Contacts of the strand formed by residues 196 - 204 (chain D) in PDB entry 5U7Z
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 LYS 196 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192D GLN* 3.1 4.3 - - - +
193D ARG 2.9 32.1 + - - +
194D ASN* 3.1 12.0 - - + +
195D ASN* 1.3 83.5 - - + +
197D THR* 1.3 67.6 - - - +
198D VAL* 4.0 1.6 - - - +
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Residues in contact with THR 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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190D ASP* 2.5 32.0 + - - +
191D PHE 3.5 5.2 - - - -
192D GLN* 3.6 8.8 + - - +
195D ASN 4.4 0.2 + - - -
196D LYS* 1.3 72.2 - - - +
198D VAL* 1.3 64.0 + - - +
199D PHE 3.9 11.7 - - - +
200D LYS* 4.1 17.8 - - + -
216D PRO* 4.1 23.6 - - + +
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Residues in contact with VAL 198 (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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54C LEU* 4.4 4.3 - - + -
191D PHE 2.6 13.7 + - - +
192D GLN 4.3 0.7 - - - -
193D ARG* 3.7 55.2 - - + +
196D LYS 4.0 0.9 - - - +
197D THR* 1.3 77.1 - - - +
199D PHE* 1.3 69.0 + - + +
215D LYS* 3.1 50.8 - - - +
216D PRO* 3.7 6.8 - - - +
258D GLU* 3.5 12.1 - - - +
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Residues in contact with PHE 199 (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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54C LEU* 4.8 0.4 - - + -
191D PHE* 2.9 83.6 + + + +
197D THR* 3.8 1.0 - - - +
198D VAL* 1.3 86.1 - - + +
200D LYS* 1.3 74.7 + - - +
201D ALA* 4.0 5.2 - - + -
210D MET* 3.9 17.9 - - + -
214D PHE 3.4 15.0 - - - +
215D LYS* 4.1 2.9 - - + -
216D PRO* 4.2 4.0 - - - -
254D ARG* 4.1 14.6 - - - -
257D LEU* 3.5 39.5 - - + +
258D GLU* 3.9 26.2 - - + -
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Residues in contact with LYS 200 (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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49C TRP* 3.5 37.4 - - + -
189D LEU 3.2 9.0 - - - +
190D ASP* 3.9 22.0 + - - +
197D THR* 4.1 18.6 - - + -
199D PHE* 1.3 81.6 - - - +
201D ALA* 1.3 61.8 + - - +
213D GLY* 3.1 2.4 - - - -
214D PHE* 3.0 61.0 + - + +
216D PRO* 4.8 3.1 - - + -
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Residues in contact with ALA 201 (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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49C TRP* 5.1 1.4 - - - -
187D VAL 4.0 0.2 - - - +
188D ASN* 3.5 7.5 - - - +
189D LEU* 3.0 34.3 + - + +
191D PHE* 4.7 2.9 - - + -
199D PHE* 4.0 10.8 - - + -
200D LYS* 1.3 76.8 - - - +
202D SER* 1.3 60.5 + - - +
203D SER 4.1 0.4 - - - -
210D MET* 3.2 36.6 - - + -
212D THR 3.1 12.3 - - - +
213D GLY* 3.9 2.7 - - - -
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Residues in contact with SER 202 (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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47C VAL* 6.1 0.7 - - - +
186D THR* 5.3 9.6 - - - +
187D VAL 3.7 5.4 - - - -
188D ASN* 3.2 17.9 + - - -
201D ALA* 1.3 70.6 - - - +
203D SER* 1.3 62.9 + - - +
210D MET* 5.0 0.2 - - - +
211D LEU* 4.4 6.9 + - - +
212D THR* 2.8 47.5 + - - +
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Residues in contact with SER 203 (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 THR* 3.7 5.8 - - - +
187D VAL* 3.1 35.0 + - - +
189D LEU* 3.9 25.1 - - - +
201D ALA 4.1 0.6 - - - -
202D SER* 1.3 76.1 - - - +
204D PHE* 1.3 74.2 + - - +
207D TYR* 3.1 25.7 + - - -
209D GLY 3.2 14.4 + - - -
210D MET* 4.1 10.3 - - - -
211D LEU* 5.3 2.5 + - - +
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Residues in contact with PHE 204 (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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133C PHE* 4.2 19.3 - + + -
161D MET* 3.9 28.3 - - + -
163D PHE* 5.5 4.9 - + + -
182D LEU* 3.8 46.7 - - + -
185D LEU* 3.8 6.3 - - + +
186D THR* 3.6 30.1 - - + -
187D VAL* 4.9 0.4 - - - -
203D SER* 1.3 81.1 + - - +
205D ALA* 1.3 55.3 + - - +
206D GLY 3.1 0.2 + - - -
207D TYR* 2.7 48.5 + + + +
211D LEU* 4.2 24.9 - - + -
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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