Contacts of the helix formed by residues 254 - 264 (chain A) in PDB entry 1EG2
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 GLY 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A ALA* 2.9 15.0 + - - -
252A GLY 3.3 1.4 + - - -
253A SER* 1.3 79.3 - - - +
255A VAL* 1.3 65.5 + - - +
256A THR* 3.1 4.2 + - - -
257A ALA* 3.1 16.6 + - - +
258A ARG 3.5 6.9 + - - -
269A CYS* 5.3 2.2 - - - -
276A PHE* 3.8 17.9 - - - -
280A TYR* 4.6 8.0 - - - -
283A GLN* 3.7 11.4 - - - +
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Residues in contact with VAL 255 (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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219A GLU* 5.2 0.4 - - - +
226A GLN* 5.3 1.8 - - + +
227A LYS* 3.8 43.3 - - + +
229A ALA* 4.0 24.9 - - + +
232A ILE* 4.2 16.4 - - + -
248A ASP* 5.6 0.4 - - - +
251A ALA 5.2 2.7 - - - +
253A SER* 3.3 16.9 + - - +
254A GLY* 1.3 77.9 - - - +
256A THR* 1.3 67.1 + - - +
258A ARG* 3.3 10.9 + - + +
259A VAL* 3.1 26.2 + - + +
283A GLN* 4.1 13.5 - - - +
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Residues in contact with THR 256 (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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63A ILE* 3.6 20.0 - - + +
227A LYS* 5.5 0.2 - - - -
232A ILE* 4.4 11.2 - - + +
236A VAL* 5.5 0.7 - - + +
246A VAL* 3.6 33.0 - - + +
248A ASP* 2.7 38.6 + - + -
251A ALA* 5.5 0.4 + - - -
254A GLY 3.1 1.2 - - - -
255A VAL* 1.3 85.6 - - - +
257A ALA* 1.3 55.9 + - - +
259A VAL* 3.4 1.9 + - - +
260A ALA* 2.9 26.7 + - - +
267A SER* 5.1 1.3 - - - -
269A CYS* 3.9 12.6 - - - -
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Residues in contact with ALA 257 (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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40A HIS* 5.0 0.7 - - - +
254A GLY 3.1 7.8 + - - +
256A THR* 1.3 75.8 - - - +
258A ARG* 1.3 65.3 + - - +
260A ALA* 3.2 1.4 + - - +
261A ILE* 2.9 34.8 + - + +
267A SER* 3.8 15.7 - - - +
269A CYS* 3.7 10.5 - - - -
280A TYR* 3.4 42.6 - - + +
283A GLN* 6.0 1.1 - - + -
284A LEU* 5.9 1.3 - - + -
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Residues in contact with ARG 258 (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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219A GLU* 3.4 50.6 + - - +
226A GLN* 5.2 1.0 - - - +
229A ALA* 3.9 18.5 - - - +
233A GLU* 5.9 0.2 + - - -
254A GLY 3.5 2.4 + - - +
255A VAL* 3.3 13.2 + - - +
257A ALA* 1.3 78.0 - - - +
259A VAL* 1.3 63.6 + - + +
261A ILE* 3.5 2.1 + - - +
262A GLN* 3.1 53.7 + - - +
283A GLN* 3.1 40.5 + - + +
284A LEU* 6.2 0.8 - - - +
286A PHE* 4.2 26.2 + - - +
287A LEU* 3.8 21.9 - - + +
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Residues in contact with VAL 259 (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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229A ALA* 4.0 24.2 - - + +
232A ILE* 3.9 22.0 - - + -
233A GLU* 3.7 33.2 - - + +
236A VAL* 3.8 18.8 - - + -
255A VAL* 3.1 19.0 + - + +
256A THR 3.8 3.8 - - - +
258A ARG* 1.3 74.2 - - + +
260A ALA* 1.3 60.1 + - - +
262A GLN* 3.3 9.5 + - - +
263A GLU* 2.8 39.4 + - + +
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Residues in contact with ALA 260 (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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40A HIS* 3.8 5.2 - - + -
236A VAL* 5.1 4.2 - - + +
246A VAL* 4.8 6.7 - - + -
256A THR 2.9 17.9 + - - +
257A ALA 3.2 4.9 + - - +
259A VAL* 1.3 78.0 - - - +
261A ILE* 1.3 62.1 + - - +
263A GLU* 3.2 3.0 + - - -
264A GLY 3.0 5.0 + - - -
265A ARG* 2.8 41.2 + - + +
266A ASN 4.2 4.5 - - - +
267A SER* 3.6 27.4 - - - -
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Residues in contact with ILE 261 (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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38A THR* 4.7 3.5 + - - -
40A HIS* 3.2 29.2 - - + +
257A ALA* 2.9 23.9 + - + +
258A ARG 3.7 3.6 - - - +
260A ALA* 1.3 75.7 - - - +
262A GLN* 1.3 63.4 + - - +
264A GLY* 3.2 12.6 + - - -
265A ARG 4.5 0.2 - - - -
284A LEU* 4.0 5.8 - - + -
287A LEU* 3.3 35.7 - - + -
297A ARG* 4.1 15.2 - - - +
299A TYR* 3.7 46.0 - - + -
301A ILE* 3.9 16.2 - - + -
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Residues in contact with GLN 262 (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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229A ALA* 5.5 0.2 - - - +
233A GLU* 3.7 21.8 + - - -
258A ARG* 3.1 42.1 + - - +
259A VAL* 3.8 11.2 - - - +
261A ILE* 1.3 76.5 - - - +
263A GLU* 1.3 69.3 + - - +
264A GLY 3.7 0.3 + - - -
286A PHE 5.2 2.8 - - - +
287A LEU* 3.4 25.5 - - + +
297A ARG* 3.7 26.0 + - - +
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Residues in contact with GLU 263 (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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233A GLU* 4.5 8.7 - - - +
236A VAL* 4.1 16.6 - - + -
237A ARG* 2.9 51.3 + - + +
242A PRO* 5.0 1.9 - - - +
259A VAL* 2.8 35.3 + - + +
260A ALA 4.0 1.8 - - - +
262A GLN* 1.3 88.0 + - - +
264A GLY* 1.3 59.2 + - - +
265A ARG* 2.7 37.9 + - - +
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Residues in contact with GLY 264 (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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38A THR* 3.5 21.5 - - - +
242A PRO* 3.8 4.5 - - - +
243A GLY* 2.8 22.7 + - - -
260A ALA 3.0 3.8 + - - -
261A ILE 3.2 8.9 + - - -
262A GLN 3.4 1.4 + - - -
263A GLU* 1.3 78.8 - - - +
265A ARG* 1.3 60.8 + - - +
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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