Contacts of the helix formed by residues 235 - 252 (chain A) in PDB entry 3LRA
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 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A VAL 4.4 1.6 + - - -
133A ILE* 3.6 26.9 + - - +
176A HIS* 5.0 0.6 - - - -
231A ARG 2.9 15.3 + - - -
232A VAL* 2.7 24.0 + - - -
234A GLN* 1.3 78.6 - - - +
236A GLU* 1.3 58.6 + - - +
237A PHE* 3.0 19.7 + - - +
238A CYS* 3.5 10.0 + - - +
239A ASN* 2.9 25.8 + - - +
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Residues in contact with GLU 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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130A PRO* 3.5 31.0 - - + +
131A VAL 5.7 1.3 - - - +
234A GLN 3.3 3.8 + - - +
235A SER* 1.3 71.4 + - - +
237A PHE* 1.3 56.4 + - - +
239A ASN* 3.8 13.0 - - + +
240A ALA* 3.2 22.9 + - - +
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Residues in contact with PHE 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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129A SER* 4.0 11.7 - - - -
130A PRO* 3.2 31.0 - - + +
131A VAL 3.7 17.2 + - - +
132A PRO* 3.5 20.9 - - + -
176A HIS* 3.5 42.2 - + - -
179A VAL* 4.2 14.1 - - + -
180A ALA* 4.0 23.6 - - + -
235A SER* 3.0 9.1 + - - +
236A GLU* 1.3 80.1 - - - +
238A CYS* 1.3 61.1 + - - +
239A ASN 3.2 0.2 - - - -
240A ALA* 3.1 7.0 + - + +
241A VAL* 2.9 45.8 + - + +
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Residues in contact with CYS 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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172A LEU* 4.3 27.4 - - - -
173A LEU* 6.2 1.8 - - - -
176A HIS* 4.2 16.2 - - - +
205A ILE* 6.4 0.2 - - - -
232A VAL* 3.0 29.6 - - - +
233A LEU* 4.2 20.6 - - - +
235A SER* 3.1 7.9 + - - +
237A PHE* 1.3 88.0 - - - +
239A ASN* 1.3 60.0 + - - +
241A VAL* 3.3 16.5 + - - +
242A ARG* 3.4 17.4 + - - +
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Residues in contact with ASN 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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205A ILE* 6.0 0.8 - - - +
233A LEU 4.0 14.6 + - - -
234A GLN* 3.7 13.8 - - - +
235A SER 2.9 14.4 + - - +
236A GLU* 3.8 12.1 - - + +
237A PHE 3.2 0.2 - - - -
238A CYS* 1.3 75.6 - - - +
240A ALA* 1.3 62.6 + - - +
242A ARG* 2.6 43.7 + - - +
243A GLU* 3.1 28.8 + - + +
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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
----------------------------------------------------------
130A PRO* 4.1 17.9 - - + -
236A GLU 3.2 14.3 + - - +
237A PHE* 3.1 14.8 + - + +
239A ASN* 1.3 76.6 - - - +
241A VAL* 1.3 65.6 + - - +
243A GLU* 3.1 13.3 + - - +
244A VAL* 3.1 32.2 + - + +
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 4.2 19.1 - - + -
175A VAL* 4.1 25.4 - - + -
176A HIS* 4.8 10.3 - - + +
179A VAL* 5.0 9.9 - - + -
195A LEU* 5.9 1.8 - - + -
237A PHE* 2.9 46.7 + - + +
238A CYS* 3.3 12.1 + - - +
240A ALA* 1.3 77.1 - - - +
242A ARG* 1.3 56.6 + - - +
244A VAL* 3.7 7.2 + - - +
245A TYR* 3.2 24.0 + - + +
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Residues in contact with ARG 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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172A LEU* 3.6 40.8 - - + +
198A PRO* 5.4 3.0 + - - +
201A LEU* 4.3 18.8 - - + -
202A GLU* 3.9 42.7 + - - +
205A ILE* 4.8 12.9 - - - +
238A CYS* 3.4 9.6 + - - +
239A ASN* 2.6 43.9 + - - +
240A ALA 3.2 0.6 - - - -
241A VAL* 1.3 75.3 - - - +
243A GLU* 1.3 66.6 + - - +
245A TYR* 3.2 11.9 + - + +
246A GLU* 3.0 21.3 + - - +
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Residues in contact with GLU 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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239A ASN* 3.1 18.6 + - + +
240A ALA* 3.1 12.8 + - - +
242A ARG* 1.3 76.8 - - + +
244A VAL* 1.3 62.0 + - + +
246A GLU* 3.0 23.0 + - - +
247A HIS* 2.6 36.2 + - + -
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Residues in contact with VAL 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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122A LEU* 6.5 1.8 - - + -
240A ALA* 3.1 20.6 + - + +
241A VAL* 3.8 7.4 - - - +
243A GLU* 1.3 78.2 - - + +
245A TYR* 1.3 58.3 + - - +
247A HIS* 3.7 9.3 + - + +
248A VAL* 3.1 31.2 + - + +
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Residues in contact with TYR 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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192A GLY* 3.4 21.5 + - - -
193A PRO* 4.7 1.6 - - - +
195A LEU* 3.5 30.3 - - + -
196A GLY* 2.6 43.0 + - - -
198A PRO* 3.8 21.8 - - + -
201A LEU* 4.5 12.1 - - + -
241A VAL* 3.2 16.0 + - + +
242A ARG* 3.4 12.3 - - - +
243A GLU 3.0 0.6 - - - -
244A VAL* 1.3 76.9 - - - +
246A GLU* 1.3 60.8 + - - +
248A VAL* 3.2 8.6 + - + -
249A TYR* 2.9 41.1 + + + +
254A ILE* 4.0 19.2 - - + +
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Residues in contact with GLU 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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198A PRO* 4.1 24.7 - - + +
242A ARG 3.0 12.3 + - - +
243A GLU* 3.0 18.3 + - - +
245A TYR* 1.3 75.2 - - - +
247A HIS* 1.3 79.3 + - - +
249A TYR* 3.3 11.6 + - - +
250A GLU* 3.3 36.3 + - - +
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Residues in contact with HIS 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 GLU* 2.6 39.6 + - + -
244A VAL* 3.9 9.3 - - + +
245A TYR 3.2 0.4 - - - -
246A GLU* 1.3 91.5 + - + +
248A VAL* 1.3 67.3 + - + +
250A GLU* 3.1 16.5 + - - +
251A THR* 3.1 32.9 + - + +
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Residues in contact with VAL 248 (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 ILE* 5.5 16.6 - - + -
244A VAL* 3.1 23.5 + - + +
245A TYR* 3.2 12.2 + - + +
247A HIS* 1.3 77.6 - - + +
249A TYR* 1.3 57.1 + - - +
251A THR* 3.7 6.0 + - - +
252A VAL* 3.1 39.7 + - + +
254A ILE* 4.1 16.8 - - + -
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Residues in contact with TYR 249 (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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196A GLY 3.9 8.1 - - - -
197A GLU* 4.0 21.1 + - + +
198A PRO* 3.2 35.2 - - + -
245A TYR* 2.9 31.9 + - + +
246A GLU 3.5 6.3 - - - +
247A HIS 3.2 0.2 - - - -
248A VAL* 1.3 76.4 - - - +
250A GLU* 1.3 62.3 + - + +
252A VAL 3.5 10.0 - - - +
253A ASP* 5.1 1.4 - - - -
254A ILE* 4.0 21.0 - - + +
255A SER* 3.7 35.7 + - - -
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Residues in contact with GLU 250 (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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65A LYS* 3.9 30.0 - - + +
246A GLU* 3.4 34.6 - - + +
247A HIS* 3.1 20.8 + - - +
249A TYR* 1.3 81.8 - - + +
251A THR* 1.3 67.8 + - + +
252A VAL* 3.2 4.0 + - - -
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Residues in contact with THR 251 (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 ASN* 3.0 28.6 + - - +
65A LYS* 3.6 36.8 - - + +
66A LEU* 3.7 25.0 - - + +
247A HIS* 3.1 19.2 + - + +
248A VAL* 3.7 7.1 + - - -
250A GLU* 1.3 78.0 - - + +
252A VAL* 1.3 72.0 + - - +
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Residues in contact with VAL 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 5.0 8.5 - - + -
56A TYR* 4.0 22.9 - - + +
58A VAL* 3.6 30.5 - - + -
63A ASN* 3.6 15.7 - - + +
66A LEU* 5.2 2.2 - - + -
248A VAL* 3.1 23.9 + - + +
249A TYR 3.5 9.6 - - - +
250A GLU 3.2 3.0 - - - -
251A THR* 1.3 96.5 + - - +
253A ASP* 1.3 66.9 + - - +
254A ILE* 3.1 21.6 + - + +
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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
------------------------------------------------------------
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