Contacts of the helix formed by residues 245 - 257 (chain A) in PDB entry 4M83
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 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A LEU* 5.6 4.7 - - + -
242A PHE 4.5 8.4 + - - +
243A THR* 3.8 2.1 - - - -
244A LYS* 1.3 84.2 + - - +
246A PRO* 1.3 76.2 - - - +
247A ALA* 4.9 4.0 + - - +
248A PHE* 3.9 21.6 + - + +
249A TYR* 3.9 30.0 + - + +
326A GLN* 2.9 35.7 + - - +
348A THR* 4.7 8.1 - - - +
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Residues in contact with PRO 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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244A LYS 3.5 9.2 - - - +
245A GLN* 1.3 89.1 - - + +
247A ALA* 1.3 59.4 + - + +
248A PHE 2.6 17.0 + - - -
249A TYR 3.9 1.4 + - - -
250A ARG* 2.9 40.0 - - - +
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Residues in contact with ALA 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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245A GLN* 3.6 4.9 + - - +
246A PRO* 1.3 81.5 - - + +
248A PHE* 1.3 63.5 + - - +
250A ARG* 4.4 14.6 - - - +
251A GLU* 4.6 12.4 - - + +
348A THR* 4.6 9.9 - - - +
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Residues in contact with PHE 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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236A VAL* 4.4 8.3 - - + -
238A LEU* 4.7 17.3 - - + -
245A GLN* 4.2 20.9 - - + +
246A PRO 2.6 11.5 + - - -
247A ALA* 1.3 76.8 - - - +
249A TYR* 1.3 75.9 + + - +
250A ARG 3.3 1.7 - - - +
251A GLU* 2.9 15.8 + - + +
252A CYS* 2.8 49.6 + - - -
303A VAL* 4.0 22.7 - - + -
324A VAL* 4.2 22.4 - - + -
326A GLN* 6.0 2.9 - - - +
348A THR* 4.6 15.3 - - + -
351A ALA* 4.3 23.1 - - + -
356A LEU* 4.5 6.1 - - + -
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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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236A VAL* 4.2 21.3 - - + -
238A LEU* 4.7 13.0 - - + +
243A THR* 3.4 38.8 + - - -
244A LYS* 5.3 0.4 - - - -
245A GLN* 3.9 28.4 - - + +
246A PRO 3.9 2.2 + - - -
248A PHE* 1.3 91.2 - + + +
250A ARG* 1.3 58.0 + - + +
252A CYS* 2.7 28.1 + - - +
253A VAL* 2.8 18.1 + - - +
266A LEU* 4.0 15.8 - - + +
267A GLN* 3.3 23.7 + - - -
268A ILE* 3.2 39.2 - - + -
270A ARG* 6.0 0.2 - - - -
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Residues in contact with ARG 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A PRO* 2.9 48.0 + - - +
247A ALA* 4.2 10.4 - - - +
249A TYR* 1.3 76.5 - - + +
251A GLU* 1.3 63.9 + - + +
253A VAL* 3.5 12.4 + - - +
254A ARG* 3.3 21.8 + - - +
276A GLU* 5.4 15.2 + - + +
277A LEU 4.7 13.9 - - - +
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Residues in contact with GLU 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 ALA* 4.6 11.2 - - + +
248A PHE* 2.9 27.9 + - + +
250A ARG* 1.3 81.9 - - + +
252A CYS* 1.3 62.8 + - - +
254A ARG* 3.5 20.1 + - - +
255A ALA* 3.3 20.8 + - - +
351A ALA 3.9 17.1 - - - +
352A THR* 4.1 4.2 - - - +
353A ALA* 3.8 23.3 + - - +
356A LEU* 4.2 4.8 - - + +
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Residues in contact with CYS 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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236A VAL* 3.8 22.2 - - + -
248A PHE* 2.8 47.6 + - - -
249A TYR* 2.7 14.9 + - - +
251A GLU* 1.3 71.4 - - - +
253A VAL* 1.3 64.0 + - - +
255A ALA* 3.2 1.9 + - - +
256A PHE* 3.2 32.0 + - + -
264A LEU* 3.7 5.4 - - + +
266A LEU* 4.0 16.4 - - + -
303A VAL* 4.7 2.2 - - - -
356A LEU* 3.9 16.6 - - - -
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Residues in contact with VAL 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 TYR 2.8 20.1 + - - +
250A ARG* 3.7 11.9 - - - +
252A CYS* 1.3 76.0 - - - +
254A ARG* 1.3 57.1 + - - +
257A GLY* 2.6 35.9 + - - -
264A LEU* 4.1 7.9 - - - -
266A LEU* 3.4 23.8 - - + -
280A LEU* 3.6 22.2 - - + -
281A PRO* 3.5 30.8 - - + +
284A VAL* 4.4 8.1 - - + -
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Residues in contact with ARG 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 ARG 3.3 13.1 + - - +
251A GLU* 3.8 20.4 - - - +
252A CYS 3.2 0.4 - - - -
253A VAL* 1.3 82.8 - - - +
255A ALA* 1.3 62.1 + - - +
257A GLY 4.3 7.0 + - - +
353A ALA* 3.7 19.0 - - + +
357A ARG* 5.7 0.9 + - - -
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Residues in contact with ALA 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 GLU 3.3 10.4 + - - +
252A CYS 3.2 9.0 + - - +
254A ARG* 1.3 81.5 - - - +
256A PHE* 1.3 70.8 + - + +
257A GLY 5.2 0.4 - - - +
259A LEU* 3.7 17.5 - - - +
353A ALA* 3.4 27.1 - - - +
356A LEU* 3.8 22.0 - - + -
357A ARG* 3.8 18.0 + - - +
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Residues in contact with PHE 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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234A VAL* 4.0 29.4 - - + -
252A CYS* 3.2 30.6 + - + +
255A ALA* 1.3 88.5 - - + +
257A GLY* 1.3 64.6 + - - +
259A LEU* 3.0 25.7 + - + +
262A TRP* 4.0 27.5 - + + +
264A LEU* 4.2 23.3 - - + -
283A ASN* 2.9 22.1 + - - +
284A VAL* 5.1 0.9 - - - -
301A LEU* 4.5 2.7 - - + -
303A VAL* 4.6 12.1 - - + -
322A ILE* 5.0 1.1 - - + -
356A LEU* 4.3 13.9 - - + -
357A ARG* 4.5 7.0 - - - -
360A ALA* 3.5 32.8 - - + -
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Residues in contact with GLY 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 VAL 2.6 26.5 + - - +
254A ARG 4.3 6.3 + - - +
255A ALA 3.7 0.6 - - - -
256A PHE* 1.3 71.1 - - - +
258A ASN* 1.3 75.2 + - - +
259A LEU* 3.1 2.1 + - - +
281A PRO* 3.6 13.9 - - - -
283A ASN* 3.5 7.9 - - - -
284A VAL* 4.0 7.3 - - - +
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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