Contacts of the strand formed by residues 185 - 197 (chain D) in PDB entry 2ZSU
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 185 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155D PHE 3.3 12.3 - - - +
156D ASP 4.2 0.7 - - - +
158D ILE* 3.7 20.2 - - + -
181D ALA 3.2 13.0 + - - +
182D TYR 3.0 10.5 + - - +
184D ALA* 1.3 79.2 - - - +
186D ASN* 1.3 67.9 + - - +
189D GLY* 3.9 10.1 - - - +
190D ILE 3.6 32.5 - - - +
191D TYR* 4.1 2.5 - - + +
216D PHE* 3.9 28.3 - - + -
238D GLY 4.2 4.3 - - - +
240D LYS* 2.8 49.8 + - + +
183E ARG* 3.6 6.7 + - - -
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Residues in contact with ASN 186 (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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78D ARG* 6.1 1.0 - - - +
79D ARG* 5.2 2.0 - - - +
154D GLY* 3.0 40.1 + - - -
155D PHE 2.9 10.5 + - - +
156D ASP* 3.0 33.4 + - - +
184D ALA 3.8 0.2 + - - -
185D LEU* 1.3 77.9 - - - +
187D ASP* 1.3 63.4 + - - +
188D PRO 3.6 5.4 - - - +
189D GLY* 3.0 18.6 + - - -
240D LYS* 3.2 7.7 - - - +
183E ARG* 4.8 5.8 + - - +
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Residues in contact with ASP 187 (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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186D ASN* 1.3 78.5 - - - +
188D PRO* 1.3 65.3 - - - +
240D LYS* 4.1 13.7 - - + +
241D GLY* 3.4 23.2 - - - -
242D SER 4.6 0.7 + - - -
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Residues in contact with PRO 188 (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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74D HIS* 2.9 21.0 + - + +
75D PRO* 3.8 31.0 - - + -
156D ASP* 4.1 1.2 - - - +
186D ASN* 3.0 17.8 - - - +
187D ASP* 1.3 85.2 - - - +
189D GLY* 1.3 57.2 + - - +
240D LYS 3.2 10.8 - - - +
241D GLY* 4.3 5.2 - - - -
242D SER* 4.4 8.3 - - - +
243D ILE* 3.8 17.9 - - + +
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Residues in contact with GLY 189 (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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74D HIS* 3.8 2.0 - - - -
156D ASP 3.1 13.7 - - - -
185D LEU* 3.9 11.6 - - - +
186D ASN 3.0 11.8 + - - -
188D PRO* 1.3 75.5 - - - +
190D ILE* 1.3 62.4 + - - +
239D VAL* 3.6 2.8 - - - -
240D LYS 2.8 30.9 + - - +
243D ILE* 3.7 7.8 - - - +
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Residues in contact with ILE 190 (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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70D ALA* 3.6 43.1 - - + +
73D ALA* 4.7 4.0 - - + -
74D HIS* 4.0 8.7 - - + -
156D ASP 2.7 11.6 + - - +
157D VAL* 3.1 34.5 - - + +
158D ILE 2.8 25.5 + - - +
185D LEU* 3.6 5.0 - - - +
189D GLY* 1.3 75.3 - - - +
191D TYR* 1.3 64.3 + - - +
237D VAL* 3.5 30.7 - - + -
238D GLY 3.5 4.5 - - - +
239D VAL* 4.3 7.0 - - + -
243D ILE* 4.3 9.2 - - + -
245D PHE* 3.8 13.5 - - + -
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Residues in contact with TYR 191 (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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158D ILE* 3.3 24.9 - - + +
160D VAL* 3.4 28.5 - - + +
172D LEU 3.7 3.5 + - - -
177D PHE* 3.3 22.0 - + - -
178D TYR* 3.6 23.7 - + - -
181D ALA* 3.9 26.2 - - + -
185D LEU* 4.1 8.2 - - + +
190D ILE* 1.3 75.1 - - - +
192D VAL* 1.3 64.5 + - - +
193D THR* 3.7 30.9 + - + +
212D MET* 4.0 17.3 - - + -
216D PHE* 3.8 18.2 - + + -
237D VAL* 3.2 5.9 - - - +
238D GLY 2.6 42.5 + - - +
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Residues in contact with VAL 192 (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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66D LEU* 3.7 19.9 - - + +
70D ALA* 3.9 21.5 - - + -
157D VAL* 5.0 0.7 - - + -
158D ILE 2.9 12.7 + - - +
159D ILE* 3.5 23.3 - - + +
160D VAL* 2.9 25.8 + - - +
191D TYR* 1.3 78.9 - - - +
193D THR* 1.3 70.7 + - - +
222D TYR* 3.6 25.4 - - + +
235D PHE* 4.8 0.9 - - + -
236D LEU 3.3 12.1 - - - +
237D VAL* 4.2 9.2 - - + -
245D PHE* 6.2 0.2 - - + -
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Residues in contact with THR 193 (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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66D LEU* 4.6 1.3 - - - -
160D VAL* 3.7 20.6 + - - +
172D LEU 5.4 0.3 + - - -
173D PHE* 3.7 20.6 - - + -
178D TYR* 4.6 6.3 - - - +
191D TYR* 3.7 31.2 + - + +
192D VAL* 1.3 77.6 - - - +
194D GLN* 1.3 77.2 + - - +
212D MET* 4.8 0.4 - - - -
235D PHE* 3.4 7.8 - - - +
236D LEU* 2.9 52.2 + - + +
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Residues in contact with GLN 194 (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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62D TYR* 3.4 33.9 - - + +
66D LEU* 4.2 2.7 - - + +
160D VAL 3.6 12.2 + - - +
162D SER* 4.0 16.8 + - - +
163D THR 3.4 26.4 + - - -
164D ASP* 4.6 4.3 + - - +
173D PHE* 3.3 18.6 - - - -
193D THR* 1.3 87.4 + - - +
195D ALA* 1.3 58.1 + - - +
196D GLY* 3.1 12.4 + - - +
204D GLU* 5.5 0.8 + - - -
233D TRP* 2.8 41.5 + - + +
234D ALA 3.7 5.4 - - - -
235D PHE* 3.9 8.7 - - + -
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Residues in contact with ALA 195 (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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173D PHE* 4.2 9.6 - - + -
193D THR 4.5 0.2 - - - +
194D GLN* 1.3 75.0 - - - +
196D GLY* 1.3 63.2 + - - +
201D PHE 4.7 0.2 - - - +
204D GLU* 3.2 24.0 - - - +
205D PHE* 3.8 35.2 - - + +
208D ALA* 5.7 0.2 - - + -
234D ALA 2.7 17.6 + - - +
235D PHE* 4.3 0.9 - - - +
236D LEU* 3.9 22.9 - - + -
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Residues in contact with GLY 196 (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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164D ASP* 4.7 2.5 - - - -
194D GLN* 3.1 11.0 + - - -
195D ALA* 1.3 80.1 - - - +
197D SER* 1.3 62.9 + - - -
198D VAL 3.3 0.2 + - - -
201D PHE* 3.9 11.0 - - - -
204D GLU* 3.9 4.4 + - - -
233D TRP* 3.4 26.0 - - - +
234D ALA* 2.7 31.0 + - - +
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Residues in contact with SER 197 (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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195D ALA 5.1 0.6 - - - +
196D GLY* 1.3 69.1 - - - -
198D VAL* 1.3 59.9 + - - +
199D TYR* 3.4 4.3 + - - +
200D LEU* 3.0 32.5 + - - +
201D PHE* 2.8 54.1 + - - +
205D PHE* 5.6 0.3 - - - +
230D ALA* 3.5 23.9 + - - +
231D SER 5.3 0.9 - - - -
232D PRO 3.7 8.7 + - - -
233D TRP* 3.5 12.2 - - - -
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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