Contacts of the helix formed by residues 228 - 240 (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 PRO 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A TRP* 3.5 36.6 - - + -
210A MET* 5.9 2.2 - - + -
211A SER 3.8 15.0 - - - +
212A ARG* 4.5 0.9 - - + -
213A LEU* 3.5 27.8 - - + +
219A GLU* 3.8 8.5 - - - +
226A GLN 4.2 4.7 - - - +
227A LYS* 1.3 85.3 - - + +
229A ALA* 1.3 65.7 + - - +
230A ALA* 3.2 8.0 + - + +
231A VAL* 2.9 32.6 - - + +
232A ILE* 3.6 2.9 + - - +
255A VAL* 4.5 0.4 - - - -
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Residues in contact with ALA 229 (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* 3.1 22.6 + - - +
227A LYS 3.7 1.2 + - - -
228A PRO* 1.3 72.3 - - - +
230A ALA* 1.3 53.0 + - - +
232A ILE* 3.1 3.4 + - - +
233A GLU* 2.7 49.0 + - - +
255A VAL* 4.0 13.0 - - + +
258A ARG* 3.9 25.8 - - - +
259A VAL* 4.1 14.6 - - + -
262A GLN* 5.5 0.9 - - - +
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Residues in contact with ALA 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A MET* 3.2 28.4 - - + +
219A GLU* 5.0 1.6 + - - -
228A PRO* 3.2 7.3 - - + +
229A ALA* 1.3 78.5 - - - +
231A VAL* 1.3 61.1 + - - +
233A GLU* 3.5 17.6 + - - +
234A ARG* 3.3 19.4 + - - +
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Residues in contact with VAL 231 (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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105A PHE* 4.1 12.3 - - + -
140A TRP* 4.7 14.8 - - + -
159A ILE* 3.9 28.0 - - + -
208A TRP* 4.0 11.6 - - + -
210A MET* 3.6 15.6 - - - +
227A LYS* 4.4 4.5 - - + -
228A PRO* 2.9 44.7 + - + +
230A ALA* 1.3 75.4 - - - +
232A ILE* 1.3 85.1 + - + +
234A ARG* 3.4 6.0 + - - +
235A LEU* 3.4 20.6 + - - +
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Residues in contact with ILE 232 (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* 4.1 16.4 - - + -
105A PHE* 3.8 30.3 - - + -
227A LYS* 3.9 18.6 - - + -
228A PRO 3.8 12.3 - - - +
229A ALA 3.1 5.7 + - - +
231A VAL* 1.3 82.6 - - + +
233A GLU* 1.3 59.8 + - - +
235A LEU* 3.2 7.0 + - + +
236A VAL* 2.9 40.8 + - + +
255A VAL* 4.2 19.3 - - + -
256A THR* 4.4 17.0 - - - +
259A VAL* 3.9 20.9 - - + -
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Residues in contact with GLU 233 (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* 2.7 39.6 + - - +
230A ALA* 3.5 17.9 - - - +
231A VAL 3.3 0.2 - - - -
232A ILE* 1.3 73.2 - - - +
234A ARG* 1.3 56.8 + - - +
236A VAL* 3.3 0.9 + - - +
237A ARG* 2.9 68.6 + - - +
259A VAL* 3.7 25.1 - - + -
262A GLN* 3.7 20.4 + - - +
263A GLU* 4.5 4.4 - - - +
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Residues in contact with ARG 234 (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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175A VAL* 3.6 27.4 + - + +
177A GLU* 3.2 30.1 + - - +
204A PRO* 3.7 23.2 + - + +
208A TRP* 3.4 69.8 - - + +
210A MET* 4.4 15.0 - - + +
230A ALA 3.3 10.3 + - - +
231A VAL 3.7 8.5 - - - +
232A ILE 3.3 0.6 - - - -
233A GLU* 1.3 80.1 - - - +
235A LEU* 1.3 63.0 + - - +
237A ARG* 4.7 2.2 - - - +
238A ALA* 3.1 26.1 + - + +
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Residues in contact with LEU 235 (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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61A LEU* 3.8 2.8 - - + +
63A ILE* 4.1 18.2 - - + -
103A ALA* 3.9 29.8 - - + -
105A PHE* 3.9 29.2 - - + -
138A ILE* 4.5 6.3 - - + -
159A ILE* 4.4 13.7 - - + -
161A TRP* 5.8 0.4 - - + -
208A TRP* 3.7 22.9 - - + -
231A VAL 3.4 12.3 + - - +
232A ILE* 3.2 10.2 + - + +
234A ARG* 1.3 75.8 - - - +
236A VAL* 1.3 58.9 + - - +
238A ALA* 5.1 0.2 - - - -
239A LEU* 2.9 53.0 + - + +
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Residues in contact with VAL 236 (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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61A LEU* 3.8 16.4 - - + -
63A ILE* 4.7 2.5 - - + -
232A ILE* 2.9 30.4 + - + +
233A GLU 3.8 3.1 - - - +
235A LEU* 1.3 77.3 - - - +
237A ARG* 1.3 61.8 + - - +
240A SER* 2.7 40.1 + - - +
246A VAL* 4.5 16.6 - - + -
256A THR 5.5 1.1 - - - +
259A VAL* 3.8 20.0 - - + +
260A ALA* 5.1 3.4 - - - +
263A GLU* 4.1 16.2 - - + -
265A ARG* 3.5 24.1 + - + +
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Residues in contact with ARG 237 (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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171A ASP* 3.5 17.5 - - - +
174A ALA* 3.9 28.2 + - + +
175A VAL* 3.8 15.3 - - + -
233A GLU* 2.9 47.1 + - - +
234A ARG* 4.9 1.3 - - - +
236A VAL* 1.3 77.3 - - - +
238A ALA* 1.3 59.6 + - - +
240A SER 3.7 7.1 - - - +
263A GLU* 2.9 47.0 + - + +
265A ARG* 3.7 12.3 + - - +
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Residues in contact with ALA 238 (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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169A PHE* 4.0 0.7 - - - -
170A PHE* 3.3 26.1 - - + -
171A ASP* 2.9 32.3 + - - +
175A VAL* 3.7 23.6 - - + -
234A ARG* 3.1 19.3 + - + +
235A LEU* 4.4 0.7 - - - +
237A ARG* 1.3 79.6 - - - +
239A LEU* 1.3 65.2 + - + +
240A SER 3.6 0.8 + - - -
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Residues in contact with LEU 239 (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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60A GLN* 3.0 22.5 + - - +
61A LEU* 3.9 28.1 - - + +
101A SER* 4.6 6.7 - - - +
103A ALA* 4.7 3.6 - - + -
138A ILE* 6.3 0.2 - - + -
161A TRP* 3.5 58.8 - - + +
169A PHE* 3.8 12.0 - - - +
170A PHE* 3.7 12.6 - - + -
235A LEU* 2.9 41.5 + - + +
236A VAL 4.2 0.2 - - - -
238A ALA* 1.3 88.1 - - + +
240A SER* 1.3 61.1 + - - +
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Residues in contact with SER 240 (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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60A GLN* 3.8 12.1 - - - -
61A LEU* 4.0 16.6 - - - -
169A PHE* 3.3 14.6 - - - -
236A VAL* 2.7 25.3 + - - +
237A ARG 3.7 1.7 - - - +
238A ALA 3.6 0.6 - - - -
239A LEU* 1.3 79.2 - - - +
241A HIS* 1.3 54.7 + - - +
244A SER* 3.5 12.6 - - - -
246A VAL* 4.2 4.9 - - - +
265A ARG* 2.6 44.7 + - - +
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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