Contacts of the helix formed by residues 241 - 258 (chain A) in PDB entry 5TE0
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 THR 241 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A HIS* 3.2 63.8 + - + +
171A PRO* 4.3 6.1 - - + -
172A ILE 3.7 13.7 - - - +
173A ILE* 3.6 15.3 - - + +
202A PHE* 4.0 15.7 - - + -
240A THR* 1.3 68.6 - - - +
242A LYS* 1.3 64.7 + - - +
243A ALA 3.1 0.2 - - - -
244A ASP* 3.0 12.6 + - - +
245A ILE* 3.5 3.0 + - - +
405A GOL 3.6 26.2 + - - -
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Residues in contact with LYS 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLU* 4.4 0.4 - - - +
240A THR* 3.1 9.5 + - - +
241A THR* 1.3 77.5 + - - +
243A ALA* 1.4 59.8 + - - +
245A ILE* 3.0 17.4 + - + +
246A TRP 3.2 4.3 + - - -
298A PRO* 2.9 44.4 + - + +
299A ASP* 4.1 6.1 + - - +
301A ARG* 2.8 36.6 + - + +
302A PRO 3.4 25.1 - - - +
303A ASP* 4.0 4.0 - - - -
402A PEG 2.7 30.3 + - - -
405A GOL 3.7 22.3 + - - +
408A GOL 3.5 18.8 + - - +
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ILE* 4.8 2.2 - - + -
225A TYR 4.9 0.9 - - - +
227A ALA* 3.9 12.1 + - + +
229A GLU* 3.5 18.5 + - - +
230A MET* 3.6 32.4 - - + +
239A ILE* 4.2 7.0 - - + -
240A THR 3.0 15.7 + - - +
242A LYS* 1.4 75.5 - - - +
244A ASP* 1.3 61.8 + - - +
246A TRP* 3.3 6.1 + - - +
247A ALA* 3.2 19.6 + - - +
301A ARG* 3.7 2.7 - - - +
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Residues in contact with ASP 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A VAL* 4.6 1.1 - - + +
165A LEU* 5.0 0.5 - - - +
166A HIS* 2.9 36.1 + - + +
173A ILE* 3.4 12.1 - - - +
174A HIS* 2.7 28.3 + - - +
175A ARG* 3.0 26.9 + - - -
177A LEU* 3.5 23.8 - - + +
241A THR 3.0 3.9 + - - +
243A ALA* 1.3 75.3 - - - +
245A ILE* 1.3 61.1 + - - +
247A ALA* 3.1 7.7 + - - +
248A LEU* 2.8 32.4 + - - +
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Residues in contact with ILE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A HIS* 4.0 13.0 - - + +
241A THR 3.8 11.0 - - - +
242A LYS* 3.0 14.2 + - + +
244A ASP* 1.3 78.1 - - - +
246A TRP* 1.3 61.4 + - - +
248A LEU* 3.2 10.2 + - + +
249A GLY 3.1 17.2 + - - -
293A MET* 3.7 13.2 - - + +
301A ARG* 3.9 12.8 - - + -
302A PRO* 3.3 27.6 - - + +
303A ASP* 3.7 4.0 - - - +
304A ILE* 3.4 47.8 - - + +
307A VAL* 3.8 20.4 - - + -
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Residues in contact with TRP 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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224A SER 5.2 0.2 + - - -
225A TYR 3.4 18.8 - - - -
226A ARG 3.4 11.5 + - - -
227A ALA* 3.5 12.1 - - + -
228A PRO* 3.5 18.8 - - + -
242A LYS 3.2 5.5 + - - -
243A ALA 3.5 9.0 - - - +
244A ASP 3.2 0.2 - - - -
245A ILE* 1.3 76.0 - - - +
247A ALA* 1.3 61.6 + - - +
249A GLY 3.0 10.4 + - - -
250A CYS* 3.1 22.8 + - - -
262A PHE* 3.3 36.4 - + - -
269A ILE* 3.4 29.9 - - + +
272A GLY* 4.0 9.6 - - - -
293A MET 4.0 8.3 - - - -
294A LEU* 3.4 39.2 - - + +
295A GLU 3.6 23.8 - - - -
296A PRO* 3.6 5.8 - - + -
301A ARG* 3.7 18.0 - - - +
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Residues in contact with ALA 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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175A ARG 6.2 2.2 - - - -
177A LEU* 3.9 32.1 - - + +
225A TYR* 3.6 28.3 - - + +
243A ALA 3.2 8.9 + - - +
244A ASP* 3.1 11.3 + - - +
246A TRP* 1.3 80.2 - - - +
248A LEU* 1.3 56.3 + - - +
250A CYS* 3.2 4.9 + - - +
251A LEU* 2.8 29.1 + - - +
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Residues in contact with LEU 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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155A PHE* 3.5 32.7 - - + -
158A THR* 3.6 30.5 - - + -
159A CYS* 4.6 3.1 - - - -
162A VAL* 4.2 17.0 - - + -
177A LEU* 4.1 11.4 - - + +
244A ASP 2.8 17.2 + - - +
245A ILE* 3.4 17.7 - - + +
247A ALA* 1.3 70.0 - - - +
249A GLY* 1.3 60.3 + - - +
251A LEU* 3.4 11.8 + - + +
252A LEU* 2.9 23.7 + - - +
293A MET* 3.8 8.7 - - - -
304A ILE* 3.6 31.0 - - + -
307A VAL* 4.8 3.4 - - + -
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Residues in contact with GLY 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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245A ILE 3.1 7.1 + - - -
246A TRP 3.0 8.4 + - - -
248A LEU* 1.3 77.3 - - - +
250A CYS* 1.4 53.7 + - - +
252A LEU* 3.4 2.8 + - - +
253A TYR* 3.0 28.2 + - - +
290A ILE* 4.1 7.0 - - - +
293A MET* 3.5 30.6 - - - -
294A LEU* 3.9 13.5 - - - -
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Residues in contact with CYS 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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224A SER 3.7 17.5 - - - -
225A TYR* 3.7 20.2 - - + -
246A TRP* 3.1 40.7 + - - -
247A ALA 3.5 6.5 - - - +
249A GLY* 1.4 70.9 - - - +
251A LEU* 1.3 59.7 + - - +
253A TYR* 3.3 3.1 + - - +
254A LYS* 2.9 30.0 + - - +
260A LEU* 3.7 13.1 - - + +
261A PRO* 4.0 12.8 - - + -
262A PHE* 3.9 11.2 - - - -
294A LEU* 3.7 7.4 - - - +
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Residues in contact with LEU 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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154A ILE* 5.3 0.4 - - + -
155A PHE* 4.4 12.1 - - + -
158A THR* 4.7 7.6 - - + +
177A LEU* 4.2 5.2 - - + -
178A LYS 3.5 36.3 - - - +
179A VAL* 4.0 11.8 - - + +
182A ILE* 4.3 20.0 - - + -
225A TYR* 3.8 10.2 - - + -
247A ALA 2.8 16.4 + - - +
248A LEU* 3.5 19.3 - - + +
250A CYS* 1.3 73.1 - - - +
252A LEU* 1.3 61.1 + - - +
254A LYS* 3.2 6.6 + - - +
255A LEU* 2.8 56.0 + - + +
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Residues in contact with LEU 252 (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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151A VAL* 3.4 33.4 - - + -
152A LEU* 5.7 1.1 - - + -
155A PHE* 3.8 25.4 - - + -
248A LEU 2.9 18.3 + - - +
249A GLY 3.8 3.8 - - - +
251A LEU* 1.3 75.7 - - - +
253A TYR* 1.3 61.6 + - - +
255A LEU* 3.2 7.7 + - + +
256A CYS* 3.1 23.6 + - - -
286A MET* 3.8 13.9 - - - -
289A LEU* 3.7 25.6 - - + -
290A ILE* 3.8 20.9 - - + +
293A MET* 3.6 23.6 - - + -
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Residues in contact with TYR 253 (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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249A GLY 3.0 13.5 + - - +
250A CYS 3.5 7.9 - - - +
252A LEU* 1.3 75.1 - - - +
254A LYS* 1.3 57.2 + - - +
256A CYS 3.2 1.7 + - - -
257A TYR* 2.8 68.2 + + + +
259A THR* 3.3 28.2 - - + +
260A LEU 4.0 2.2 - - - -
261A PRO* 3.5 39.9 + - + +
274A PHE* 3.9 12.3 - + - -
275A THR* 2.8 30.2 + - - -
276A ILE* 4.0 2.5 - - + -
277A PRO* 4.4 6.8 - - - +
290A ILE* 4.0 28.4 - - + +
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Residues in contact with LYS 254 (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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135A VAL* 5.8 1.1 - - - +
138A MET* 4.3 15.7 - - + +
179A VAL* 3.7 26.5 - - + +
180A GLU* 4.1 17.6 + - - -
225A TYR* 3.8 11.9 + - - +
250A CYS 2.9 17.1 + - - +
251A LEU 3.2 4.2 + - - +
253A TYR* 1.3 73.2 - - - +
255A LEU* 1.3 61.7 - - - +
258A PHE* 2.8 38.3 + - - -
259A THR* 3.3 23.3 + - - +
260A LEU* 3.8 32.2 - - + +
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Residues in contact with LEU 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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134A VAL* 3.7 29.8 - - + -
138A MET* 5.2 1.8 - - - -
146A PHE* 3.5 15.4 - - + -
151A VAL* 4.0 34.7 - - + +
154A ILE* 3.8 29.2 - - + -
155A PHE* 4.4 4.9 - - + +
179A VAL* 3.8 15.9 - - + -
182A ILE* 6.3 0.2 - - + -
251A LEU* 2.8 39.9 + - + +
252A LEU* 3.2 13.7 + - + +
254A LYS* 1.3 73.5 - - - +
256A CYS* 1.3 60.1 + - - +
258A PHE* 3.4 18.9 - - - -
282A TYR* 4.4 1.4 + - - -
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Residues in contact with CYS 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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151A VAL* 4.0 12.3 - - - -
252A LEU 3.1 15.6 + - - +
253A TYR* 3.6 7.4 - - - +
255A LEU* 1.3 78.0 - - - +
257A TYR* 1.3 76.4 + - + +
282A TYR* 3.2 42.7 + - + -
286A MET* 3.8 36.6 - - - -
290A ILE* 4.2 6.1 - - - -
403A GOL 2.8 17.5 + - - -
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Residues in contact with TYR 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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253A TYR* 2.8 57.8 + + + +
256A CYS* 1.3 91.3 - - + +
258A PHE* 1.3 69.7 + - - +
259A THR* 3.2 11.7 + - + +
276A ILE* 3.7 22.3 - - + +
277A PRO* 3.7 24.2 - - + -
280A SER* 2.7 37.1 + - - -
282A TYR* 4.0 3.3 - + - -
287A HIS* 3.3 20.3 - - - -
290A ILE* 4.0 5.6 - - + +
403A GOL 3.8 11.2 + - - -
407A GOL 3.5 28.1 + - - +
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Residues in contact with PHE 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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138A MET* 3.3 64.4 - - + +
141A ARG* 3.3 30.7 - - + -
142A LEU* 4.2 12.8 - - + -
145A GLY* 3.8 11.4 - - - -
146A PHE* 3.9 9.6 - + - -
254A LYS* 2.8 36.1 + - - -
255A LEU 3.4 19.1 - - - -
257A TYR* 1.3 72.1 - - - +
259A THR* 1.3 57.7 + - - +
403A GOL 3.5 28.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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