Contacts of the helix formed by residues 251 - 262 (chain B) in PDB entry 1U5Q
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 SER 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B GLU* 2.4 36.3 + - - -
249B HIS 3.8 1.6 + - - -
250B TRP* 1.3 77.2 - - - +
252B GLU* 1.3 59.0 + - - +
253B TYR* 3.7 2.8 + - - -
254B PHE* 3.3 9.7 + - - +
255B ARG* 3.0 24.3 + - - +
283B ARG* 2.9 20.1 + - - -
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Residues in contact with GLU 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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250B TRP 3.7 1.3 + - - -
251B SER* 1.3 70.6 - - - +
253B TYR* 1.3 67.9 + - + +
255B ARG* 3.7 10.0 - - + +
256B ASN* 2.7 44.0 + - - +
279B ARG* 2.6 33.9 + - - -
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Residues in contact with TYR 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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251B SER* 3.7 0.9 + - - -
252B GLU* 1.3 96.0 - - + +
254B PHE* 1.3 58.3 + - - +
256B ASN 3.3 0.2 + - - -
257B PHE* 2.8 25.8 + - - +
278B HIS* 3.4 9.0 - - - -
279B ARG* 3.4 57.4 - - + +
280B PHE* 4.0 12.3 - - - +
283B ARG* 3.5 44.4 - - + +
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Residues in contact with PHE 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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125B GLU* 3.5 24.7 - - + +
128B ILE* 3.5 26.2 - - + -
215B CYS* 3.8 22.7 - - + -
219B ALA* 3.9 10.3 - - + -
245B LEU* 3.8 20.4 - - + -
250B TRP* 3.7 35.7 - + + -
251B SER* 3.3 7.8 + - - +
253B TYR* 1.3 78.2 - - - +
255B ARG* 1.3 64.0 + - - +
257B PHE* 2.9 11.9 + - + +
258B VAL* 3.0 30.1 + - + +
280B PHE* 3.2 39.0 - + + -
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Residues in contact with ARG 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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244B ALA* 4.7 6.1 - - - +
245B LEU* 3.1 49.4 + - + +
247B SER 2.2 39.4 + - - -
248B GLY* 3.4 12.2 + - - -
250B TRP* 4.1 11.1 + - - +
251B SER 3.0 15.8 + - - +
252B GLU* 3.7 10.9 - - + +
254B PHE* 1.3 76.8 - - - +
256B ASN* 1.3 62.7 + - - +
258B VAL* 3.3 2.1 + - - +
259B ASP* 3.0 43.6 + - - +
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Residues in contact with ASN 256 (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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252B GLU* 2.7 36.4 + - - +
253B TYR 3.7 3.6 - - - +
255B ARG* 1.3 72.1 - - - +
257B PHE* 1.3 65.8 + - - +
259B ASP* 3.8 7.2 - - - +
260B SER* 2.8 40.2 + - - -
278B HIS* 2.6 26.3 + - - -
279B ARG* 2.7 25.0 + - - +
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Residues in contact with PHE 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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132B THR* 3.5 31.2 - - + -
136B LEU* 4.1 17.7 - - + -
211B LEU* 4.0 12.6 - - + -
215B CYS* 3.9 15.9 - - - -
253B TYR 2.8 14.8 + - - +
254B PHE 2.9 8.3 + - - +
256B ASN* 1.3 77.4 - - - +
258B VAL* 1.3 65.6 + - + +
260B SER* 3.2 3.3 + - - -
261B CYS* 3.0 41.8 + - - -
275B LEU* 3.9 31.4 - - + -
278B HIS* 3.7 30.5 + + + -
280B PHE* 3.5 26.2 - + + -
281B VAL* 4.2 7.0 - - + -
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Residues in contact with VAL 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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212B GLY* 4.3 4.7 - - - +
215B CYS* 3.8 17.5 - - + -
216B ILE* 3.9 19.1 - - + -
244B ALA* 4.7 0.2 - - - -
245B LEU* 3.8 21.8 - - + +
254B PHE* 3.0 41.2 + - + +
255B ARG 3.7 6.5 - - - +
257B PHE* 1.3 77.8 - - - +
259B ASP* 1.3 64.7 + - - +
261B CYS* 3.1 5.9 + - - +
262B LEU* 2.9 49.2 + - + +
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Residues in contact with ASP 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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243B PRO 4.5 2.1 - - - +
244B ALA* 3.5 29.8 - - - +
245B LEU 4.9 0.7 + - - -
255B ARG* 3.0 40.1 + - - +
256B ASN* 4.0 8.1 - - - +
258B VAL* 1.3 78.3 - - - +
260B SER* 1.3 61.3 + - - +
262B LEU* 3.5 11.5 + - - +
263B GLN* 3.1 26.7 + - - +
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Residues in contact with SER 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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256B ASN* 2.8 39.8 + - - -
257B PHE* 3.5 5.6 - - - -
259B ASP* 1.3 75.2 - - - +
261B CYS* 1.3 66.7 + - - +
262B LEU 3.3 0.3 + - - -
263B GLN* 3.3 24.3 + - - +
269B ARG* 3.6 1.0 - - - +
270B PRO* 3.4 31.3 - - - +
275B LEU* 4.5 9.0 - - - -
278B HIS* 4.3 3.1 + - - -
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Residues in contact with CYS 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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208B VAL* 3.3 28.0 - - - +
209B TRP* 3.6 8.7 - - - -
211B LEU* 4.6 2.7 - - - -
212B GLY* 3.6 17.9 - - - -
257B PHE* 3.0 46.5 + - - -
258B VAL 3.6 5.8 - - - +
260B SER* 1.3 76.2 - - - +
262B LEU* 1.3 59.1 + - - +
263B GLN 3.4 0.2 - - - -
269B ARG* 3.0 26.9 + - - +
275B LEU* 3.6 21.3 - - - -
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Residues in contact with LEU 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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209B TRP* 3.1 53.9 - - + +
212B GLY* 4.0 6.5 - - - -
213B ILE* 3.9 18.2 - - + +
216B ILE* 3.7 24.9 - - + -
242B SER* 2.9 34.5 + - - +
243B PRO* 3.4 25.8 - - + +
258B VAL* 2.9 25.3 + - + +
259B ASP* 3.5 8.5 + - - +
260B SER 3.2 1.0 - - - -
261B CYS* 1.3 78.6 - - - +
263B GLN* 1.3 59.7 + - - -
264B LYS 3.4 0.2 + - - -
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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