Contacts of the helix formed by residues 240 - 247 (chain A) in PDB entry 1EGA
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 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A ARG* 1.3 72.2 - - - +
241A GLY* 1.3 62.6 + - - +
242A GLN 3.0 1.8 - - - -
243A LYS* 2.6 53.5 + - - +
244A LYS* 2.7 35.0 + - - +
281A VAL* 3.8 14.9 - - + +
286A ALA* 5.2 5.7 - - - +
289A GLU* 4.3 0.5 - - - +
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Residues in contact with GLY 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ARG* 4.3 4.0 - - - +
240A GLU* 1.3 78.7 - - - +
242A GLN* 1.3 61.1 + - - +
244A LYS* 3.3 21.3 + - - +
245A MET* 3.4 16.6 + - - +
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Residues in contact with GLN 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A PRO* 3.3 39.1 - - + +
212A TYR 4.7 3.6 + - - +
237A VAL* 2.9 26.1 - - + +
238A GLU* 3.3 12.4 + - - +
239A ARG* 2.9 39.4 + - + +
241A GLY* 1.3 76.4 - - - +
243A LYS* 1.3 57.2 + - - +
245A MET* 2.9 42.0 + - + +
246A VAL* 3.3 9.9 + - - +
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Residues in contact with LYS 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A VAL* 4.0 10.7 - - + +
239A ARG 3.5 7.6 + - - +
240A GLU* 2.6 47.2 + - - +
242A GLN* 1.3 81.0 - - - +
244A LYS* 1.3 78.4 + - - +
246A VAL 3.6 1.0 + - - -
247A ILE* 3.2 36.1 + - + +
279A VAL* 3.6 26.2 - - + +
280A LYS* 4.5 4.9 - - - +
281A VAL* 4.1 17.5 - - + +
286A ALA* 5.0 3.2 - - - +
289A GLU* 2.6 31.8 + - - +
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Residues in contact with LYS 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A GLU* 2.7 33.9 + - - +
241A GLY* 3.3 14.3 + - - +
242A GLN 3.1 0.6 - - - -
243A LYS* 1.3 97.6 - - - +
245A MET* 1.3 55.6 + - - +
247A ILE* 3.8 10.9 - - + +
248A GLY* 2.8 31.0 + - - +
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Residues in contact with MET 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LEU* 4.7 7.4 - - + +
209A GLU* 3.2 61.7 - - + +
211A PRO* 5.4 3.6 - - + -
241A GLY 3.4 8.2 + - - +
242A GLN* 2.9 44.6 + - + +
244A LYS* 1.3 75.1 - - - +
246A VAL* 1.3 69.4 + - + +
247A ILE 3.0 1.3 - - - -
248A GLY* 2.9 16.7 + - - -
253A LYS* 4.1 9.7 + - - +
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Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LEU* 4.1 20.2 - - + -
206A LEU* 4.0 26.2 - - + -
211A PRO* 5.8 4.3 - - + -
214A VAL* 5.7 3.4 - - + -
235A ILE* 4.2 11.9 - - + -
237A VAL* 5.0 7.4 - - + -
242A GLN 3.3 13.6 + - - +
243A LYS 4.0 0.2 - - - +
245A MET* 1.3 76.4 - - + +
247A ILE* 1.3 60.0 + - - +
253A LYS* 3.6 6.1 - - - +
254A ILE* 3.3 30.7 + - + +
257A ILE* 4.7 2.8 - - + +
279A VAL* 3.5 36.3 - - + -
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Residues in contact with ILE 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A LYS* 3.2 41.1 + - + +
244A LYS* 3.8 11.2 - - + +
245A MET 3.0 0.6 - - - -
246A VAL* 1.3 78.9 - - - +
248A GLY* 1.3 71.4 + - - +
251A GLY* 3.3 31.3 - - - +
253A LYS* 3.5 0.6 + - - -
254A ILE* 3.3 21.3 + - + -
279A VAL* 4.0 17.9 - - + -
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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