Contacts of the helix formed by residues 305 - 311 (chain R) in PDB entry 3EXG
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 ALA 305 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304R TYR* 1.3 77.4 - - - +
306R LYS* 1.3 66.6 + - - +
307R ILE 3.3 2.0 - - - +
308R LEU* 2.9 23.1 + - + +
309R GLU 2.9 10.0 + - - -
59S ARG* 5.6 0.2 - - - +
111S GLY* 3.5 26.7 - - - +
119S GLY 2.9 21.5 + - - +
329S GLU* 4.8 0.9 - - - +
330S PRO* 3.6 24.0 - - + -
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Residues in contact with LYS 306 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304R TYR 3.2 2.2 + - - -
305R ALA* 1.3 71.2 - - - +
307R ILE* 1.3 59.4 + - - +
309R GLU* 4.3 0.4 - - - -
310R ASP* 2.8 72.8 + - - +
59S ARG* 3.4 46.9 - - - +
329S GLU* 3.9 8.5 + - - +
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Residues in contact with ILE 307 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305R ALA 3.2 0.2 + - - -
306R LYS* 1.3 74.4 - - - +
308R LEU* 1.3 82.2 + - + +
310R ASP* 3.4 6.4 + - + +
311R ASN* 2.9 30.5 + - - +
329S GLU* 2.8 39.6 + - + +
330S PRO* 3.6 27.8 - - + +
332S LEU* 4.0 23.2 - - + +
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Residues in contact with LEU 308 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303R PRO* 3.9 18.8 - - + -
305R ALA* 2.9 13.3 + - + +
307R ILE* 1.3 95.1 - - + +
309R GLU* 1.3 61.0 + - - +
311R ASN* 3.1 13.1 + - - +
312R SER* 2.8 19.5 + - - -
118S LYS 4.7 1.6 - - - +
119S GLY 4.5 3.1 - - - +
120S LYS* 4.2 27.8 - - + -
330S PRO* 3.7 25.4 - - + -
331S PRO 3.7 23.3 - - - +
332S LEU* 4.2 6.1 - - - -
334S GLU 5.0 0.2 - - - -
335S LEU* 3.6 27.6 - - + +
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Residues in contact with GLU 309 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121R SER 3.9 7.6 - - - +
122R ALA* 3.6 6.9 - - - +
123R GLY* 2.9 32.2 + - - -
124R VAL 3.9 3.8 + - - -
125R ALA 4.4 0.9 + - - -
129R SER* 5.0 0.7 + - - -
302R MET* 3.8 23.8 - - + +
303R PRO* 3.3 23.1 - - - +
304R TYR 3.7 1.7 - - - +
305R ALA 2.9 14.2 + - - +
306R LYS 3.8 3.4 - - - +
308R LEU* 1.3 74.1 - - - +
310R ASP* 1.3 60.6 + - - +
311R ASN 2.9 4.9 - - - -
312R SER* 2.8 28.1 + - - -
313R ILE* 3.7 16.2 + - + +
59S ARG* 2.7 26.0 + - - +
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Residues in contact with ASP 310 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306R LYS* 2.8 69.3 + - - +
307R ILE* 3.8 8.3 - - + +
308R LEU 3.4 0.2 - - - -
309R GLU* 1.3 75.6 - - - +
311R ASN* 1.3 64.5 + - - +
312R SER 3.2 0.4 - - - -
313R ILE* 3.5 4.9 - - - +
315R GLN* 2.6 45.9 + - + +
59S ARG* 5.2 1.2 + - - -
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Residues in contact with ASN 311 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298R ALA* 3.9 7.4 - - - +
307R ILE* 2.9 25.1 + - - +
308R LEU 3.1 7.4 + - - +
309R GLU 2.9 1.2 - - - -
310R ASP* 1.3 86.8 - - - +
312R SER* 1.3 63.3 + - - +
313R ILE 3.6 2.7 - - - -
315R GLN* 5.3 3.8 - - - +
317R LYS* 5.3 6.9 + - - -
318R ASP* 5.9 1.6 - - - -
332S LEU* 3.2 37.3 - - + +
335S LEU* 3.6 14.9 - - + +
351S ALA* 5.4 5.5 + - - +
357S PHE* 4.3 10.8 - - + -
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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