Contacts of the helix formed by residues 248 - 260 (chain D) in PDB entry 3SZ9
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 GLU 248 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246D SER* 3.2 9.2 + - - +
247D THR* 1.3 78.9 - - - +
249D ILE* 1.3 75.1 + - - +
251D ARG* 3.2 28.8 + - - +
252D VAL* 4.0 6.9 + - + +
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Residues in contact with ILE 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D PHE* 3.4 32.5 - - + -
246D SER* 2.8 26.8 + - - +
248D GLU* 1.3 80.9 - - - +
250D GLY* 1.3 57.5 + - - +
251D ARG 2.8 11.4 + - - -
252D VAL* 3.2 24.0 + - + +
253D ILE* 3.3 17.6 + - + +
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Residues in contact with GLY 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C LEU* 3.9 7.0 - - - +
243D PHE* 3.6 20.1 - - - -
246D SER 3.3 4.9 + - - -
247D THR 3.3 11.1 + - - -
248D GLU 3.2 1.4 - - - -
249D ILE* 1.3 77.3 - - - +
251D ARG* 1.3 58.9 + - - +
253D ILE* 4.0 6.5 - - - +
254D GLN* 3.7 10.4 + - - +
267D LEU* 3.6 22.0 - - - +
269D LEU* 4.0 10.8 - - - -
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Residues in contact with ARG 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C GLY 3.4 21.2 + - - +
259C SER* 4.5 8.0 + - - +
260C SER 2.7 29.4 + - - -
262C LEU* 3.7 16.5 - - + +
247D THR* 4.1 23.3 - - - +
248D GLU* 3.2 17.9 + - - +
249D ILE 2.8 1.4 + - - -
250D GLY* 1.3 76.9 - - - +
252D VAL* 1.3 67.8 + - + +
253D ILE 3.1 1.3 - - - -
254D GLN* 3.4 1.3 + - - +
255D VAL* 3.0 31.7 + - + +
470D MET* 3.8 26.9 - - - +
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Residues in contact with VAL 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D ALA* 5.7 9.0 - - + -
233D ALA* 5.7 0.4 - - - -
248D GLU* 4.0 9.9 - - + +
249D ILE* 3.6 21.8 - - + +
251D ARG* 1.3 74.0 - - + +
253D ILE* 1.3 54.9 + - + +
255D VAL* 3.3 7.5 + - + +
256D ALA* 2.8 39.7 + - + +
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Residues in contact with ILE 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D ILE* 4.1 23.1 - - + -
229D GLY 5.2 2.9 - - - +
230D ALA* 5.9 1.1 - - - +
233D ALA* 4.0 20.5 - - + +
241D VAL* 4.0 25.6 - - + +
243D PHE* 3.9 24.9 - - + -
249D ILE* 3.3 20.0 - - + +
250D GLY* 4.0 9.4 - - - +
251D ARG 3.1 0.2 - - - -
252D VAL* 1.3 78.1 - - + +
254D GLN* 1.3 57.2 + - - +
256D ALA* 3.4 6.7 + - - +
257D ALA* 3.1 26.2 + - - +
265D VAL* 4.5 6.5 - - + -
267D LEU* 4.0 17.9 - - + -
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Residues in contact with GLN 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C GLN* 3.9 24.6 + - + +
257C ALA* 3.6 9.7 - - - +
258C GLY* 3.5 30.9 - - - +
262C LEU* 3.6 25.5 - - - +
263C LYS 3.5 21.3 + - - +
265C VAL* 3.8 9.1 - - - +
250D GLY 3.7 12.5 + - - +
251D ARG 3.4 2.4 + - - +
253D ILE* 1.3 78.5 - - - +
255D VAL* 1.3 63.6 + - - +
257D ALA* 3.8 5.4 + - - +
258D GLY* 3.2 16.1 + - - -
265D VAL* 4.8 12.3 - - + -
267D LEU* 4.1 13.0 - - + +
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Residues in contact with VAL 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C VAL* 4.4 17.9 - - + +
258C GLY* 4.1 11.9 - - - +
259C SER* 3.8 22.4 - - - +
251D ARG* 3.0 29.5 + - + +
252D VAL* 3.5 8.1 - - + +
254D GLN* 1.3 75.5 - - - +
256D ALA* 1.3 54.1 + - - +
258D GLY* 3.2 1.6 + - - -
259D SER* 2.7 46.0 + - - +
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Residues in contact with ALA 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D ALA* 3.7 29.3 - - + +
234D SER* 3.8 15.0 - - - +
252D VAL* 2.8 23.6 + - + +
253D ILE 3.4 5.1 + - - +
255D VAL* 1.3 74.5 - - - +
257D ALA* 1.3 51.6 + - - +
259D SER* 3.9 5.4 - - - -
260D SER* 2.7 39.5 + - - -
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Residues in contact with ALA 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C GLN* 4.1 3.8 - - - +
233D ALA 3.9 1.2 + - - -
253D ILE 3.1 11.1 + - - +
254D GLN 4.0 4.5 - - - +
255D VAL 3.4 0.2 - - - -
256D ALA* 1.3 75.0 - - - +
258D GLY* 1.3 60.4 + - - +
260D SER* 3.3 11.3 + - - -
261D ASN 3.5 0.3 + - - -
262D LEU* 3.0 28.8 + - - -
263D LYS* 3.3 35.2 - - + +
265D VAL* 3.7 25.8 - - + -
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Residues in contact with GLY 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C ARG* 3.8 25.6 - - - +
254C GLN* 3.8 30.6 - - - +
255C VAL* 3.9 12.3 - - - +
254D GLN 3.2 10.8 + - - -
255D VAL 3.2 3.1 + - - -
257D ALA* 1.3 80.2 - - - +
259D SER* 1.3 60.2 - - - +
260D SER 4.0 1.2 - - - +
262D LEU* 3.8 4.4 - - - +
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Residues in contact with SER 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C ARG* 4.1 8.1 + - - +
255C VAL* 3.9 9.5 - - - +
236D GLU* 4.7 1.4 - - - +
255D VAL* 2.7 36.3 + - - +
256D ALA* 3.9 5.7 - - - -
258D GLY* 1.3 72.3 - - - +
260D SER* 1.3 64.0 + - - +
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Residues in contact with SER 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C ARG* 3.2 23.4 + - - -
233D ALA 4.0 0.3 + - - -
234D SER* 3.5 24.9 - - - -
236D GLU* 3.6 21.7 - - - +
256D ALA 2.7 24.7 + - - -
257D ALA* 3.3 4.4 + - - -
258D GLY 3.4 0.9 - - - +
259D SER* 1.3 82.2 - - - +
261D ASN* 1.3 67.8 + - - -
262D LEU 3.6 3.3 + - - -
263D LYS* 3.0 21.0 + - - -
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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