Contacts of the strand formed by residues 235 - 243 (chain D) in PDB entry 1ZVM
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 VAL 235 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200D ALA 3.4 28.0 - - - +
202D ASP 3.4 12.6 - - - +
204D VAL* 3.9 16.2 - - + -
230D LEU* 4.1 15.3 - - + -
231D GLN 2.7 30.6 + - - +
232D PRO* 2.8 25.7 - - - +
234D LYS* 1.3 71.2 - - - +
236D GLN* 1.3 66.0 + - - +
237D THR 3.8 17.5 - - - +
270D ASN 5.2 0.9 - - - +
271D ILE* 3.9 26.5 - - + +
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Residues in contact with GLN 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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202D ASP* 2.7 45.8 + - - +
203D VAL* 4.0 15.6 - - - +
234D LYS 4.4 2.5 - - - +
235D VAL* 1.3 74.7 - - - +
237D THR* 1.3 68.9 + - + +
270D ASN 5.2 0.2 - - - +
271D ILE* 3.3 5.9 - - - +
272D GLN* 3.1 23.0 + - - +
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Residues in contact with THR 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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202D ASP 3.1 2.6 + - - +
203D VAL* 3.3 22.6 - - + +
204D VAL 2.8 31.7 + - - +
235D VAL* 3.8 4.2 - - - +
236D GLN* 1.3 95.2 - - + +
238D LEU* 1.3 62.2 + - - +
239D GLU* 4.1 1.7 + - - +
271D ILE* 3.5 5.8 - - - -
272D GLN* 3.2 29.0 + - + -
273D PHE 5.6 0.2 - - - -
274D SER* 4.6 9.2 - - - -
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Residues in contact with LEU 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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124D LEU* 5.2 0.4 - - + -
204D VAL* 3.1 34.8 - - + +
206D VAL* 3.9 28.9 - - + -
222D PHE* 4.1 15.5 - - + -
230D LEU* 4.4 14.4 - - + -
235D VAL* 5.4 0.2 - - + -
237D THR* 1.3 74.1 - - - +
239D GLU* 1.3 59.3 + - - +
262D LEU* 4.0 16.4 - - + -
266D ILE* 3.6 38.4 - - + -
271D ILE* 3.9 3.7 - - + +
272D GLN 2.8 11.7 + - - +
273D PHE* 3.5 9.9 - - + -
274D SER 2.9 23.2 + - - +
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Residues in contact with GLU 239 (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 VAL* 4.7 8.5 - - + -
204D VAL 2.8 9.5 + - - +
205D HIS* 3.1 29.1 + - + +
206D VAL* 3.0 24.0 + - - +
237D THR* 4.0 2.5 + - - +
238D LEU* 1.3 72.6 - - - +
240D ALA* 1.3 66.8 + - - +
241D TRP* 3.0 26.9 + - - +
274D SER* 2.9 32.8 + - - +
276D LYS* 3.5 23.4 - - + +
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Residues in contact with ALA 240 (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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206D VAL* 3.3 21.8 - - + +
208D LEU* 4.3 16.2 - - + -
238D LEU 4.0 0.6 + - - -
239D GLU* 1.3 74.4 - - - +
241D TRP* 1.3 66.5 + - - +
242D VAL* 3.9 1.6 - - + -
259D ILE* 5.2 1.1 - - + -
262D LEU* 4.6 0.7 - - + -
273D PHE* 4.0 19.3 - - + -
274D SER 2.7 16.2 + - - +
275D CYS* 4.4 7.0 - - - -
276D LYS* 2.9 26.2 + - - +
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Residues in contact with TRP 241 (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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123D LEU* 4.5 9.9 - - + -
135D PHE* 3.6 45.8 - + - -
142D MET* 4.7 4.9 - - + -
205D HIS* 3.5 34.1 - + + -
206D VAL 2.8 12.8 + - - +
207D MET* 3.5 26.2 - - + -
208D LEU* 2.9 25.8 + - - -
239D GLU* 3.0 25.1 + - + -
240D ALA* 1.3 81.7 - - - +
242D VAL* 1.3 63.4 + - - +
243D ILE* 3.4 6.3 + - + +
276D LYS* 3.5 17.8 - - + +
278D ILE* 3.4 20.4 - - + -
284D PHE* 3.9 15.9 - + - -
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Residues in contact with VAL 242 (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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208D LEU* 3.7 7.2 - - + -
210D GLY* 3.5 28.5 - - - +
215D ILE* 3.8 14.4 - - + -
240D ALA* 5.0 0.9 - - + -
241D TRP* 1.3 73.0 - - - +
243D ILE* 1.3 61.2 + - - +
244D HIS* 3.5 4.0 + - - -
253D LEU* 3.8 26.5 - - + +
254D CYS* 4.4 1.3 - - - -
259D ILE* 4.0 21.1 - - + -
275D CYS* 3.7 28.5 - - - -
276D LYS 3.0 9.2 + - - +
277D ASN* 4.8 3.6 - - - +
278D ILE 3.0 24.1 + - - -
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Residues in contact with ILE 243 (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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128D ILE* 3.4 27.6 - - + -
131D LEU* 3.4 27.1 - - + -
207D MET* 3.5 25.8 - - + -
208D LEU 2.8 14.7 + - - +
209D ASP* 4.2 2.6 - - - +
210D GLY* 2.7 27.8 + - - -
211D SER 4.2 0.3 + - - -
241D TRP 3.8 2.0 - - - +
242D VAL* 1.3 71.1 - - - +
244D HIS* 1.3 68.0 + - - +
245D GLY 3.9 0.2 + - - -
278D ILE* 3.4 35.0 - - + +
281D PRO* 3.5 20.2 - - + -
284D PHE* 5.5 1.3 - - + -
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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