Contacts of the helix formed by residues 241 - 258 (chain A) in PDB entry 4ZSL
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 GLN 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A HIS* 3.0 66.8 + - + +
177A GLN* 4.3 17.2 + - - +
178A VAL 4.4 2.0 - - - +
179A ILE* 3.8 19.2 - - + +
207A LEU* 3.6 22.9 - - - +
240A THR* 1.4 75.2 - - - +
242A ALA* 1.3 56.0 + - - +
243A ILE 3.1 0.2 - - - -
244A ASP* 2.9 28.5 + - - +
245A LEU* 3.6 4.6 + - + +
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Residues in contact with ALA 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A THR* 3.3 16.6 + - - +
241A GLN* 1.3 74.5 - - - +
243A ILE* 1.4 62.6 + - - +
245A LEU* 3.3 18.1 + - - -
246A TRP 3.4 4.7 + - - -
332A PRO* 3.5 32.3 - - + +
335A ARG* 2.9 31.8 + - + +
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Residues in contact with ILE 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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179A ILE* 4.0 11.0 - - + -
181A ARG* 3.9 36.1 - - + +
229A ALA* 4.0 7.5 - - + +
231A GLU* 3.4 27.5 + - + +
232A LEU* 3.9 35.7 - - + -
239A TYR* 3.8 29.2 - - + -
240A THR 2.9 20.8 + - - +
242A ALA* 1.4 76.5 - - - +
244A ASP* 1.3 63.2 + - - +
246A TRP* 3.4 12.0 + - - +
247A SER* 3.5 14.9 + - - +
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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
----------------------------------------------------------
170A LEU* 4.0 2.8 - - + +
173A MET* 4.4 0.2 - - - +
174A HIS* 2.7 32.0 + - + +
179A ILE* 3.6 8.2 - - - +
180A HIS* 3.0 26.1 + - - +
181A ARG* 2.9 28.2 + - - -
183A LEU* 3.7 22.5 + - + +
241A GLN 2.9 9.6 + - - +
243A ILE* 1.3 74.7 - - - +
245A LEU* 1.3 59.1 + - - +
247A SER* 3.2 8.3 + - - -
248A VAL* 2.9 30.7 + - - +
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Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 4.1 25.4 - - + -
170A LEU* 5.0 2.2 - - + -
174A HIS* 3.6 29.2 - - + +
241A GLN 3.8 7.2 - - - +
242A ALA* 3.3 13.3 + - - +
244A ASP* 1.3 77.0 - - - +
246A TRP* 1.4 63.2 + - - +
248A VAL* 3.4 7.6 + - + +
249A GLY 3.1 17.5 + - - -
327A MET* 3.7 29.9 - - + +
335A ARG* 4.5 8.5 - - + -
336A ILE* 3.1 28.7 - - + +
337A SER* 4.1 5.4 - - - +
338A ALA* 3.8 20.9 - - + +
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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
----------------------------------------------------------
226A TRP 5.1 0.8 + - - -
227A TYR 3.4 22.5 + - - -
228A ARG 3.7 9.9 + - - -
229A ALA* 3.5 21.5 - - + -
230A PRO* 3.5 21.5 - - + -
242A ALA 3.4 6.1 + - - -
243A ILE 3.7 9.0 - - - +
244A ASP 3.3 0.4 - - - -
245A LEU* 1.4 76.6 - - - +
247A SER* 1.3 61.5 + - - +
249A GLY 3.2 2.4 + - - -
250A CYS* 3.0 35.8 + - - -
262A PHE* 3.8 26.4 - + - -
270A GLN* 6.2 0.2 - - - +
274A ILE* 3.8 28.0 - - + +
278A LEU* 3.7 33.0 - - + -
327A MET 4.2 3.4 - - - -
328A LEU* 3.3 26.1 - - + +
329A ARG 3.7 23.3 - - - -
335A ARG* 4.0 11.3 - - - +
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Residues in contact with SER 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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181A ARG 5.4 3.1 + - - -
182A ASP* 5.6 0.2 - - - -
183A LEU* 3.7 36.8 + - - -
227A TYR* 2.8 25.2 + - - +
229A ALA 5.2 0.2 + - - -
243A ILE* 3.5 12.6 + - - +
244A ASP* 3.2 11.9 + - - -
246A TRP* 1.3 78.3 - - - +
248A VAL* 1.4 55.0 + - - +
250A CYS* 3.1 8.3 + - - +
251A ILE* 2.9 34.2 + - - +
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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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163A LEU* 3.8 21.5 - - + +
166A LEU* 4.0 13.9 - - + -
167A LEU* 4.0 8.7 - - + -
170A LEU* 3.3 32.1 - - + -
183A LEU* 4.0 4.5 - - + -
244A ASP 2.9 23.2 + - - +
245A LEU* 3.6 14.4 - - + +
246A TRP 3.3 0.2 - - - -
247A SER* 1.4 70.3 - - - +
249A GLY* 1.3 52.6 + - - +
251A ILE* 3.2 9.1 + - + +
252A PHE* 2.7 33.1 + - - +
327A MET* 3.7 23.3 - - + -
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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 LEU 3.1 12.0 + - - -
246A TRP 3.2 4.4 + - - -
248A VAL* 1.3 75.0 - - - +
250A CYS* 1.3 55.6 + - - +
252A PHE* 3.4 0.6 + - - -
253A GLY* 2.9 26.7 + - - -
324A LEU* 3.3 12.8 - - - +
327A MET* 3.8 17.9 - - - -
328A LEU* 3.7 24.1 - - - +
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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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226A TRP 3.9 16.2 - - - +
227A TYR* 3.7 22.9 - - + -
246A TRP* 3.0 44.9 + - - -
247A SER 3.1 8.3 + - - +
249A GLY* 1.3 74.2 - - - +
251A ILE* 1.3 57.1 + - - +
253A GLY* 3.5 1.0 + - - -
254A GLU* 2.9 29.9 + - - +
261A LEU* 4.4 17.6 + - + +
262A PHE* 4.3 15.7 - - - +
328A LEU* 3.9 4.9 - - - +
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Residues in contact with ILE 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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144A LEU* 3.9 28.7 - - + -
166A LEU* 4.4 10.8 - - + -
183A LEU* 3.8 14.1 - - + -
184A LYS* 3.7 27.6 - - - +
185A PRO* 4.0 22.4 - - + -
188A LEU* 3.8 18.6 - - + -
227A TYR* 4.3 4.0 - - + -
247A SER 2.9 20.6 + - - +
248A VAL* 3.5 10.8 - - - +
250A CYS* 1.3 71.6 - - - +
252A PHE* 1.4 58.0 + - - +
254A GLU* 3.2 10.2 + - - +
255A MET* 3.0 36.3 + - + +
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Residues in contact with PHE 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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159A VAL* 3.9 19.5 - - + -
163A LEU* 3.7 28.2 - - + +
248A VAL 2.7 20.6 + - - +
249A GLY* 3.4 6.0 + - - +
251A ILE* 1.4 70.9 - - - +
253A GLY* 1.3 62.1 + - - +
255A MET* 3.3 12.2 + - + +
256A LEU* 3.2 31.0 + - + +
320A ALA* 3.3 34.1 - - + -
323A LEU* 3.9 9.0 - - + -
324A LEU* 3.6 28.0 - - + -
327A MET* 4.0 9.9 - - - -
346A PHE* 3.6 35.0 - + - -
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Residues in contact with GLY 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 2.9 16.0 + - - -
250A CYS 3.8 1.8 - - - -
252A PHE* 1.3 75.6 - - - +
254A GLU* 1.3 61.2 + - - +
256A LEU* 3.3 5.5 + - - +
257A ALA* 3.2 18.9 + - - +
259A ARG 4.3 1.0 - - - +
261A LEU* 4.9 2.2 - - - -
313A TYR* 3.0 40.0 + - - -
324A LEU* 4.0 6.0 - - - +
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Residues in contact with GLU 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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145A HIS* 4.7 1.7 + - - -
148A ILE* 3.8 9.4 - - + +
149A HIS* 2.7 31.6 + - - +
185A PRO* 3.7 16.4 - - - +
227A TYR* 2.7 36.3 + - - -
250A CYS 2.9 16.4 + - - +
251A ILE* 3.2 7.4 + - - +
253A GLY* 1.3 76.8 - - - +
255A MET* 1.3 52.6 + - - +
258A ARG* 2.7 36.4 + - - -
259A ARG 3.3 24.2 + - - +
260A GLN* 3.5 21.4 + - - +
261A LEU* 5.0 0.8 - - - +
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Residues in contact with MET 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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144A LEU* 4.0 15.0 - - + -
148A ILE* 3.6 22.2 - - + -
154A LEU* 3.3 28.1 - - + +
159A VAL* 3.7 46.8 - - + +
162A PHE* 3.9 24.7 - - + -
163A LEU* 4.1 20.6 - - + +
166A LEU* 5.7 1.1 - - + -
251A ILE* 3.0 30.6 + - + +
252A PHE* 3.3 15.9 + - - +
254A GLU* 1.3 75.7 - - - +
256A LEU* 1.3 61.7 + - - +
257A ALA 3.7 0.2 + - - -
258A ARG* 3.8 5.5 - - - +
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Residues in contact with LEU 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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156A LEU* 4.3 20.2 - - + -
159A VAL* 3.9 22.9 - - + -
252A PHE* 3.2 37.1 + - + +
253A GLY* 3.3 11.6 + - - +
255A MET* 1.3 79.0 - - - +
257A ALA* 1.3 57.3 + - - +
258A ARG* 5.0 1.9 - - - +
313A TYR* 4.4 12.3 - - + -
316A ALA* 5.1 11.2 - - + -
317A ASP 5.8 0.4 - - - +
320A ALA* 4.4 9.6 - - + -
321A LEU* 4.3 23.3 - - + -
324A LEU* 4.6 7.4 - - + -
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Residues in contact with ALA 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 GLY 3.2 5.6 + - - +
256A LEU* 1.3 77.2 - - - +
258A ARG* 1.4 71.2 + - - +
259A ARG* 3.4 35.5 + - + +
313A TYR* 3.5 29.4 - - + -
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Residues in contact with ARG 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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147A ILE 2.8 29.1 + - - -
148A ILE* 2.8 34.1 + - - +
149A HIS* 3.8 13.4 + - - -
150A SER* 3.2 15.3 + - - -
151A SER* 5.2 0.4 - - - +
152A GLN 2.8 29.9 + - - -
154A LEU* 3.5 26.1 - - + +
254A GLU 2.7 18.9 + - - -
255A MET 3.8 13.5 - - - +
256A LEU 3.6 2.2 - - - +
257A ALA* 1.4 74.6 - - - +
259A ARG* 1.4 57.2 - - - +
402A GOL 3.1 45.1 + - - -
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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