Contacts of the helix formed by residues 235 - 241 (chain D) in PDB entry 3GXM
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 GLU 235 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233D GLU* 4.6 0.9 - - - +
234D ASN* 1.3 87.1 + - - +
236D PRO* 1.4 70.1 - - - +
237D SER 3.1 2.5 - - - -
238D ALA* 3.0 27.2 + - + +
239D GLY 4.2 1.2 + - - -
244D TYR* 4.1 15.2 + - - +
246D PHE* 5.9 2.0 - - - -
248D CYS* 5.1 2.3 - - - +
249D LEU 4.7 0.5 - - - +
282D ASP 2.8 24.4 + - - +
283D ASP* 3.4 21.9 - - - +
284D GLN* 4.3 5.3 + - - -
311D HIS* 2.9 22.4 + - + -
313D TYR* 2.7 29.8 + - - -
340D GLU* 4.1 3.5 - - - +
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Residues in contact with PRO 236 (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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233D GLU* 3.7 25.8 - - + +
234D ASN 3.3 0.4 - - - -
235D GLU* 1.4 87.4 - - - +
237D SER* 1.3 59.4 + - - +
238D ALA 3.3 0.7 + - - -
239D GLY 3.5 0.7 + - - -
240D LEU* 4.0 0.7 - - - +
249D LEU 3.7 3.1 - - - +
250D GLY* 3.1 12.3 - - - -
251D PHE* 3.0 35.0 + - + +
256D GLN* 4.3 6.3 - - - +
281D LEU* 3.0 28.5 - - + +
283D ASP* 3.5 7.2 - - + +
291D TRP* 3.5 34.1 - - + -
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Residues in contact with SER 237 (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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235D GLU* 5.2 0.2 - - - +
236D PRO* 1.3 79.3 - - - +
238D ALA* 1.3 64.2 + - - +
239D GLY 3.4 0.2 - - - -
240D LEU* 3.3 33.8 - - - +
241D LEU* 3.9 11.3 - - - +
251D PHE 4.4 1.1 - - - -
283D ASP* 2.6 27.9 + - - -
284D GLN* 5.6 0.7 - - - +
287D LEU* 3.8 22.6 - - - +
291D TRP* 4.8 5.4 - - - -
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Residues in contact with ALA 238 (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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235D GLU* 3.0 25.2 + - + +
237D SER* 1.3 77.8 + - - +
239D GLY* 1.3 58.1 + - - +
240D LEU 3.0 9.8 + - - -
241D LEU* 3.3 17.6 + - - +
244D TYR* 3.5 57.8 - - + +
248D CYS* 4.4 4.9 - - + -
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Residues in contact with GLY 239 (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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193D GLY 4.2 2.5 - - - -
194D LYS* 4.0 2.0 - - - +
195D GLY 3.0 33.3 + - - +
235D GLU 4.2 1.0 + - - -
236D PRO 3.5 4.6 + - - -
237D SER 3.4 0.8 - - - -
238D ALA* 1.3 76.0 - - - +
240D LEU* 1.3 56.7 + - - +
241D LEU 3.4 1.1 - - - -
248D CYS* 3.6 23.8 - - - +
250D GLY* 3.4 25.8 - - - +
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Residues in contact with LEU 240 (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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194D LYS* 2.9 32.5 - - - -
196D SER* 6.0 2.7 - - - -
236D PRO 4.0 4.5 - - - +
237D SER* 3.3 25.4 - - - +
238D ALA 3.0 1.2 - - - -
239D GLY* 1.3 78.5 - - - +
241D LEU* 1.3 61.6 + - + +
242D SER 4.2 0.2 + - - -
250D GLY* 4.3 5.4 - - - -
251D PHE 3.6 33.4 - - - +
252D THR* 4.0 28.5 - - + -
253D PRO* 5.7 0.9 - - + -
291D TRP* 5.5 1.6 - - + -
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Residues in contact with LEU 241 (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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346C LYS* 5.1 15.0 - - + +
348C TRP* 4.2 15.3 - - + -
194D LYS* 3.5 13.4 + - - -
237D SER 3.9 15.3 - - - +
238D ALA* 3.3 10.5 + - - +
239D GLY 3.4 0.4 - - - -
240D LEU* 1.3 82.4 - - + +
242D SER* 1.3 67.3 + - - +
244D TYR* 3.3 38.2 + - + +
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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