Contacts of the helix formed by residues 251 - 263 (chain B) in PDB entry 4DBW
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 THR 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245B ALA* 3.5 4.0 - - - -
250B ARG* 1.3 82.4 - - - +
252B PRO* 1.3 76.4 - - + +
253B ALA* 3.8 4.2 + - - -
254B LEU* 3.0 29.8 + - + +
255B ILE* 3.1 14.0 + - - +
279B GLN* 2.7 43.2 + - + +
401B NAP 5.4 1.8 - - - -
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Residues in contact with PRO 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 LEU* 3.5 40.5 - - + +
241B LEU* 4.3 15.1 - - + +
242B CYS* 4.0 17.0 - - - -
245B ALA* 3.5 16.8 - - + -
250B ARG 4.7 0.4 - - - +
251B THR* 1.3 88.4 - - + +
253B ALA* 1.3 63.1 + - - +
255B ILE* 3.1 9.5 + - + +
256B ALA* 3.0 22.2 + - - +
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Residues in contact with ALA 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 3.5 21.7 - - + +
236B LEU* 3.7 10.1 - - + +
251B THR* 3.1 4.4 + - - +
252B PRO* 1.3 80.0 - - - +
254B LEU* 1.3 63.3 + - - +
256B ALA* 3.1 4.9 + - - +
257B LEU* 3.0 26.5 + - - +
280B ASN* 4.5 2.5 - - - +
401B NAP 3.5 45.1 - - + +
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Residues in contact with LEU 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* 3.9 28.0 - - + -
251B THR* 3.0 26.7 + - + +
253B ALA* 1.3 79.0 - - - +
255B ILE* 1.3 57.7 + - - +
257B LEU* 3.4 6.1 + - + +
258B ARG* 2.9 30.8 + - - +
279B GLN* 3.4 40.2 - - + +
280B ASN* 3.9 17.0 - - - +
282B GLN* 4.3 11.0 - - + +
283B VAL* 3.9 24.2 - - + +
286B PHE* 3.6 16.1 - - + -
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Residues in contact with ILE 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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241B LEU* 4.0 16.2 - - + +
244B LEU* 3.8 35.2 - - + +
245B ALA* 3.8 19.7 - - - +
248B HIS* 4.4 4.7 - - + -
250B ARG* 4.6 2.7 - - + -
251B THR 3.1 14.5 + - - +
252B PRO* 3.1 8.3 + - + +
254B LEU* 1.3 76.7 - - - +
256B ALA* 1.3 58.0 + - - +
258B ARG* 3.3 2.7 + - - +
259B TYR* 2.9 29.6 + - - +
286B PHE* 4.1 16.2 - - + -
288B LEU* 3.9 20.9 - - + +
296B ILE* 3.8 23.3 - - + -
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Residues in contact with ALA 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B PRO* 4.8 13.5 - - + +
218B ALA* 3.5 23.7 - - - +
219B LEU* 4.1 6.5 - - + -
235B LEU* 4.7 10.3 - - + -
236B LEU* 4.7 2.9 - - + -
241B LEU* 4.9 6.5 - - + +
252B PRO 3.0 12.6 + - - +
253B ALA* 3.4 8.3 - - - +
255B ILE* 1.3 79.5 - - - +
257B LEU* 1.3 62.5 + - - +
259B TYR* 3.5 17.2 - - - +
260B GLN* 3.6 14.6 + - - +
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Residues in contact with LEU 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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19B LEU* 4.7 5.4 - - + -
218B ALA* 4.4 2.7 - - + -
219B LEU* 3.7 19.5 - - + -
253B ALA 3.0 19.2 + - - +
254B LEU* 3.9 7.9 - - + +
256B ALA* 1.3 74.1 - - - +
258B ARG* 1.3 66.4 + - - +
260B GLN* 3.2 13.3 + - - +
261B LEU* 3.2 15.8 + - - +
267B VAL* 3.8 33.1 - - + +
268B LEU 4.0 11.4 - - - +
269B ALA* 4.0 11.9 - - + -
280B ASN* 4.0 44.6 - - + +
283B VAL* 3.7 14.6 - - + -
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Residues in contact with ARG 258 (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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254B LEU 2.9 18.6 + - - +
255B ILE 3.8 2.7 - - - +
257B LEU* 1.3 73.3 - - - +
259B TYR* 1.3 66.0 + - - +
261B LEU* 3.1 19.2 + - - +
262B GLN* 2.8 61.5 + - - +
283B VAL* 2.9 32.3 + - + +
284B PHE* 3.8 16.6 + - - +
286B PHE* 3.0 39.0 + - + +
287B GLN* 4.0 10.9 + - - +
288B LEU* 3.8 15.9 - - + +
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Residues in contact with TYR 259 (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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195B PRO* 4.3 12.8 - - + -
198B ASN* 3.4 26.2 + - + +
255B ILE 2.9 17.6 + - - +
256B ALA* 3.5 7.6 - - - +
258B ARG* 1.3 77.2 - - - +
260B GLN* 1.3 78.4 + - - +
263B ARG* 3.2 57.4 + - - +
288B LEU* 3.6 8.9 - - - +
293B MET* 3.3 32.2 - - + +
296B ILE* 3.4 45.9 + - + -
297B ASP* 2.7 32.6 + - - -
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Residues in contact with GLN 260 (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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193B CYS* 3.4 35.9 + - - -
194B HIS* 3.6 13.5 - - - +
195B PRO* 4.8 0.4 - - - +
215B ALA* 4.3 2.7 - - + -
218B ALA* 4.6 3.2 + - + +
256B ALA 3.6 13.8 + - - +
257B LEU 3.2 8.3 + - - +
259B TYR* 1.3 88.9 - - - +
261B LEU* 1.3 63.4 + - - +
263B ARG* 3.0 32.9 + - - +
264B GLY 3.3 0.2 + - - -
265B VAL* 2.9 42.5 + - + +
267B VAL* 3.8 29.8 - - + -
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Residues in contact with LEU 261 (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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18B VAL* 3.6 39.9 - - + +
19B LEU* 5.5 0.4 - - + -
257B LEU 3.2 9.8 + - - +
258B ARG* 3.1 23.1 + - - +
260B GLN* 1.3 76.6 - - - +
262B GLN* 1.3 61.4 + - + +
264B GLY* 3.3 13.3 + - - -
265B VAL 3.8 11.2 - - - +
267B VAL* 3.8 11.7 - - + -
283B VAL* 3.8 28.0 - - + -
284B PHE* 3.9 28.9 - - + -
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Residues in contact with GLN 262 (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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258B ARG* 2.8 53.8 + - - +
259B TYR 3.9 0.2 - - - -
260B GLN 3.2 0.4 - - - -
261B LEU* 1.3 76.7 - - - +
263B ARG* 1.3 58.6 + - - +
264B GLY 3.3 1.5 + - - -
287B GLN* 3.4 4.6 - - - +
288B LEU* 2.6 55.1 + - - +
293B MET* 3.8 24.9 - - + +
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Residues in contact with ARG 263 (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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193B CYS* 3.5 10.1 - - - -
198B ASN* 2.9 49.7 + - - +
200B SER* 4.1 7.9 + - - +
203B LEU* 3.8 26.1 - - + +
207B LYS* 3.0 23.1 + - - -
259B TYR* 3.2 44.6 + - - +
260B GLN* 3.0 40.3 + - - +
262B GLN* 1.3 76.9 - - - +
264B GLY* 1.3 59.0 + - - +
265B VAL* 3.6 9.9 + - + +
293B MET* 4.0 8.1 - - + -
297B ASP* 4.6 2.6 + - - +
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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