Contacts of the helix formed by residues 241 - 255 (chain A) in PDB entry 3H9R
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 ASP 241 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ARG 4.7 2.0 - - - +
219A TYR* 3.6 29.9 - - - +
235A LYS* 5.1 0.3 + - - -
237A PHE* 3.4 20.4 - - + -
238A SER* 2.7 29.9 + - - +
240A ARG* 1.3 77.0 - - + +
242A GLU* 1.3 61.2 + - - +
243A LYS* 3.3 3.3 - - - +
244A SER* 2.9 35.5 + - - -
375A ARG* 3.5 27.4 + - - +
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Residues in contact with GLU 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A PHE* 5.0 0.4 - - - -
238A SER 4.3 1.1 - - - +
239A SER* 3.3 37.1 + - - +
240A ARG 3.8 0.6 - - - -
241A ASP* 1.3 72.7 - - - +
243A LYS* 1.3 61.3 + - + +
244A SER 3.1 2.2 - - - -
245A TRP* 3.0 8.8 + - + +
246A PHE* 3.0 27.6 + - - +
277A THR* 4.9 13.2 - - - +
279A LEU* 3.6 30.4 - - + +
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Residues in contact with LYS 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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241A ASP* 3.3 1.6 - - - +
242A GLU* 1.3 78.5 - - + +
244A SER* 1.3 62.1 + - - +
246A PHE* 3.9 14.4 - - + +
247A ARG* 3.0 26.3 + - - +
356A GLY 4.2 1.0 - - - +
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Residues in contact with SER 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A PHE* 3.8 11.4 - - - -
241A ASP* 2.9 36.1 + - - -
242A GLU 3.1 0.6 - - - -
243A LYS* 1.3 77.7 - - - +
245A TRP* 1.3 58.6 + - - +
248A GLU* 2.9 34.8 + - - +
354A ASP* 5.4 0.2 - - - -
356A GLY* 3.7 14.8 + - - -
357A LEU* 5.5 0.2 - - - +
375A ARG* 2.7 35.5 + - - +
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Residues in contact with TRP 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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237A PHE* 3.5 39.7 - + + -
241A ASP 3.5 2.8 + - - -
242A GLU 3.0 10.0 + - - +
244A SER* 1.3 78.3 - - - +
246A PHE* 1.3 80.0 + + + +
248A GLU* 4.1 1.0 - - - +
249A THR* 2.7 38.6 + - - -
268A SER* 2.9 27.4 + - - -
269A ASP* 4.2 14.6 - - - -
270A MET* 4.3 6.1 - - + -
279A LEU* 3.7 49.6 - - + -
280A TRP 3.1 20.7 + - - +
281A LEU* 4.4 2.0 - - + -
86B THR* 4.0 21.1 - - + -
87B GLY 5.1 0.4 - - - -
88B HIS* 5.0 4.5 - + - -
89B PRO* 3.9 30.7 - - + -
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Residues in contact with PHE 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 GLU 3.0 13.4 + - - +
243A LYS* 4.0 15.9 - - + +
245A TRP* 1.3 92.2 - + + +
247A ARG* 1.3 57.9 + - + +
250A GLU* 2.8 55.6 + - - +
86B THR* 4.5 16.4 - - + -
89B PRO* 3.5 34.9 - - + +
90B GLY 5.0 1.3 - - - -
94B PRO* 5.8 7.6 - - + -
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Residues in contact with ARG 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 LYS 3.0 18.3 + - - +
246A PHE* 1.3 80.4 - - + +
248A GLU* 1.3 59.7 + - - +
250A GLU* 3.4 21.2 + - - +
251A LEU* 2.9 33.0 + - + +
355A LEU 4.4 5.6 - - - +
356A GLY 3.6 19.1 - - - +
357A LEU 5.0 1.1 - - - -
358A ALA 2.8 28.5 + - - +
359A VAL* 3.6 5.9 - - - +
360A MET* 3.5 46.3 + - - +
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Residues in contact with GLU 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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1A TAK 5.1 2.8 + - - -
235A LYS* 4.4 3.8 + - - +
237A PHE* 3.6 16.5 - - - -
244A SER 2.9 18.0 + - - +
245A TRP* 4.2 2.7 - - - +
247A ARG* 1.3 76.6 - - - +
249A THR* 1.3 61.4 + - - +
251A LEU* 3.4 3.2 + - - +
252A TYR* 3.1 49.0 + - + -
263A LEU* 5.5 2.3 - - - +
281A LEU* 3.4 32.6 - - + +
354A ASP* 3.4 17.8 + - - +
355A LEU* 3.1 42.7 + - + +
356A GLY* 4.0 8.3 + - - -
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Residues in contact with THR 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 TRP* 2.7 27.7 + - - -
246A PHE 3.8 2.9 - - - -
248A GLU* 1.3 76.1 - - - +
250A GLU* 1.3 61.9 - - - +
252A TYR* 3.5 3.1 + - - +
253A ASN* 3.0 41.9 + - - +
265A PHE* 5.1 1.1 - - + -
268A SER* 2.9 41.3 + - - +
281A LEU* 3.6 11.3 - - - +
88B HIS* 4.3 1.8 - - + -
89B PRO* 4.1 22.2 - - + -
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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 PHE* 2.8 42.2 + - + +
247A ARG* 3.7 33.6 + - - +
249A THR* 1.3 74.0 - - - +
251A LEU* 1.3 58.6 + - - +
253A ASN 3.8 0.3 - - - -
254A THR* 2.6 46.2 + - - +
360A MET* 4.8 10.3 - - + -
89B PRO* 3.6 21.5 - - + +
90B GLY* 4.1 10.9 + - - +
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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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247A ARG* 2.9 20.0 + - + +
248A GLU* 3.7 6.1 - - - +
250A GLU* 1.3 78.8 - - - +
252A TYR* 1.3 64.1 + - - +
254A THR* 4.7 0.2 - - - -
255A VAL* 3.1 32.4 + - + +
257A LEU* 3.6 31.9 - - + -
332A ILE* 3.7 20.9 - - + -
355A LEU* 3.9 19.1 - - + +
358A ALA* 3.3 37.7 - - + +
360A MET* 4.2 27.4 - - + -
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Residues in contact with TYR 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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194A SER* 2.7 45.7 + - - -
195A GLY 4.4 0.3 + - - -
248A GLU* 3.1 43.3 + - + +
249A THR 4.2 1.8 - - - +
251A LEU* 1.3 81.0 - - - +
253A ASN* 1.3 59.1 + - - +
255A VAL 2.9 6.3 - - - +
257A LEU* 4.2 21.8 - - + -
262A ILE* 4.1 4.2 - - + +
263A LEU* 2.7 36.6 + - + +
265A PHE* 3.2 54.0 + + + -
281A LEU* 4.9 3.1 - - + -
283A THR* 5.9 1.6 - - + -
352A ILE 5.1 0.9 + - - -
354A ASP 5.5 1.2 + - - -
355A LEU* 3.6 33.5 - - + +
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Residues in contact with ASN 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 GLY 4.1 3.5 - - - +
193A GLY* 3.5 16.9 + - - -
195A GLY 5.3 1.2 + - - -
198A PHE* 3.8 28.9 - - + -
201A GLN* 3.3 21.2 + - - -
249A THR* 3.0 37.9 + - - +
250A GLU 4.2 0.2 - - - +
252A TYR* 1.3 75.8 - - - +
254A THR* 1.3 61.6 + - - +
255A VAL 3.5 0.2 - - - -
265A PHE* 3.7 12.8 - - - -
88B HIS* 3.6 26.1 + - - -
89B PRO 3.6 14.8 + - - +
90B GLY 4.6 2.6 - - - +
91B ILE* 4.1 8.2 - - + +
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Residues in contact with THR 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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191A GLY* 5.3 8.7 - - - -
193A GLY* 5.3 1.3 - - - -
250A GLU* 2.6 26.4 + - - +
251A LEU* 4.0 3.8 - - - -
253A ASN* 1.3 77.2 - - - +
255A VAL* 1.3 70.0 + - + +
360A MET* 5.0 10.3 - - + -
90B GLY* 3.6 23.5 + - - +
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Residues in contact with VAL 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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193A GLY* 3.9 3.3 - - - -
194A SER* 2.5 29.3 + - - -
251A LEU* 3.1 17.3 + - + +
252A TYR 2.9 7.4 - - - +
254A THR* 1.3 87.1 - - + +
256A MET* 1.3 63.9 + - - +
257A LEU* 4.0 11.9 - - + +
328A GLY 5.2 2.0 - - - -
329A LYS* 3.7 26.0 - - + -
330A PRO* 3.7 23.1 - - + -
332A ILE* 4.4 12.1 - - + -
360A MET* 3.8 22.4 - - - -
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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