Contacts of the helix formed by residues 305 - 311 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111U GLY* 3.8 12.8 - - - +
119U GLY 2.9 20.0 + - - +
329U GLU* 4.6 2.7 - - - +
330U PRO* 3.6 35.0 - - + -
303X PRO* 4.6 0.6 - - - +
304X TYR* 1.3 81.4 - - - +
306X LYS* 1.3 61.5 + - - +
307X ILE 3.4 0.2 - - - -
308X LEU* 3.3 12.0 + - + +
309X GLU* 2.8 25.1 + - - +
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Residues in contact with LYS 306 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59U ARG* 3.4 47.4 - - - +
111U GLY 5.2 0.4 + - - -
329U GLU* 3.4 12.1 + - - +
304X TYR 3.3 1.4 + - - -
305X ALA* 1.3 69.0 - - - +
307X ILE* 1.3 62.9 + - - +
309X GLU* 3.1 1.4 + - - +
310X ASP* 2.7 73.4 + - - +
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Residues in contact with ILE 307 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329U GLU* 2.8 41.3 + - + +
330U PRO 3.8 21.3 - - - +
332U LEU* 4.0 24.2 - - + +
305X ALA* 4.9 2.0 - - + -
306X LYS* 1.3 74.0 - - - +
308X LEU* 1.3 76.3 + - + +
310X ASP* 3.4 10.1 + - - +
311X ASN* 2.6 40.4 + - - +
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Residues in contact with LEU 308 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119U GLY 4.6 0.4 - - - +
120U LYS* 4.0 31.0 - - + -
330U PRO* 3.6 27.1 - - + -
331U PRO 3.9 19.1 - - - +
332U LEU* 4.3 11.4 - - + +
334U GLU 4.6 1.3 - - - +
335U LEU* 3.3 38.6 - - + +
303X PRO* 3.6 15.9 - - + -
305X ALA* 3.3 19.2 + - + +
306X LYS 3.2 0.2 - - - -
307X ILE* 1.3 84.9 - - + +
309X GLU* 1.3 61.7 + - - +
311X ASN* 3.3 7.1 + - - -
312X SER* 2.8 19.6 + - - -
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Residues in contact with GLU 309 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59U ARG* 2.7 34.1 + - - +
121X SER 3.3 22.2 - - - +
122X ALA* 3.6 5.6 - - - +
123X GLY* 2.8 19.7 + - - -
125X ALA 5.6 0.2 + - - -
302X MET* 3.8 20.2 - - - -
303X PRO* 3.6 20.4 - - - +
304X TYR 4.1 0.7 - - - +
305X ALA 2.8 19.4 + - - +
306X LYS* 3.1 5.4 + - - +
308X LEU* 1.3 69.8 - - - +
310X ASP* 1.3 71.2 + - - +
311X ASN 3.0 2.7 - - - -
312X SER* 2.9 16.5 + - - -
313X ILE* 3.9 16.4 + - + +
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Residues in contact with ASP 310 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306X LYS* 2.7 61.9 + - - +
307X ILE* 3.8 8.4 - - - +
309X GLU* 1.3 78.6 - - - +
311X ASN* 1.3 61.5 + - - +
312X SER 3.3 0.4 - - - -
313X ILE* 3.5 22.7 + - - +
315X GLN* 3.4 25.0 - - - +
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Residues in contact with ASN 311 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332U LEU* 3.4 35.6 - - + +
335U LEU* 4.1 8.1 - - + +
351U ALA* 5.4 5.8 + - - +
357U PHE* 4.6 12.6 - - + -
298X ALA* 4.0 9.9 - - - +
307X ILE* 2.6 31.6 + - - +
308X LEU 3.3 4.8 + - - +
309X GLU 3.0 1.0 - - - -
310X ASP* 1.3 84.0 - - - +
312X SER* 1.3 61.6 + - - +
313X ILE 3.5 4.7 - - - -
315X GLN* 3.7 19.0 + - - +
317X LYS* 5.3 2.9 + - - -
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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