Contacts of the helix formed by residues 237 - 254 (chain A) in PDB entry 4PYP
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 VAL 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A LEU* 4.0 15.9 - - + +
232A ARG* 4.5 8.3 - - + +
235A ALA* 3.9 24.5 - - + +
236A ASP* 1.3 72.5 - - - +
238A THR* 1.3 62.2 + - - +
239A HIS* 3.9 16.4 - - + +
240A ASP* 3.5 46.2 - - + +
241A LEU* 3.6 22.3 + - - +
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Residues in contact with THR 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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236A ASP 3.7 5.6 + - - -
237A VAL* 1.3 71.0 - - - +
239A HIS* 1.3 64.9 + - + +
241A LEU* 3.3 9.0 + - + +
242A GLN* 2.9 46.0 + - + +
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Residues in contact with HIS 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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237A VAL* 3.9 14.2 - - + +
238A THR* 1.3 85.2 - - + +
240A ASP* 1.3 56.6 + - - +
242A GLN* 3.5 9.4 + - - +
243A GLU* 3.0 29.0 + - - +
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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
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148A SER 5.3 0.3 - - - +
149A PRO* 4.7 1.9 - - - +
150A THR* 4.1 19.2 + - - -
228A LEU* 3.7 15.4 - - + +
232A ARG* 2.5 42.1 + - - -
237A VAL* 3.5 28.2 - - + +
238A THR 3.4 0.4 - - - -
239A HIS* 1.3 78.6 - - - +
241A LEU* 1.3 57.6 + - - +
243A GLU* 3.3 8.8 + - - +
244A MET* 2.9 38.7 + - - +
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Residues in contact with LEU 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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215A LEU* 3.7 30.3 - - + -
221A GLU* 5.4 4.9 - - - +
224A ALA 5.9 0.7 - - - +
225A LYS* 4.6 33.2 - - + +
228A LEU* 5.3 12.1 - - + -
237A VAL 3.6 13.9 + - - +
238A THR* 3.3 12.7 + - + +
239A HIS 3.3 0.6 - - - -
240A ASP* 1.3 76.7 - - - +
242A GLN* 1.3 63.9 + - + +
244A MET* 3.3 15.3 + - + +
245A LYS* 3.2 42.1 + - + +
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Residues in contact with GLN 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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238A THR* 2.9 31.8 + - + +
239A HIS* 4.0 9.9 - - - +
241A LEU* 1.3 76.4 - - + +
243A GLU* 1.3 56.3 + - - +
245A LYS* 3.3 6.9 + - - +
246A GLU* 2.8 34.3 + - + +
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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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150A THR* 2.5 31.8 + - + +
153A ARG* 3.5 11.1 + - - -
212A ARG* 4.0 14.8 + - - -
239A HIS 3.0 18.4 + - - +
240A ASP* 3.5 12.9 - - - +
241A LEU 3.2 0.2 - - - -
242A GLN* 1.3 77.9 - - - +
244A MET* 1.3 58.4 + - - +
246A GLU* 3.4 5.3 - - + +
247A GLU* 2.5 64.0 + - + +
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Residues in contact with MET 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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146A GLU 6.0 1.8 - - - +
211A PRO* 3.3 47.1 - - + +
212A ARG* 3.6 25.6 - - + +
215A LEU* 3.6 33.0 - - + -
216A ILE* 3.4 10.4 - - - +
224A ALA* 5.1 1.6 - - + -
228A LEU* 4.9 9.4 - - + -
240A ASP* 2.9 25.4 + - - +
241A LEU* 3.7 15.5 - - + +
242A GLN 3.3 0.2 - - - -
243A GLU* 1.3 85.2 - - - +
245A LYS* 1.3 59.5 + - - +
246A GLU 3.4 0.2 - - - -
247A GLU* 3.9 3.7 - - - +
248A SER* 3.0 24.4 + - - -
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Residues in contact with LYS 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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215A LEU* 3.8 35.4 - - + +
221A GLU* 3.6 28.8 + - - +
241A LEU* 3.2 27.7 + - + +
242A GLN* 3.5 7.2 - - - +
243A GLU 3.1 0.4 - - - -
244A MET* 1.3 79.2 - - - +
246A GLU* 1.3 57.7 + - - +
248A SER* 3.2 14.0 + - - +
249A ARG* 3.3 23.4 + - - +
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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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242A GLN* 2.8 18.4 + - + +
243A GLU* 3.8 6.7 - - + +
245A LYS* 1.3 77.8 - - - +
247A GLU* 1.3 59.2 + - - +
248A SER 3.1 0.9 - - - -
249A ARG* 2.5 67.2 + - - +
250A GLN* 3.1 22.2 + - - +
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Residues in contact with GLU 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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153A ARG* 3.9 12.0 + - - -
212A ARG* 3.7 32.8 + - + +
216A ILE* 5.4 3.1 - - + -
243A GLU* 2.5 45.4 + - + +
244A MET* 4.1 6.1 - - - +
246A GLU* 1.3 71.2 - - - +
248A SER* 1.3 57.6 + - - +
249A ARG 3.1 1.6 - - - -
250A GLN* 4.8 1.8 - - - +
251A MET* 3.0 62.2 + - + +
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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
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215A LEU* 5.3 0.2 - - - +
216A ILE* 3.6 27.0 - - - +
244A MET 3.0 20.9 + - - -
245A LYS* 3.2 16.4 + - - +
247A GLU* 1.3 74.2 - - - +
249A ARG* 1.3 59.1 - - - +
251A MET* 5.0 0.2 - - - -
252A MET* 3.2 34.1 - - - +
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Residues in contact with ARG 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 LYS 3.3 15.8 + - - +
246A GLU* 2.5 59.2 + - - +
248A SER* 1.3 77.4 - - - +
250A GLN* 1.3 57.3 + - + +
252A MET 2.8 6.2 + - - -
253A ARG* 2.5 89.6 + - - +
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Residues in contact with GLN 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 GLU* 3.1 21.6 + - - +
247A GLU* 5.0 1.6 - - - +
249A ARG* 1.3 80.9 - - + +
251A MET* 1.3 61.4 + - + +
252A MET 3.2 0.7 + - - -
253A ARG* 3.5 14.2 + - - -
254A GLU* 3.5 18.7 + - - +
397A GLN* 3.5 42.6 + - + +
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Residues in contact with MET 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 GLU* 3.0 47.5 + - + +
250A GLN* 1.3 76.0 - - + +
252A MET* 1.3 68.9 + - + +
254A GLU 3.8 10.7 - - - +
256A LYS* 5.4 7.1 + - - +
397A GLN* 3.8 39.6 - - + +
400A ARG* 5.3 8.1 - - - -
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Residues in contact with MET 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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216A ILE* 4.4 24.2 - - + -
248A SER* 3.2 38.6 - - - +
249A ARG 2.8 2.9 + - - -
251A MET* 1.3 91.8 - - + +
253A ARG* 1.3 60.2 + - - +
254A GLU 3.6 4.5 - - - +
255A LYS* 5.7 0.7 - - - -
256A LYS* 6.3 5.4 - - - -
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Residues in contact with ARG 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 ARG* 2.5 82.5 + - - +
250A GLN* 3.5 8.5 + - - +
252A MET* 1.3 77.3 - - - +
254A GLU* 1.3 64.5 + - + +
255A LYS* 3.9 4.4 + - - +
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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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250A GLN* 3.5 17.1 + - - +
251A MET 3.8 15.2 - - - +
252A MET* 4.1 3.2 - - - -
253A ARG* 1.3 82.2 + - + +
255A LYS* 1.3 66.3 + - - +
256A LYS 3.4 1.9 + - - -
396A SER* 2.3 33.0 + - - -
397A GLN* 2.8 26.3 - - - +
398A GLY* 4.0 15.0 - - - +
399A PRO* 4.8 0.4 - - + +
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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
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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