Contacts of the helix formed by residues 240 - 246 (chain x) in PDB entry 5GJQ
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 SER 240 (chain x).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211x GLN* 3.2 23.8 - - - -
214x LEU 3.5 10.3 - - - -
216x ALA* 3.7 10.0 - - - +
238x LYS 3.8 0.2 - - - -
239x LYS* 1.3 81.8 + - - +
241x LEU* 1.3 69.5 + - - +
242x ILE 2.8 2.3 + - - -
243x ASP* 2.3 56.5 + - - +
244x GLN* 3.1 10.7 + - - +
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Residues in contact with LEU 241 (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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127x GLU 4.3 16.8 - - - +
128x LEU* 4.5 16.4 - - + +
131x ALA* 4.1 19.3 - - + -
134x ARG* 6.2 1.6 - - - +
214x LEU* 3.3 30.8 + - + +
215x GLU 3.5 21.1 + - - +
216x ALA* 4.5 2.0 - - - +
217x ILE* 4.0 26.7 - - + +
240x SER* 1.3 70.9 - - - +
242x ILE* 1.3 64.0 + - - +
244x GLN* 3.2 9.0 + - - +
245x PHE* 3.1 40.8 + - + -
246x PHE* 5.4 2.2 - - + -
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Residues in contact with ILE 242 (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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128x LEU* 5.1 3.4 - - + -
207x MET* 3.0 48.7 - - + +
210x LEU* 3.3 16.2 - - + -
211x GLN* 3.2 31.7 - - + +
214x LEU* 4.9 6.0 - - + +
240x SER* 2.8 4.4 + - - -
241x LEU* 1.3 72.2 - - - +
243x ASP* 1.3 67.9 + - - +
244x GLN 2.9 1.8 - - - -
245x PHE 2.7 14.2 + - - -
246x PHE* 2.8 33.9 + - + -
247x GLY 3.7 0.9 + - - -
272x LEU* 2.9 34.3 - - + -
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Residues in contact with ASP 243 (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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211x GLN* 3.7 23.6 + - - +
238x LYS* 4.1 28.3 + - + -
240x SER* 2.3 39.2 + - - +
242x ILE* 1.3 78.4 - - - +
244x GLN* 1.3 60.2 + - - +
247x GLY* 3.6 22.5 + - - +
270x ASN* 6.0 1.4 - - - +
272x LEU* 4.7 10.7 - - - +
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Residues in contact with GLN 244 (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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216x ALA* 3.4 21.6 - - + +
217x ILE* 3.3 36.6 + - - +
218x GLU* 5.2 1.0 - - - +
238x LYS* 4.1 26.3 - - + +
240x SER 3.1 13.3 + - - +
241x LEU* 3.2 10.5 - - - +
242x ILE 2.8 1.4 + - - -
243x ASP* 1.3 78.9 - - - +
245x PHE* 1.3 67.3 + - + +
246x PHE 3.7 0.2 - - - -
409x ILE 4.5 7.6 - - - +
410x GLY 4.4 0.3 - - - -
411x SER* 3.2 45.5 + - - +
412x ASN* 2.8 23.3 - - - +
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Residues in contact with PHE 245 (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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125x VAL* 5.7 0.4 - - + -
127x GLU* 3.4 30.3 - - + -
128x LEU 6.0 0.2 - - - -
217x ILE* 4.0 29.2 - - + -
241x LEU* 3.1 33.4 + - + +
242x ILE 2.7 9.9 + - - -
244x GLN* 1.3 86.7 - - + +
246x PHE* 1.3 67.4 + - + -
320x PRO* 4.0 5.2 - - - -
321x ALA* 3.8 16.4 - - + +
322x TYR* 3.0 59.6 + + + +
411x SER* 4.2 18.8 - - - -
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Residues in contact with PHE 246 (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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122x ILE* 6.0 0.2 - - - -
125x VAL* 3.8 34.8 - - + -
128x LEU* 4.1 23.8 - - + -
207x MET* 4.1 22.0 - - + -
241x LEU* 5.4 1.8 - - + -
242x ILE* 2.8 31.7 + - + -
245x PHE* 1.3 91.1 - - + +
247x GLY* 1.3 63.1 + - - +
248x VAL* 3.8 1.6 + - - +
272x LEU* 3.3 39.8 - - + +
320x PRO* 3.2 17.9 - - - +
322x TYR* 3.3 26.9 - - + +
323x LEU* 5.0 1.9 - - - +
324x THR* 3.7 16.8 - - - +
478x LEU* 4.3 10.3 - - + -
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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