Contacts of the helix formed by residues 258 - 270 (chain B) in PDB entry 1QS0
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 ASP 258 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212B ASP 3.2 22.3 + - - +
213B LYS* 3.4 8.8 - - - +
214B ALA* 3.0 37.6 + - + +
251B LEU* 5.6 1.4 + - - +
253B SER* 4.6 1.8 + - - -
257B LEU* 1.3 73.2 - - - +
259B LEU* 1.3 60.5 + - - +
260B ASP* 3.1 9.5 + - - +
261B THR* 2.8 34.5 + - - -
262B ILE* 3.2 23.4 + - - +
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Residues in contact with LEU 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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399A ASP* 5.1 6.3 - - + +
403A ARG* 3.5 25.8 - - - +
257B LEU* 3.0 23.3 + - + +
258B ASP* 1.3 70.7 + - - +
260B ASP* 1.3 62.4 + - - +
262B ILE* 3.9 6.4 - - + +
263B VAL* 2.9 52.1 + - + +
291B LEU* 4.3 31.4 - - + -
295B HIS* 3.3 31.6 - - + +
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Residues in contact with ASP 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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399A ASP* 5.3 4.3 - - - +
403A ARG* 5.3 5.4 + - - -
258B ASP* 3.1 8.1 + - - +
259B LEU* 1.3 78.8 - - - +
261B THR* 1.3 57.5 + - - +
262B ILE 2.7 15.3 + - - -
263B VAL* 3.0 4.0 + - - +
264B GLU* 2.8 34.9 + - + +
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Residues in contact with THR 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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214B ALA* 4.2 18.5 - - + -
215B ALA* 4.9 2.9 - - - +
216B ILE* 4.2 25.1 - - + -
249B ILE* 4.2 3.9 - - + +
258B ASP* 2.8 31.9 + - - -
260B ASP* 1.3 77.2 - - - +
262B ILE* 1.3 56.7 + - - +
264B GLU* 4.1 9.7 - - - +
265B SER* 3.0 23.6 + - - +
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Residues in contact with ILE 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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214B ALA* 5.0 1.3 - - + -
226B LEU* 3.6 33.7 - - + -
249B ILE* 4.5 9.4 - - + -
251B LEU* 3.4 33.9 - - + -
257B LEU* 4.4 21.5 - - + -
258B ASP 3.2 23.3 + - - +
259B LEU* 3.9 7.0 - - + +
260B ASP 2.7 2.2 + - - -
261B THR* 1.3 78.1 - - - +
263B VAL* 1.3 65.0 + - + +
264B GLU 3.0 5.3 + - - -
265B SER* 3.1 11.4 + - - -
266B VAL* 3.2 19.1 + - + +
288B LEU* 4.6 6.1 - - + -
292B VAL* 4.7 8.3 - - + -
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LEU* 2.9 46.1 + - + +
260B ASP* 4.0 4.5 - - - +
262B ILE* 1.3 77.7 - - + +
264B GLU* 1.3 56.3 + - - +
266B VAL* 4.8 0.4 - - - -
267B LYS* 3.0 40.1 + - - +
291B LEU 5.5 1.6 - - - +
292B VAL* 5.9 3.8 - - + -
295B HIS* 3.7 30.5 - - + +
296B CYS* 3.4 27.0 - - - -
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Residues in contact with GLU 264 (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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260B ASP* 2.8 24.8 + - + +
261B THR* 4.2 8.1 - - - +
263B VAL* 1.3 79.0 - - - +
265B SER* 1.3 63.3 + - - +
267B LYS* 3.6 17.7 - - + +
268B LYS* 3.4 21.7 + - - +
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Residues in contact with SER 265 (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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216B ILE* 3.7 8.5 - - - +
224B SER* 2.8 13.6 + - - -
247B GLU* 2.9 27.5 + - - +
249B ILE* 3.6 26.6 - - - +
261B THR* 3.0 14.4 + - - +
262B ILE 3.1 3.2 + - - -
264B GLU* 1.3 76.5 - - - +
266B VAL* 1.3 60.7 + - - +
268B LYS* 4.0 5.6 - - - +
269B THR* 3.0 25.5 + - - -
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Residues in contact with VAL 266 (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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224B SER* 3.2 24.5 - - - +
226B LEU* 5.2 0.4 - - + -
262B ILE* 3.2 26.6 + - + +
263B VAL* 5.0 0.4 - - - -
265B SER* 1.3 75.0 - - - +
267B LYS* 1.3 62.0 + - - +
268B LYS 3.3 0.2 - - - -
269B THR* 4.2 1.6 - - - -
270B GLY* 2.7 28.5 + - - -
271B ARG 4.2 14.6 - - - +
272B CYS* 3.8 16.2 - - + -
292B VAL* 4.3 11.0 - - + -
296B CYS* 4.2 26.0 - - + -
299B HIS* 4.3 3.1 - - - +
300B LEU* 4.3 14.8 - - + -
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Residues in contact with LYS 267 (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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263B VAL* 3.0 34.3 + - - +
264B GLU* 3.6 19.9 - - + +
266B VAL* 1.3 80.4 - - - +
268B LYS* 1.3 64.0 + - - +
270B GLY* 4.3 1.7 + - - -
295B HIS 5.8 0.7 - - - -
296B CYS* 4.5 3.8 - - - -
299B HIS* 3.2 48.6 + - + +
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Residues in contact with LYS 268 (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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220B GLY 3.2 23.3 + - - +
221B ASN* 3.5 27.7 + - + +
247B GLU* 3.3 21.7 + - - -
264B GLU 3.4 13.9 + - - +
265B SER* 4.0 2.9 - - - +
267B LYS* 1.3 83.8 - - - +
269B THR* 1.3 71.1 + - - +
270B GLY* 4.3 0.3 - - - -
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Residues in contact with THR 269 (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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220B GLY 4.3 4.7 + - - -
221B ASN* 3.5 29.3 + - - +
222B ASP 2.9 28.1 - - - +
223B VAL* 3.2 10.3 + - - -
224B SER* 3.5 7.6 + - - -
247B GLU* 4.8 2.3 + - - +
265B SER 3.0 18.5 + - - -
266B VAL 4.2 0.2 - - - -
268B LYS* 1.3 84.1 - - - +
270B GLY* 1.3 58.7 + - - +
271B ARG* 2.9 33.1 + - + +
301B GLU* 5.1 3.5 - - - +
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Residues in contact with GLY 270 (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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266B VAL 2.7 18.8 + - - -
267B LYS 4.7 1.3 - - - -
268B LYS 3.5 1.5 + - - -
269B THR* 1.3 73.2 - - - +
271B ARG* 1.3 65.0 + - - +
299B HIS 3.2 21.1 - - - -
300B LEU* 3.5 6.5 - - - +
301B GLU* 2.5 40.1 + - - -
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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