Contacts of the helix formed by residues 246 - 264 (chain A) in PDB entry 5D9K
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 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A ILE* 3.6 7.7 - - - +
238A GLU* 4.9 2.3 + - - +
244A GLY* 3.7 11.1 + - - +
245A HIS* 1.3 88.4 - - - +
247A GLN* 1.3 61.8 + - - +
248A SER* 3.5 19.2 + - - -
249A ALA* 3.1 19.1 + - - +
250A ASP 3.8 0.9 + - - -
307A PRO* 4.8 6.2 - - - +
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Residues in contact with GLN 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A HIS* 3.4 55.7 + - + +
190A ILE* 3.6 12.6 - - + +
246A THR* 1.3 75.7 - - - +
248A SER* 1.3 61.5 + - - +
250A ASP* 3.2 19.0 + - - +
251A TRP* 3.3 15.6 - - + +
312A GLY 4.3 15.1 + - - +
313A ALA* 5.6 3.0 - - - +
317A GLY* 6.0 1.2 - - - -
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Residues in contact with SER 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A THR* 3.1 12.0 + - - -
247A GLN* 1.3 78.9 - - - +
249A ALA* 1.4 58.6 + - - +
251A TRP* 3.1 23.7 + - - -
252A TRP 3.3 5.7 + - - -
307A PRO* 2.6 45.1 + - - +
310A ARG* 3.1 28.2 + - - +
313A ALA* 4.0 9.7 + - - +
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Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ALA* 3.9 7.9 + - + +
238A GLU* 3.7 18.0 + - - +
239A VAL* 3.8 20.4 - - + -
245A HIS* 3.6 20.4 - - + +
246A THR* 3.1 18.1 + - - +
248A SER* 1.4 77.4 - - - +
250A ASP* 1.4 60.4 + - - +
252A TRP* 3.4 5.4 + - - +
253A SER* 3.2 25.1 + - - -
310A ARG* 3.7 3.9 - - - +
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Residues in contact with ASP 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU* 4.0 11.6 - - + +
184A LEU* 5.9 0.2 - - - +
185A HIS* 2.7 30.1 + - + +
190A ILE* 3.4 10.9 - - - +
191A TYR* 2.9 48.6 + - - +
194A LEU* 3.9 6.0 - - + +
245A HIS* 3.0 15.6 + - - -
247A GLN 3.2 11.8 + - - +
248A SER 3.2 0.4 - - - -
249A ALA* 1.4 76.7 - - - +
251A TRP* 1.4 57.5 + - - +
253A SER* 3.5 8.2 + - - -
254A PHE* 3.1 25.8 + - - +
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Residues in contact with TRP 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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178A ALA* 3.7 30.7 - - + -
181A LEU* 3.8 19.1 - - + -
182A ASP* 4.5 2.2 - - - -
185A HIS* 3.5 32.5 + + - -
247A GLN* 3.3 24.1 + - + +
248A SER* 3.1 12.7 + - - +
250A ASP* 1.4 74.6 - - - +
252A TRP* 1.3 61.3 + - - +
254A PHE* 3.4 33.7 - + + +
255A GLY 3.2 15.4 + - - -
302A LEU* 3.4 18.5 - - + +
310A ARG* 4.7 3.6 - - - -
311A LEU 3.6 24.9 - - - +
312A GLY* 4.1 18.8 + - - -
313A ALA 5.0 0.2 - - - -
318A VAL* 3.8 26.9 - - + +
321A ILE* 3.7 20.0 - - + -
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Residues in contact with TRP 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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233A GLU 5.3 0.2 + - - -
234A TYR 3.6 11.9 - - - -
235A MET 3.3 11.9 + - - -
236A ALA* 3.5 22.0 - - + -
237A PRO* 3.6 35.7 - - + -
248A SER 3.3 4.6 + - - -
249A ALA 3.5 9.2 - - - +
250A ASP 3.3 0.4 - - - -
251A TRP* 1.3 75.9 - - - +
253A SER* 1.3 57.4 + - - +
255A GLY* 2.8 21.8 + - - -
256A VAL* 2.9 26.5 + - + +
268A PHE* 3.4 33.2 - + - -
280A ILE* 3.9 19.0 - - + +
302A LEU 3.7 23.3 - - - -
303A PHE* 3.6 35.5 - + - -
304A LYS 3.7 7.2 - - - -
305A ARG* 4.0 10.1 - - - -
310A ARG* 3.7 16.7 - - - +
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Residues in contact with SER 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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191A TYR 5.4 2.4 + - - -
194A LEU* 3.9 35.2 + - - +
234A TYR* 2.7 27.6 + - - +
235A MET* 4.9 1.6 - - - -
236A ALA 4.9 0.5 + - - -
245A HIS* 5.7 3.1 - - - -
249A ALA 3.2 12.6 + - - -
250A ASP* 3.7 11.1 - - - -
252A TRP* 1.3 76.1 - - - +
254A PHE* 1.4 52.2 + - - +
256A VAL* 3.3 6.9 + - - +
257A LEU* 2.8 33.4 + - - +
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Residues in contact with PHE 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 3.3 55.5 - - + +
177A LEU* 3.9 18.8 - - + -
178A ALA* 3.9 21.1 - - + -
181A LEU* 4.2 4.5 - - + -
194A LEU* 3.9 7.8 - - + +
250A ASP 3.1 14.2 + - - +
251A TRP* 3.4 30.7 - + + +
253A SER* 1.4 72.1 - - - +
255A GLY* 1.3 58.9 + - - +
257A LEU* 3.5 5.6 + - - +
258A MET* 2.9 28.3 + - + +
298A LEU* 5.0 2.5 - - + -
302A LEU* 3.8 22.0 - - + -
321A ILE* 4.3 15.9 - - + -
327A PHE* 4.1 13.7 - + - -
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Residues in contact with GLY 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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251A TRP 3.2 4.2 + - - -
252A TRP 2.8 9.3 + - - -
254A PHE* 1.3 75.2 - - - +
256A VAL* 1.4 54.5 + - - +
258A MET* 3.2 6.8 + - - +
259A PHE* 2.8 32.1 + - - +
299A LEU* 3.4 9.5 - - - +
302A LEU* 3.7 22.0 - - - +
303A PHE* 3.5 15.5 - - - -
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Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A GLU 3.4 21.5 - - - +
234A TYR* 3.4 30.7 - - + +
252A TRP* 2.9 44.6 + - + +
253A SER* 3.5 7.6 - - - +
255A GLY* 1.4 72.9 - - - +
257A LEU* 1.3 56.3 + - - +
259A PHE* 3.4 2.1 + - - +
260A GLU* 2.9 29.1 + - - +
266A LEU* 3.7 14.8 - - + -
267A PRO* 3.9 16.2 - - + +
268A PHE* 5.0 1.1 - - + -
303A PHE* 3.5 12.7 - - + -
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Residues in contact with LEU 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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155A LEU* 5.1 5.4 - - + -
174A LEU* 4.6 2.0 - - + -
177A LEU* 3.5 31.6 - - + -
194A LEU* 4.4 6.3 - - + +
195A LYS* 3.9 9.6 - - - -
196A PRO* 3.7 43.5 - - + -
199A ILE* 3.8 14.1 - - + -
234A TYR* 4.4 5.4 - - + -
253A SER 2.8 20.7 + - - +
254A PHE* 3.6 6.1 - - - +
256A VAL* 1.3 71.0 - - - +
258A MET* 1.3 58.7 + - - +
260A GLU* 3.4 6.2 + - - +
261A MET* 3.0 54.1 + - + +
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Residues in contact with MET 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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170A VAL* 4.5 0.4 - - + -
174A LEU* 3.5 33.9 - - + +
254A PHE* 2.9 16.1 + - - +
255A GLY* 3.3 10.3 - - - +
257A LEU* 1.3 72.9 - - - +
259A PHE* 1.3 61.5 + - - +
261A MET* 3.2 8.2 + - - +
262A LEU* 3.2 33.6 + - + +
295A ALA* 3.3 47.1 - - + +
298A LEU* 3.7 33.9 - - + -
299A LEU* 3.8 15.0 - - + -
302A LEU* 4.7 5.2 - - - -
326A PHE* 4.1 10.8 - - + -
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Residues in contact with PHE 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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255A GLY 2.8 19.4 + - - +
256A VAL 3.6 4.9 - - - +
258A MET* 1.3 71.9 - - - +
260A GLU* 1.3 55.9 + - - +
262A LEU* 3.4 2.7 + - - -
263A THR* 2.9 55.1 + - + +
265A THR* 3.2 25.6 - - + -
266A LEU 4.1 2.2 - - - -
267A PRO* 3.6 33.4 - - + -
285A LEU* 3.9 34.5 - - + -
286A GLY 4.5 1.3 - - - -
287A MET* 4.3 4.9 - - - -
288A PRO* 3.7 35.9 - - + -
291A LEU* 4.5 0.9 - - + -
299A LEU* 3.8 27.6 - - + -
303A PHE* 4.4 0.4 - + + -
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Residues in contact with GLU 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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156A PHE* 5.9 2.8 - - - -
159A LEU* 3.9 23.5 - - + +
196A PRO* 3.7 12.5 - - - +
234A TYR* 2.7 39.0 + - - -
256A VAL 2.9 16.3 + - - +
257A LEU* 3.7 5.0 - - - +
259A PHE* 1.3 75.6 - - - +
261A MET* 1.3 58.9 + - + +
264A GLY* 2.9 31.9 + - - -
265A THR* 3.4 25.5 + - - +
266A LEU* 4.1 17.2 - - + +
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Residues in contact with MET 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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155A LEU* 4.0 18.6 - - + -
159A LEU* 3.6 13.9 - - + +
164A MET* 3.5 5.5 - - - -
165A PHE* 2.8 59.8 + - + -
170A VAL* 3.4 21.8 - - + -
173A TYR* 4.4 13.5 - - + -
174A LEU* 3.3 39.3 - - + -
196A PRO* 6.2 2.0 - - + -
257A LEU* 3.0 34.8 + - + +
258A MET* 3.2 5.1 + - - +
260A GLU* 1.3 77.0 - - + +
262A LEU* 1.3 53.6 + - - +
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Residues in contact with LEU 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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164A MET* 3.3 24.6 - - - +
165A PHE 4.1 8.0 - - - +
167A GLU* 3.8 32.5 - - + +
170A VAL* 3.7 26.9 - - + -
258A MET* 3.2 45.5 + - + +
259A PHE* 4.1 3.4 - - - +
261A MET* 1.3 76.3 - - - +
263A THR* 1.3 59.6 + - - +
290A PHE* 3.3 6.8 - - - -
291A LEU* 3.6 25.4 - - + -
295A ALA* 4.3 9.6 - - + -
299A LEU* 5.2 1.6 - - + -
326A PHE* 4.8 2.2 - - + -
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Residues in contact with THR 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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163A VAL* 5.6 1.0 - - - +
164A MET* 4.1 16.7 - - - +
259A PHE* 2.9 42.2 + - + +
262A LEU* 1.3 76.8 - - - +
264A GLY* 1.3 58.9 + - - +
265A THR* 2.9 33.6 + - - -
288A PRO* 4.0 13.7 - - + -
290A PHE* 3.6 27.8 - - + -
291A LEU* 4.2 12.8 - - + -
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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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159A LEU* 5.2 2.7 - - - -
163A VAL* 3.3 28.0 - - - +
164A MET* 4.0 1.6 - - - +
260A GLU* 2.9 22.5 + - - +
262A LEU 3.7 0.8 - - - -
263A THR* 1.3 74.5 - - - +
265A THR* 1.4 62.8 + - - +
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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
------------------------------------------------------------
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