Contacts of the helix formed by residues 248 - 260 (chain B) in PDB entry 1R74
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 CYS 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B TYR* 4.9 0.9 - - - -
180B ASP* 3.5 23.1 - - - +
183B LEU* 3.5 31.4 - - - -
215B ALA* 6.0 0.7 - - - -
246B PRO 3.3 6.7 + - - -
247B HIS* 1.3 73.6 - - - +
249B LEU* 1.3 66.0 + - - +
250B ALA* 3.4 3.6 - - + +
251B SER* 3.2 16.2 + - - +
252B PHE* 3.1 19.5 + - - +
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Residues in contact with LEU 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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176B HIS* 4.1 10.6 - - - +
180B ASP* 2.9 22.0 + - - +
247B HIS 3.7 2.2 + - - -
248B CYS* 1.3 67.9 - - - +
250B ALA* 1.3 70.6 + - - +
252B PHE* 4.0 0.4 - - - +
253B THR* 3.1 34.1 + - - +
268B VAL* 4.3 12.3 - - + -
275B TYR* 3.8 30.5 - - + +
286B PHE* 3.9 37.9 - - + -
288B HIS* 3.9 21.3 - - - +
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Residues in contact with ALA 250 (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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180B ASP* 5.0 2.2 + - - +
248B CYS* 3.4 3.1 - - + +
249B LEU* 1.3 83.4 - - - +
251B SER* 1.3 62.5 + - - +
253B THR* 3.5 6.2 - - - +
254B GLU* 3.3 26.8 + - - +
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Residues in contact with SER 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLN* 4.7 11.1 + - - -
247B HIS* 5.8 1.9 + - - +
248B CYS* 3.2 19.7 + - - +
249B LEU 3.1 0.4 - - - -
250B ALA* 1.3 79.2 - - - +
252B PHE* 1.3 60.1 + - - +
254B GLU* 3.1 14.8 + - - +
255B LEU* 2.9 41.1 + - - +
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Residues in contact with PHE 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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142B PHE* 3.3 32.5 - + + -
159B LEU* 4.5 8.1 - - + -
174B ILE* 4.1 25.1 - - + -
175B ASP 4.8 3.1 - - - -
176B HIS* 3.8 18.8 - + + +
247B HIS* 2.7 42.4 - + + -
248B CYS 3.1 15.3 + - - +
249B LEU 3.4 2.2 + - - +
251B SER* 1.3 75.2 + - - +
253B THR* 1.3 56.7 + - - +
255B LEU* 3.1 12.2 + - + +
256B LEU* 2.8 52.9 + - + +
288B HIS* 3.2 32.5 - + + -
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Residues in contact with THR 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 LEU* 3.1 22.7 + - - +
250B ALA* 3.5 7.5 - - - +
252B PHE* 1.3 76.1 - - - +
254B GLU* 1.3 66.7 + - + +
256B LEU* 3.0 7.3 + - - +
257B GLN* 2.8 45.6 + - - +
266B HIS* 3.7 24.6 + - + +
268B VAL* 4.4 2.3 - - + +
288B HIS* 3.3 20.4 + - - -
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Residues in contact with GLU 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 ALA* 3.3 17.4 + - - +
251B SER* 3.1 15.8 + - - +
253B THR* 1.3 81.0 - - + +
255B LEU* 1.3 55.1 + - + +
257B GLN* 3.0 17.9 + - - +
258B ALA* 2.8 36.3 + - - +
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Residues in contact with LEU 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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152B GLN* 4.0 22.7 - - - +
155B HIS* 4.6 9.2 - - + +
156B ARG* 3.8 42.2 - - + +
159B LEU* 3.8 25.4 - - + +
247B HIS* 4.2 17.7 - - + +
251B SER* 2.9 31.4 + - - +
252B PHE* 3.4 15.7 - - + +
254B GLU* 1.3 73.1 - - + +
256B LEU* 1.4 63.2 - - - +
258B ALA* 3.3 7.2 + - + +
259B ALA* 3.1 21.4 + - - +
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Residues in contact with LEU 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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159B LEU* 3.9 29.4 - - + -
172B LEU* 4.1 22.0 - - + -
174B ILE* 3.9 7.2 - - + -
252B PHE* 2.8 35.1 + - + +
253B THR* 3.4 5.6 - - - +
255B LEU* 1.4 71.9 - - - +
257B GLN* 1.3 64.0 + - - +
259B ALA* 3.3 10.9 + - + +
260B PHE* 3.3 23.6 - - + -
266B HIS* 4.6 2.7 - - + +
288B HIS* 3.6 40.2 - - + -
290B LEU* 3.9 18.6 - - + +
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Residues in contact with GLN 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 THR* 2.8 35.4 + - + +
254B GLU* 3.5 26.7 + - - +
256B LEU* 1.3 72.2 - - - +
258B ALA* 1.3 65.2 + - - +
259B ALA 3.1 0.7 + - - -
260B PHE* 3.2 3.8 + - - +
261B GLY 3.2 15.4 + - - -
262B GLY* 3.2 15.0 + - - +
264B CYS* 4.5 7.2 - - - -
266B HIS* 4.9 6.1 - - + +
290B LEU* 5.6 0.2 - - + -
2264B BME 2.9 45.1 + - + +
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Residues in contact with ALA 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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156B ARG* 5.7 10.5 - - + +
254B GLU 2.8 15.1 + - - +
255B LEU* 3.7 8.3 - - + +
257B GLN* 1.3 77.9 - - - +
259B ALA* 1.3 58.0 + - - +
261B GLY* 3.1 18.5 + - - +
262B GLY 5.1 0.2 - - - +
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Residues in contact with ALA 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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156B ARG 5.1 1.8 - - - +
159B LEU* 3.7 38.6 - - + +
160B LYS* 4.1 10.5 - - - +
163B ALA* 3.6 16.2 - - + +
255B LEU 3.1 12.7 + - - +
256B LEU* 3.5 13.0 - - + +
257B GLN 3.1 0.4 - - - -
258B ALA* 1.3 78.7 - - - +
260B PHE* 1.3 63.0 + - + +
261B GLY 3.3 0.4 + - - -
292B ARG* 5.1 0.9 + - - -
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Residues in contact with PHE 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ALA* 3.8 24.5 - - + -
166B VAL* 4.2 9.0 - - + -
172B LEU* 4.1 31.4 - - + -
256B LEU* 3.3 15.9 - - + -
257B GLN 3.2 2.8 + - - -
259B ALA* 1.3 80.3 - - + +
261B GLY* 1.3 62.1 + - - +
262B GLY 3.3 0.4 - - - -
263B LYS* 3.5 15.5 + - - +
264B CYS* 3.9 23.8 - - + -
290B LEU* 3.8 24.9 - - + -
292B ARG* 3.5 66.0 + - + +
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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