Contacts of the helix formed by residues 231 - 238 (chain D) in PDB entry 1USK
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 ALA 231 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D GLN* 4.4 17.3 - - - +
21D MET* 5.8 1.2 - - - +
230D ASN* 1.3 78.0 + - - +
232D SER* 1.3 61.8 + - - +
233D LEU 3.2 0.9 + - - -
234D SER* 3.7 14.9 + - - -
235D ASN* 3.4 15.0 - - - +
271D ASP* 4.9 11.4 - - - +
336D TRP* 5.3 2.0 - - - -
340D GLY* 5.6 5.5 - - - -
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Residues in contact with SER 232 (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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17D GLN* 3.1 20.9 + - - +
203D TYR* 3.4 35.4 + - - -
230D ASN* 3.1 6.5 + - - -
231D ALA* 1.3 76.8 - - - +
233D LEU* 1.3 56.3 + - - +
234D SER 3.5 0.2 - - - -
235D ASN* 3.2 12.2 + - - +
236D ILE* 3.0 38.5 + - - +
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Residues in contact with LEU 233 (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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203D TYR* 3.9 13.3 - - + +
206D MET* 3.8 16.2 - - + -
207D GLY* 3.7 27.8 - - - +
210D LEU* 4.3 6.1 - - + -
228D VAL 3.4 20.6 - - - +
230D ASN 3.2 14.9 + - - +
232D SER* 1.3 79.7 - - - +
234D SER* 1.3 58.5 + - - +
236D ILE* 3.4 5.1 + - - +
237D ALA* 2.9 32.9 + - - +
241D ALA* 4.8 4.5 - - + -
244D MET* 3.2 38.4 - - + -
336D TRP* 3.9 19.1 - - + +
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Residues in contact with SER 234 (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 ASN 4.4 1.0 + - - -
231D ALA 3.7 8.7 + - - -
233D LEU* 1.3 76.6 - - - +
235D ASN* 1.3 68.1 + - - +
238D GLY* 2.9 27.7 + - - +
241D ALA* 4.0 14.8 - - - -
336D TRP* 4.3 3.3 + - - +
337D HIS 3.8 9.4 - - - -
338D ALA 3.4 22.7 + - - +
339D ASP 4.1 1.2 - - - -
340D GLY* 3.3 29.8 + - - -
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Residues in contact with ASN 235 (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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211D ARG* 3.6 12.6 + - - -
231D ALA* 3.4 16.0 + - - +
232D SER* 3.2 12.9 + - - +
233D LEU 3.2 0.2 - - - -
234D SER* 1.3 85.7 + - - +
236D ILE* 1.3 62.7 + - + +
238D GLY* 4.7 0.7 - - - -
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Residues in contact with ILE 236 (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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203D TYR* 4.2 17.5 - - + +
204D PRO* 4.1 24.2 - - + +
207D GLY* 3.5 26.9 - - - +
208D GLN* 3.7 27.9 - - + +
211D ARG* 2.9 25.5 + - - +
232D SER* 3.0 22.4 + - - +
233D LEU 3.9 3.4 - - - +
235D ASN* 1.3 79.3 - - + +
237D ALA* 1.3 58.8 + - - +
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Residues in contact with ALA 237 (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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207D GLY* 3.4 22.4 - - - +
210D LEU* 4.0 15.7 - - + -
211D ARG* 3.8 17.8 + - - +
233D LEU 2.9 18.5 + - - +
236D ILE* 1.3 77.4 - - - +
238D GLY* 1.3 62.9 + - - +
239D ASP 3.6 0.2 + - - -
240D ALA* 3.4 15.9 + - - +
241D ALA* 4.0 23.3 - - + +
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Residues in contact with GLY 238 (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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211D ARG* 3.8 14.0 - - - +
234D SER 2.9 20.4 + - - +
235D ASN 4.1 1.1 + - - -
236D ILE 3.5 1.6 - - - -
237D ALA* 1.3 73.1 - - - +
239D ASP* 1.3 64.4 + - - -
240D ALA 3.1 5.5 + - - -
241D ALA* 3.3 16.8 + - - +
338D ALA* 3.9 11.5 - - - +
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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