Contacts of the helix formed by residues 233 - 252 (chain A) in PDB entry 4N78
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 GLY 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A CYS* 3.6 12.7 - - - +
149A ARG* 5.0 2.5 - - - -
231A ILE 3.3 1.4 + - - -
232A SER* 1.3 74.5 + - - +
234A TYR* 1.3 60.0 + - - +
235A GLU* 3.1 22.8 + - - -
236A GLU* 2.8 34.9 + - - +
278A VAL* 6.3 0.8 - - - +
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Residues in contact with TYR 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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140A VAL* 4.0 17.3 - - + +
144A CYS* 3.8 12.3 - - - -
228A LEU* 3.3 42.6 - - + +
229A GLU* 3.8 34.2 + - + +
231A ILE* 3.5 14.6 - - + +
232A SER 3.3 3.8 + - - -
233A GLY* 1.3 77.0 - - - +
235A GLU* 1.3 93.7 + - + +
236A GLU 3.0 1.4 + - - -
237A LEU* 3.0 13.9 + - - +
238A LEU* 3.2 34.0 + - + +
273A LEU 2.8 29.4 + - - -
274A MET* 4.2 0.7 - - - -
276A GLY 4.6 1.9 + - - -
278A VAL* 4.7 8.7 - - + -
279A SER* 3.9 17.8 + - - -
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Residues in contact with GLU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A GLY* 3.4 19.9 + - - -
234A TYR* 1.3 103.9 + - + +
236A GLU* 1.3 63.7 + - + +
237A LEU 3.4 0.2 - - - -
238A LEU* 4.0 6.1 - - - -
239A ALA* 3.1 27.0 + - - +
274A MET* 3.7 11.4 - - + +
278A VAL* 5.0 8.5 - - - +
279A SER* 3.2 35.0 - - - +
284A LEU* 4.5 20.8 - - + +
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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
----------------------------------------------------------
149A ARG* 3.9 24.8 + - - +
233A GLY* 2.8 22.2 + - - +
235A GLU* 1.3 87.4 - - + +
237A LEU* 1.3 61.9 + - - +
239A ALA* 3.5 1.2 - - - +
240A ASP* 3.2 19.4 + - - +
284A LEU* 4.2 15.5 - - - +
287A LYS* 4.7 9.0 + - - -
289A ARG* 2.5 54.7 + - - +
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Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A VAL* 3.8 42.6 - - + +
143A LEU* 4.2 28.3 - - + -
144A CYS* 3.7 13.0 - - - -
149A ARG* 4.2 17.0 - - - +
153A VAL* 5.5 2.7 - - + -
158A LEU* 4.0 23.6 - - + -
161A LEU* 4.5 8.7 - - + -
233A GLY 3.7 1.4 + - - -
234A TYR 3.0 8.6 + - - +
236A GLU* 1.3 76.9 - - - +
238A LEU* 1.3 62.7 + - + +
240A ASP* 2.9 25.1 + - - +
241A ILE* 3.0 20.2 + - + +
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Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 4.6 9.6 - - + -
140A VAL* 5.8 2.5 - - + -
165A ILE* 4.6 23.8 - - + -
228A LEU* 4.6 5.8 - - + -
234A TYR* 3.2 32.8 + - + +
235A GLU 4.2 0.4 - - - +
237A LEU* 1.3 81.8 - - + +
239A ALA* 1.3 57.8 + - - +
241A ILE* 3.1 23.6 + - + +
242A VAL* 2.8 34.2 + - + +
270A GLY* 4.3 4.3 - - - +
273A LEU* 3.8 27.4 - - + -
274A MET* 3.5 31.0 - - + -
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Residues in contact with ALA 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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235A GLU 3.1 20.3 + - - +
236A GLU* 3.5 8.7 - - - +
237A LEU 3.1 0.2 - - - -
238A LEU* 1.3 77.0 - - - +
240A ASP* 1.3 54.4 + - - +
242A VAL* 4.0 1.0 - - - +
243A ASN* 2.7 41.1 + - - +
274A MET* 3.8 18.4 - - + -
284A LEU* 5.6 0.7 - - + -
289A ARG* 4.0 22.9 - - + -
290A ILE* 4.1 13.9 - - + -
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Residues in contact with ASP 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ARG* 3.2 34.3 + - - -
158A LEU* 4.1 23.1 - - + +
236A GLU 3.2 4.5 + - - +
237A LEU* 2.9 10.5 + - + +
239A ALA* 1.3 75.1 - - - +
241A ILE* 1.3 64.4 + - - +
243A ASN* 3.6 5.7 + - - +
244A LEU* 3.1 23.7 + - - +
289A ARG* 2.4 32.5 + - - -
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Residues in contact with ILE 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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136A PHE* 5.3 3.1 - - + -
158A LEU* 3.7 28.3 - - + +
159A ILE* 6.4 0.2 - - + -
161A LEU* 3.6 33.9 - - + +
162A GLY* 3.7 26.2 - - - +
165A ILE* 5.1 4.5 - - + -
237A LEU* 3.0 16.9 + - + +
238A LEU* 3.1 28.7 + - + +
240A ASP* 1.3 76.6 - - - +
242A VAL* 1.3 63.3 + - + +
244A LEU* 3.3 7.2 + - - +
245A CYS* 3.2 24.0 + - - -
266A VAL* 3.7 14.1 - - + -
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Residues in contact with VAL 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A LEU 2.8 23.4 + - - +
239A ALA* 4.0 5.2 - - - +
241A ILE* 1.3 72.0 - - + +
243A ASN* 1.3 68.6 + - - +
245A CYS* 3.1 9.2 + - - +
246A VAL* 2.9 25.3 + - + +
266A VAL* 4.4 7.0 - - + +
267A MET* 4.3 12.6 - - - +
270A GLY* 4.0 22.4 - - - -
271A LEU* 4.3 7.6 - - + +
274A MET* 4.0 17.0 - - - -
290A ILE* 5.1 4.9 - - + -
295A ILE* 3.7 30.5 - - + -
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Residues in contact with ASN 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ALA 2.7 28.4 + - - +
240A ASP* 3.9 5.9 - - - +
242A VAL* 1.3 78.0 - - - +
244A LEU* 1.3 57.3 + - - +
246A VAL* 3.5 10.6 + - - +
247A ASP* 3.0 27.2 + - - +
289A ARG* 2.9 45.8 + - - +
290A ILE* 3.5 18.2 - - - +
291A ASN 4.4 2.6 + - - -
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Residues in contact with LEU 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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155A GLU* 3.4 52.5 - - + +
158A LEU* 3.6 23.6 - - + -
159A ILE* 3.9 16.2 - - + +
240A ASP 3.1 18.2 + - - +
241A ILE 3.5 5.8 - - - +
242A VAL 3.1 0.2 - - - -
243A ASN* 1.3 75.6 - - - +
245A CYS* 1.3 59.7 + - - +
247A ASP* 3.1 10.1 + - + +
248A TYR* 2.8 57.7 + - + +
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Residues in contact with CYS 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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159A ILE* 4.5 12.8 - - - -
162A GLY* 5.8 0.9 - - - -
241A ILE* 3.2 18.3 + - - -
242A VAL* 3.1 8.1 + - - +
244A LEU* 1.3 77.2 - - - +
246A VAL* 1.3 57.8 + - - +
248A TYR* 3.8 0.9 - - - +
249A TYR* 2.9 26.3 + - - +
263A LEU* 3.7 41.0 - - + +
266A VAL* 3.5 33.9 - - - -
267A MET* 3.2 16.0 - - + +
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Residues in contact with VAL 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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242A VAL* 2.9 20.4 + - + +
243A ASN* 3.6 13.0 - - - +
245A CYS* 1.3 75.6 - - - +
247A ASP* 1.3 58.7 + - - +
249A TYR* 4.0 0.5 - - - +
250A GLU* 3.0 30.2 + - - +
267A MET* 3.6 14.8 - - - -
291A ASN* 5.3 7.0 - - + +
294A LYS* 3.9 31.0 - - + +
295A ILE* 3.7 33.4 - - + -
298A TYR* 3.8 10.8 + - + -
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Residues in contact with ASP 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 ASN 3.0 13.9 + - - +
244A LEU* 3.1 14.6 + - + +
246A VAL* 1.3 76.7 - - - +
248A TYR* 1.3 72.9 + - + +
250A GLU* 3.5 6.9 + - - +
251A ASN* 2.9 53.0 + - - +
253A MET* 5.0 1.7 - - - +
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Residues in contact with TYR 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 GLU* 2.4 43.0 + - - +
156A ALA* 5.6 0.5 - - - -
159A ILE* 3.7 33.8 - - + +
244A LEU* 2.8 32.8 + - + +
245A CYS 3.8 1.6 - - - +
247A ASP* 1.3 84.9 - - - +
249A TYR* 1.3 53.7 + - - +
251A ASN 3.1 0.5 + - - -
252A ARG 2.7 32.2 + - - -
253A MET* 2.7 45.5 + - + +
263A LEU* 3.8 20.2 - - + -
563A ARG* 5.3 1.2 + - - -
600A PHE* 4.0 27.3 - + - -
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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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245A CYS 2.9 17.9 + - - +
246A VAL 4.0 1.3 - - - +
248A TYR* 1.3 77.0 - - - +
250A GLU* 1.3 62.8 + - - +
251A ASN 3.4 0.2 + - - -
252A ARG* 3.4 11.3 + - - -
254A TYR* 4.0 17.2 + + - -
260A LYS* 3.9 41.4 - - + -
263A LEU* 3.6 13.2 - - + +
264A LEU* 3.6 38.2 - - + +
267A MET* 3.6 12.3 - - + -
298A TYR* 3.7 45.8 + + + -
301A GLN* 5.6 8.4 + - - +
302A LEU* 4.0 12.0 - - - +
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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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246A VAL* 3.0 16.8 + - - +
247A ASP* 3.8 8.0 - - - +
249A TYR* 1.3 78.4 - - - +
251A ASN* 1.3 73.7 + - - +
252A ARG* 3.4 8.0 + - - +
294A LYS* 3.1 35.4 + - - +
297A LYS* 6.3 0.9 - - - +
298A TYR* 3.2 26.2 + - + +
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Residues in contact with ASN 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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247A ASP* 2.9 43.4 + - - +
250A GLU* 1.3 92.5 + - - +
252A ARG* 1.3 74.7 + - - +
253A MET* 3.3 23.8 + - + +
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Residues in contact with ARG 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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248A TYR 2.7 7.4 + - - -
249A TYR 3.4 8.2 + - - -
250A GLU 3.4 7.1 + - - +
251A ASN* 1.3 84.4 - - - +
253A MET* 1.3 55.3 + - - +
254A TYR* 2.9 49.9 + - + +
399A GLN* 5.5 2.8 + - - +
403A GLN* 4.9 13.5 - - - +
601A PHE* 3.8 10.7 - - - -
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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