 40.6 + - - -
579B LEU* 3.9 21.9 - - + +
682D ARG 4.7 6.9 + - - +
684D GLY 3.2 16.7 + - - +
685D LEU* 3.6 6.9 - - - +
687D GLY* 1.4 72.8 - - - +
689D PHE* 1.3 64.3 + - - +
691D ARG* 3.1 38.1 + - - +
692D LEU* 3.4 16.3 - - - +
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Residues in contact with PHE 689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578B MET* 3.7 20.2 - - + -
579B LEU* 3.5 44.6 - - + -
582B PHE* 4.0 14.2 - + + -
614B PHE* 4.8 3.6 - + - -
647B ILE* 5.4 1.1 - - + -
650B ILE* 3.6 20.6 - - + -
651B MET* 3.5 33.7 - - + -
654B VAL* 3.8 17.9 - - + -
685D LEU* 3.1 42.8 + - + +
686D ALA* 4.8 0.7 - - - -
688D GLU* 1.3 70.4 - - - +
690D GLN* 1.4 56.6 + - - +
691D ARG 3.0 4.7 - - - -
692D LEU* 3.0 30.5 + - + +
693D LEU* 3.4 16.9 + - - +
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Residues in contact with GLN 690 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650B ILE* 3.7 17.3 - - + +
653B MET* 5.8 0.8 - - - -
682B ARG* 3.5 22.3 + - - +
683B GLY* 3.5 29.3 - - - +
691B ARG* 2.9 19.9 + - - -
289C LYS* 3.0 28.1 + - - -
686D ALA 3.0 16.8 + - - +
687D GLY* 3.7 7.5 - - - +
689D PHE* 1.4 74.1 - - - +
691D ARG* 1.3 56.6 + - - +
692D LEU 3.4 0.7 - - - -
693D LEU* 4.2 13.1 - - + +
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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