Contacts of the strand formed by residues 214 - 221 (chain D) in PDB entry 3U1K
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 LEU 214 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193D ILE* 3.8 8.1 - - + +
194D GLY* 3.4 9.7 - - - -
195D ILE* 3.9 27.1 - - + +
204D PRO* 5.9 0.3 - - - +
212D SER* 2.6 25.2 + - - -
213D THR* 1.3 84.5 - - + +
215D ASN* 1.3 61.6 + - - +
216D LEU* 3.7 23.6 - - + -
231D ALA* 4.7 0.4 - - + -
232D SER 3.5 16.8 - - - +
233D ALA* 3.5 17.9 - - + -
236D ILE* 4.1 4.3 - - + -
241D PHE* 3.7 23.3 - - + -
244D ALA* 3.4 32.8 - - + -
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Residues in contact with ASN 215 (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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192D ARG* 2.9 33.5 + - - +
193D ILE 4.1 1.3 - - - -
209D MET* 3.4 24.9 - - + +
214D LEU* 1.3 72.8 - - - +
216D LEU* 1.3 59.4 + - - +
217D VAL* 4.3 4.7 - - - +
230D GLU 3.7 1.6 - - - +
231D ALA* 3.2 3.1 - - - -
232D SER* 2.7 48.6 + - - +
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Residues in contact with LEU 216 (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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191D VAL 3.8 0.3 - - - +
192D ARG* 3.2 3.7 - - - +
193D ILE* 2.8 40.6 + - + +
214D LEU* 3.7 22.0 - - + -
215D ASN* 1.3 75.2 + - - +
217D VAL* 1.3 74.4 + - - +
218D VAL* 3.8 15.7 - - + -
229D LEU* 4.4 11.9 - - + -
230D GLU 3.4 12.3 - - - +
231D ALA* 3.8 11.9 - - + -
241D PHE* 4.7 7.0 - - + +
244D ALA* 3.8 19.5 - - + +
245D ILE* 3.7 38.1 - - + +
557D LEU* 5.2 0.2 - - + -
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Residues in contact with VAL 217 (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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133D ILE* 4.5 9.6 - - + -
167D VAL* 4.6 4.9 - - + -
170D ILE* 3.8 22.0 - - + -
190D ALA* 5.0 0.4 - - + -
191D VAL 3.4 10.3 - - - +
192D ARG* 3.8 35.4 - - + +
215D ASN* 4.3 4.0 - - - +
216D LEU* 1.3 80.6 - - - +
218D VAL* 1.3 65.9 + - - +
228D MET* 3.5 24.9 - - + +
229D LEU* 3.6 6.1 - - - -
230D GLU* 2.8 40.7 + - + +
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Residues in contact with VAL 218 (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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190D ALA* 3.1 24.1 - - - +
191D VAL* 2.9 16.0 + - + +
193D ILE* 5.1 1.3 - - + -
216D LEU* 3.8 27.1 - - + +
217D VAL* 1.3 80.5 - - - +
219D ALA* 1.3 71.9 + - - +
220D GLY 4.6 0.2 - - - +
226D ILE* 4.9 2.0 - - + -
228D MET 3.7 2.0 - - - -
229D LEU* 3.8 20.9 - - + -
245D ILE* 4.5 4.7 - - - +
248D GLY* 4.1 22.4 - - - -
249D VAL* 4.0 30.1 - - + +
252D THR* 3.7 5.0 - - + +
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Residues in contact with ALA 219 (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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137D SER* 3.5 32.3 - - - +
188D VAL* 4.0 11.9 - - + -
189D GLY 3.3 4.3 - - - +
190D ALA* 4.2 5.2 - - + -
218D VAL* 1.3 77.5 - - - +
220D GLY* 1.3 59.3 + - - +
226D ILE* 3.8 2.9 - - - -
227D VAL* 2.9 27.2 + - + -
228D MET* 3.0 28.5 + - + +
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Residues in contact with GLY 220 (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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188D VAL* 3.1 6.9 - - - +
189D GLY 2.7 35.9 + - - -
218D VAL* 5.2 2.0 - - - -
219D ALA* 1.3 74.8 - - - +
221D ALA* 1.3 61.4 - - - -
225D GLN 3.2 9.6 - - - -
226D ILE* 4.6 0.9 - - - -
227D VAL* 4.1 4.3 - - - -
249D VAL* 5.7 2.5 - - - -
252D THR* 3.6 19.1 - - - +
253D GLN* 4.5 0.4 - - - -
256D ILE* 3.5 4.0 - - - +
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Residues in contact with ALA 221 (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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141D LEU* 4.7 11.9 - - + -
185D ASN 5.5 0.2 - - - +
187D PRO 3.9 3.6 - - - +
188D VAL* 4.7 0.4 - - - +
220D GLY* 1.3 72.1 - - - -
222D PRO* 1.3 80.4 - - + +
225D GLN* 2.8 27.2 + - + +
227D VAL* 3.6 20.1 - - + +
253D GLN* 3.0 17.5 + - - -
256D ILE* 3.3 6.3 - - - -
564D PRO 4.7 7.6 - - - +
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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