Contacts of the helix formed by residues 245 - 257 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238B LEU* 3.9 14.8 - - + -
242B PHE* 4.3 3.2 + - - +
243B THR 2.5 14.5 + - - +
244B LYS* 1.3 86.6 + - - +
246B PRO* 1.3 61.6 - - - +
247B ALA* 3.3 2.5 - - - -
248B PHE* 3.6 23.4 + - + +
249B TYR* 2.7 32.3 + - + -
272B VAL* 4.2 0.2 - - - +
326B GLN* 3.2 27.5 + - - +
348B THR* 4.0 14.9 - - + +
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Residues in contact with PRO 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B LYS* 3.3 15.7 - - + +
245B GLN* 1.3 88.6 - - - +
247B ALA* 1.3 54.8 + - + +
249B TYR* 3.5 11.8 - - + +
250B ARG* 2.6 43.6 + - - +
272B VAL* 4.6 12.6 - - + -
276B GLU* 3.4 39.3 - - + +
277B LEU* 4.4 2.2 - - + +
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B GLN 3.3 0.2 - - - -
246B PRO* 1.3 83.5 - - + +
248B PHE* 1.3 52.8 + - - +
250B ARG* 3.2 23.1 + - - +
251B GLU* 2.5 42.1 + - + +
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Residues in contact with PHE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B VAL* 4.3 6.3 - - + -
238B LEU* 4.1 26.9 - - + -
245B GLN* 3.3 25.1 + - + +
246B PRO 3.2 0.2 - - - -
247B ALA* 1.3 79.6 - - - +
249B TYR* 1.3 61.7 + + - +
251B GLU* 3.0 8.6 + - - +
252B CYS* 2.5 60.0 + - - -
303B VAL* 3.9 7.2 - - + -
324B VAL* 3.7 26.5 - - + -
348B THR* 3.7 25.8 - - + +
351B ALA* 3.6 35.4 - - + -
356B LEU* 4.0 8.3 - - + -
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Residues in contact with TYR 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B VAL* 4.3 19.1 - - + -
238B LEU* 3.8 14.7 - - + +
243B THR* 2.0 55.4 + - - -
245B GLN* 2.7 26.1 + - + +
246B PRO* 3.6 8.3 - - + +
248B PHE* 1.3 88.0 - + - +
250B ARG* 1.3 54.0 + - - +
252B CYS* 2.9 5.4 + - - +
253B VAL* 2.5 40.0 + - - +
266B LEU* 4.3 6.6 - - + +
267B GLN 3.7 14.6 + - - -
268B ILE* 3.7 35.7 - - + -
272B VAL* 4.2 9.2 - - + -
277B LEU* 3.6 15.0 - - + -
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Residues in contact with ARG 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B PRO* 2.6 22.8 + - - +
247B ALA* 3.5 29.1 - - - +
249B TYR* 1.3 71.4 - - - +
251B GLU* 1.3 61.8 + - - +
253B VAL* 3.6 9.5 - - + +
254B ARG* 2.8 57.3 + - - +
276B GLU* 3.6 39.0 + - - +
277B LEU* 4.1 28.4 - - + +
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Residues in contact with GLU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B ALA* 2.5 28.9 + - + +
248B PHE* 3.2 13.5 - - - +
250B ARG* 1.3 75.5 - - - +
252B CYS* 1.3 54.3 + - - +
254B ARG* 3.5 26.0 + - - -
255B ALA* 2.9 29.3 + - - +
351B ALA 3.6 22.9 - - - +
352B THR* 3.5 12.2 - - + +
353B ALA* 3.0 32.2 + - - +
356B LEU* 3.9 2.8 - - - +
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Residues in contact with CYS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B VAL* 3.8 23.6 - - + -
248B PHE* 2.5 58.2 + - - +
249B TYR* 2.9 9.4 + - - +
251B GLU* 1.3 72.0 - - - +
253B VAL* 1.3 66.4 + - - +
255B ALA* 3.3 5.1 + - - -
256B PHE* 3.3 31.1 + - + -
264B LEU* 3.6 4.4 - - - +
266B LEU* 3.8 18.2 - - + -
303B VAL* 4.7 2.9 - - - -
356B LEU* 4.3 6.1 - - - -
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Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B TYR 2.5 29.4 + - - +
250B ARG* 3.6 9.0 - - + +
252B CYS* 1.3 70.2 - - - +
254B ARG* 1.3 58.4 + - + +
257B GLY* 2.7 34.0 + - - -
264B LEU* 4.1 9.1 - - - +
266B LEU* 3.4 23.3 - - + -
277B LEU* 4.0 31.2 - - + +
279B GLU 5.5 1.6 - - - +
280B LEU* 4.6 8.3 - - + -
281B PRO* 4.2 25.4 - - + -
284B VAL* 4.9 3.8 - - + -
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Residues in contact with ARG 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B ARG* 2.8 46.2 + - - +
251B GLU* 3.5 21.3 + - - -
253B VAL* 1.3 75.4 - - + +
255B ALA* 1.3 66.3 + - - +
256B PHE 3.3 0.3 + - - -
257B GLY* 3.7 10.0 + - - +
353B ALA* 3.9 19.6 - - + +
357B ARG* 5.2 1.9 - - - -
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Residues in contact with ALA 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B GLU 2.9 20.1 + - - +
252B CYS* 3.3 8.5 + - - +
254B ARG* 1.3 79.2 - - - +
256B PHE* 1.3 75.9 + - + +
257B GLY 5.2 0.3 - - - +
259B LEU* 4.5 1.4 - - - +
353B ALA* 3.4 25.7 - - - +
356B LEU* 3.9 15.5 - - + -
357B ARG* 3.2 34.2 - - - +
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Residues in contact with PHE 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B VAL* 3.7 40.4 - - + -
236B VAL* 4.8 3.4 - - + -
252B CYS* 3.3 21.1 + - + +
255B ALA* 1.3 91.2 - - + +
257B GLY* 1.3 67.6 + - - +
259B LEU* 3.4 18.5 + - + +
262B TRP* 3.8 19.2 - + + +
264B LEU* 4.0 26.9 - - + +
283B ASN* 2.9 20.3 + - - +
284B VAL* 4.8 1.8 - - - -
301B LEU* 4.3 5.4 - - + -
303B VAL* 4.4 12.8 - - + -
322B ILE* 5.0 0.4 - - + -
356B LEU* 4.6 12.1 - - + -
357B ARG* 4.8 3.8 - - - -
360B ALA* 3.6 29.4 - - + -
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Residues in contact with GLY 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B VAL* 2.7 25.3 + - - -
254B ARG* 3.7 8.4 + - - +
255B ALA 3.7 1.5 - - - +
256B PHE* 1.3 71.2 - - - +
258B ASN* 1.3 72.4 + - - +
259B LEU* 3.3 1.9 + - - +
281B PRO* 3.9 17.5 - - - -
283B ASN* 4.0 2.9 - - - -
284B VAL* 4.3 2.9 - - - -
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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