Contacts of the helix formed by residues 228 - 242 (chain A) in PDB entry 3RIG
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 ASP 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A ILE 5.2 1.6 + - - -
221A VAL* 5.2 3.2 - - - +
226A ASN 3.8 0.8 + - - -
227A LEU* 1.3 72.5 - - - +
229A PRO* 1.4 73.2 - - - +
230A ALA* 2.9 24.5 + - - +
231A ILE* 3.1 34.1 + - + +
232A LEU* 3.0 20.8 + - - +
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Residues in contact with PRO 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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226A ASN* 5.9 1.3 - - + -
227A LEU 3.4 8.5 - - - +
228A ASP* 1.4 91.2 - - - +
230A ALA* 1.3 56.8 + - - +
232A LEU* 3.3 10.7 + - + +
233A GLU* 3.0 42.6 + - - +
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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
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228A ASP* 2.9 12.0 + - - +
229A PRO* 1.3 78.4 - - - +
231A ILE* 1.3 65.5 + - + +
233A GLU* 3.5 12.4 + - - +
234A GLU* 3.1 22.7 + - - +
237A ARG* 5.2 1.4 + - - -
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Residues in contact with ILE 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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155A LEU* 4.7 11.0 - - + -
156A GLU 4.0 18.8 - - - +
157A ILE* 3.9 38.1 - - + +
159A GLY 6.2 0.2 - - - +
227A LEU* 6.1 0.9 - - + -
228A ASP* 3.1 33.7 + - + +
230A ALA* 1.3 77.9 - - + +
232A LEU* 1.3 58.1 + - + +
234A GLU* 3.2 11.9 + - - +
235A VAL* 3.0 28.3 + - + +
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Residues in contact with LEU 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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157A ILE* 5.8 0.4 - - + -
227A LEU* 4.0 37.5 - - + +
228A ASP 3.0 18.6 + - - +
229A PRO* 3.3 10.7 + - + +
231A ILE* 1.3 78.5 - - + +
233A GLU* 1.3 57.2 + - + +
235A VAL* 3.4 7.3 + - + +
236A ASP* 2.9 35.8 + - - +
256A PRO* 4.5 7.4 - - + -
260A PHE* 4.2 22.0 - - + -
6C THR* 6.2 0.9 - - + -
7C ALA* 3.7 34.8 - - + -
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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 PRO* 3.0 30.8 + - + +
230A ALA* 3.8 8.8 - - - +
232A LEU* 1.3 75.6 - - + +
234A GLU* 1.3 62.3 + - - +
236A ASP* 3.2 11.7 + - - +
237A ARG* 3.1 45.4 + - - +
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Residues in contact with GLU 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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134A ARG* 5.6 1.7 + - - -
155A LEU* 2.9 40.5 - - + +
230A ALA 3.1 14.8 + - - +
231A ILE* 3.2 13.8 + - - +
233A GLU* 1.3 70.9 - - - +
235A VAL* 1.3 67.5 + - - +
237A ARG* 3.0 36.7 + - + +
238A GLU* 3.0 25.5 + - + +
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Residues in contact with VAL 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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138A ILE* 4.0 14.6 - - + -
155A LEU* 3.8 19.0 - - + +
157A ILE* 3.9 24.2 - - + -
231A ILE 3.0 17.9 + - - +
232A LEU* 3.5 12.8 - - + +
234A GLU* 1.3 75.9 - - - +
236A ASP* 1.3 66.3 + - - +
238A GLU* 3.1 2.5 + - - +
239A LEU* 2.8 45.8 + - + +
260A PHE* 3.7 31.6 - - + -
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Residues in contact with ASP 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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232A LEU* 2.9 21.3 + - - +
233A GLU* 3.2 13.6 + - - +
235A VAL* 1.3 79.3 - - - +
237A ARG* 1.3 56.8 + - - +
239A LEU* 3.4 9.1 + - - +
240A ALA* 2.9 30.5 + - - +
260A PHE* 5.6 2.6 - - - -
263A GLN* 4.0 18.9 + - - -
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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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230A ALA 5.2 1.0 + - - -
233A GLU* 3.1 40.7 + - - +
234A GLU* 3.0 36.4 + - + +
236A ASP* 1.3 72.6 - - + +
238A GLU* 1.3 67.3 + - + +
240A ALA* 3.4 4.6 + - - +
241A HIS* 3.2 36.7 + - + +
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Residues in contact with GLU 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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52A HIS* 2.6 43.6 + - - -
54A VAL* 3.6 12.9 - - + +
134A ARG* 2.7 30.5 + - - -
136A VAL* 3.3 17.1 - - + +
138A ILE* 4.3 9.0 - - + -
155A LEU* 4.7 11.1 - - + +
234A GLU* 3.0 30.2 + - + +
235A VAL 3.6 5.2 - - - +
237A ARG* 1.3 77.4 - - + +
239A LEU* 1.3 57.0 + - - +
241A HIS 3.3 1.2 + - - -
242A CYS* 3.0 33.4 + - - +
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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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54A VAL* 4.0 24.2 - - + -
56A ILE* 4.4 3.1 - - + -
138A ILE* 4.1 9.2 - - + -
235A VAL* 2.8 40.2 + - + +
236A ASP* 3.7 8.1 - - - +
238A GLU* 1.3 75.2 - - - +
240A ALA* 1.3 55.8 + - - +
241A HIS 3.4 0.3 + - - -
242A CYS* 3.7 7.9 + - - -
260A PHE* 3.8 34.1 - - + +
263A GLN* 3.8 25.4 - - + +
264A VAL* 3.7 27.2 - - + +
267A ARG* 2.8 24.9 + - - -
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Residues in contact with ALA 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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236A ASP 2.9 19.1 + - - +
237A ARG* 3.9 6.1 - - - +
238A GLU 3.3 0.2 - - - -
239A LEU* 1.3 75.9 - - - +
241A HIS* 1.3 70.0 + - + +
267A ARG* 3.3 30.7 + - - +
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Residues in contact with HIS 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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52A HIS* 3.8 25.4 + - + +
237A ARG* 3.2 31.8 + - + +
239A LEU 3.2 0.2 - - - -
240A ALA* 1.3 89.0 + - + +
242A CYS* 1.3 69.9 + - - +
243A ASP* 3.6 3.1 + - - +
267A ARG* 5.4 0.2 - - - -
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Residues in contact with CYS 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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52A HIS* 3.2 19.7 - - + +
54A VAL* 3.3 32.1 - - + -
238A GLU 3.0 5.6 + - - +
239A LEU 3.8 9.0 - - - -
240A ALA 3.6 0.4 - - - -
241A HIS* 1.3 81.7 - - - +
243A ASP* 1.3 60.0 + - - +
244A LEU 3.8 15.5 - - - +
245A CYS* 4.2 3.6 - - - -
264A VAL* 3.7 31.9 - - - -
267A ARG* 2.9 22.4 + - - -
269A VAL* 4.0 2.9 - - - +
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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