Contacts of the helix formed by residues 245 - 258 (chain B) in PDB entry 3RU0
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 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244B MET* 1.3 74.6 - - - +
246B SER* 1.3 64.5 + - - +
247B GLU* 3.7 9.3 + - - +
248B GLU* 3.0 36.2 + - - +
249B ARG* 3.0 21.8 + - - +
272B ASP* 3.5 16.4 - - - +
275B MET* 3.9 8.7 - - + -
276B LEU* 3.8 42.0 - - + -
325B ILE* 4.2 7.9 - - + -
326B TYR* 4.4 2.7 - - - +
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Residues in contact with SER 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B THR* 1.3 71.2 - - - +
247B GLU* 1.3 57.0 + - - +
249B ARG* 3.3 29.7 + - - +
250B ARG* 2.9 29.6 + - - +
266B CYS* 4.4 17.6 - - - +
269B GLN* 3.6 26.2 + - - +
272B ASP* 2.7 34.2 + - - -
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Residues in contact with GLU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B THR* 3.2 9.2 + - - +
246B SER* 1.3 82.9 + - - +
248B GLU* 1.3 58.2 + - + +
250B ARG* 3.4 7.8 + - - +
251B LYS* 3.0 27.8 + - + +
272B ASP* 4.5 1.3 + - - +
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU 4.4 0.9 - - - +
244B MET* 3.4 31.0 - - + +
245B THR* 3.0 34.0 + - - +
247B GLU* 1.3 75.0 - - + +
249B ARG* 1.3 66.0 + - - +
251B LYS* 3.4 8.2 + - - +
252B GLN* 3.1 18.7 + - - +
287B GLN* 3.4 16.3 + - - +
325B ILE* 3.9 4.7 - - - +
326B TYR* 2.6 33.2 + - - -
329B LYS* 6.0 0.2 - - - -
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Residues in contact with ARG 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B CYS* 3.3 23.1 - - - +
240B LEU* 3.6 26.6 - - + +
241B ASP 4.9 5.2 - - - -
242B MET* 5.5 2.0 + - - +
244B MET* 3.0 40.3 + - + +
245B THR* 3.0 13.3 + - - +
246B SER* 3.3 32.3 - - - +
248B GLU* 1.3 73.5 - - - +
250B ARG* 1.3 64.2 + - - +
252B GLN* 3.2 1.2 + - - -
253B LEU* 2.9 37.5 + - + +
265B ARG* 3.8 39.1 + - - +
266B CYS* 3.5 33.0 - - - +
270B ASP 4.8 1.8 + - - -
272B ASP* 4.5 3.0 + - - -
275B MET* 4.9 0.2 - - - +
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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 SER 2.9 18.3 + - - +
247B GLU* 3.5 9.4 - - - +
248B GLU 3.3 0.2 - - - -
249B ARG* 1.3 74.2 - - - +
251B LYS* 1.3 64.2 + - - +
253B LEU* 3.9 5.0 - - - +
254B ARG* 3.0 26.4 + - - +
259B PHE 4.7 1.0 - - - +
260B GLU* 4.6 17.0 - - - +
261B CYS* 6.2 2.9 - - - +
266B CYS* 5.8 2.6 - - - -
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Residues in contact with LYS 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 GLU* 3.0 18.4 + - + +
248B GLU* 3.7 7.4 - - - +
249B ARG 3.3 0.2 - - - -
250B ARG* 1.3 77.8 - - - +
252B GLN* 1.3 58.9 + - - +
254B ARG* 3.4 2.9 + - - -
255B ASP* 2.9 55.8 + - - +
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Residues in contact with GLN 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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239B TYR 5.3 1.4 + - - -
240B LEU* 3.3 28.4 - - + +
244B MET* 3.5 23.5 - - + +
248B GLU 3.1 17.1 + - - +
249B ARG 4.0 2.2 - - - +
251B LYS* 1.3 76.5 - - - +
253B LEU* 1.3 58.6 + - - +
255B ASP* 4.5 4.0 - - + +
256B GLN* 2.8 63.1 + - + +
257B TYR* 4.6 2.0 + - + -
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Residues in contact with LEU 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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206B HIS* 3.6 32.1 - - + +
208B CYS* 4.9 0.4 - - - -
239B TYR* 4.5 1.8 - - + -
240B LEU* 3.8 32.1 - - + -
249B ARG* 2.9 26.5 + - + +
250B ARG* 4.1 3.4 - - - +
252B GLN* 1.3 74.6 - - - +
254B ARG* 1.3 59.0 + - - +
257B TYR* 3.1 23.3 + - + +
258B CYS 3.0 21.5 + - - -
259B PHE* 3.2 44.3 + - + +
261B CYS* 3.7 18.8 - - + +
266B CYS* 5.6 0.2 - - - -
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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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135B LYS* 5.2 9.5 + - - +
137B THR* 6.3 3.8 - - - -
250B ARG 3.0 19.5 + - - +
251B LYS* 3.8 3.6 - - - +
253B LEU* 1.3 77.3 - - - +
255B ASP* 1.3 70.6 + - - +
258B CYS* 3.1 46.7 + - - +
259B PHE* 3.4 37.2 + - - +
260B GLU* 3.8 15.9 - - + +
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Residues in contact with ASP 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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136B LEU* 6.2 0.2 - - - +
140B LYS* 3.2 22.2 + - - +
251B LYS* 2.9 52.1 + - - +
252B GLN* 3.3 4.2 + - + +
254B ARG* 1.3 87.5 - - - +
256B GLN* 1.3 61.2 + - + +
258B CYS* 5.1 3.5 + - - -
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Residues in contact with GLN 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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136B LEU* 6.0 1.0 - - - +
140B LYS* 4.2 6.1 - - - +
179B ILE* 3.3 44.1 + - + +
180B CYS* 3.9 9.0 - - - +
182B SER* 5.6 5.1 + - - -
252B GLN* 2.8 50.0 + - + +
255B ASP* 1.3 75.3 - - + +
257B TYR* 1.3 89.3 + - + +
258B CYS* 3.7 4.7 + - - -
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Residues in contact with TYR 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 ASN* 3.4 3.3 - - - +
180B CYS* 3.4 42.0 - - + -
181B ASN* 5.4 0.4 - - - -
182B SER 4.6 10.6 + - - -
239B TYR* 3.5 49.2 + + + +
240B LEU* 4.6 0.9 - - + -
252B GLN* 4.3 7.5 + - - -
253B LEU* 3.1 31.6 + - + +
256B GLN* 1.3 116.1 + - + +
258B CYS* 1.3 72.8 + - - +
259B PHE* 3.3 14.9 + - + -
437B SFG 2.7 31.0 + - - +
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Residues in contact with CYS 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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132B ASN* 3.9 25.1 - - - +
135B LYS* 3.9 47.3 + - + +
136B LEU* 4.1 19.3 - - - -
253B LEU 3.0 3.8 + - - -
254B ARG* 3.1 35.0 + - - +
255B ASP 5.2 3.1 - - - -
256B GLN 5.0 5.2 - - - -
257B TYR* 1.3 81.7 - - - +
259B PHE* 1.3 61.0 + - - +
437B SFG 4.7 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