Contacts of the strand formed by residues 213 - 218 (chain D) in PDB entry 3RZL
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 213 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D VAL* 3.7 17.5 - - + -
197D PHE 3.3 13.0 - - - +
198D ARG* 3.7 23.6 - - + +
211D VAL 3.3 12.0 + - - +
212D ALA* 1.3 81.1 - - - +
214D VAL* 1.3 77.0 + - - +
215D ARG* 4.1 27.1 + - + +
234D TRP* 4.4 3.7 - - - -
275F C 5.9 2.9 - - - +
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Residues in contact with VAL 214 (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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58D ARG* 5.7 4.3 - - - +
60D ILE* 4.1 27.1 - - + -
65D LEU* 4.3 12.6 - - + -
195D PHE 3.7 1.2 - - - +
196D VAL* 3.6 4.2 - - - -
197D PHE* 2.9 56.4 + - + -
213D VAL* 1.3 79.5 - - - +
215D ARG* 1.3 62.9 + - - +
216D LEU* 4.1 16.6 - - + -
234D TRP* 4.4 6.3 - - + -
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Residues in contact with ARG 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D ARG* 4.8 5.9 + - - -
194D ASP* 6.2 4.7 - - + -
195D PHE 3.8 4.7 - - - +
196D VAL* 3.8 28.9 - - + +
213D VAL* 4.1 18.1 + - + +
214D VAL* 1.3 76.2 - - - +
216D LEU* 1.3 62.4 + - - +
217D PRO* 4.6 1.9 - - - +
239D PRO* 5.4 0.8 - - - +
241D ARG* 4.3 8.2 - - - +
274F G 2.9 39.9 + - - -
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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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58D ARG* 4.5 19.7 - - - +
60D ILE* 4.4 13.0 - - + -
69D TYR* 3.5 44.4 - - + -
194D ASP* 4.8 2.9 - - - +
195D PHE* 3.0 50.3 + - + +
197D PHE* 3.9 27.4 - - + -
214D VAL* 4.0 13.2 + - + -
215D ARG* 1.3 76.0 - - - +
217D PRO* 1.3 69.2 - - + +
218D LEU* 3.7 14.4 - - + -
224D LEU* 4.8 5.2 - - + -
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Residues in contact with PRO 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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58D ARG* 4.8 9.9 - - - +
69D TYR* 3.4 21.1 + - - -
192D SER* 4.0 14.6 - - - +
193D ARG 3.7 7.2 - - - +
194D ASP* 4.2 15.7 - - - +
215D ARG 4.6 2.0 - - - +
216D LEU* 1.3 88.5 - - + +
218D LEU* 1.3 61.0 + - - +
219D ALA 3.8 0.8 + - - -
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Residues in contact with LEU 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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69D TYR* 3.6 24.0 - - + -
186D SER* 5.0 6.3 - - - +
188D SER* 3.8 18.7 - - - +
191D ALA 4.3 1.7 - - - +
192D SER* 3.2 22.3 + - - -
193D ARG 3.2 13.3 + - - +
195D PHE* 3.6 39.0 - - + -
216D LEU* 3.7 21.8 - - + -
217D PRO* 1.3 72.2 - - - +
219D ALA* 1.3 62.5 + - - +
222D SER* 4.0 3.6 - - - +
224D LEU* 4.1 22.0 - - + +
238D LEU* 4.7 1.3 - - + -
248D ARG* 3.4 25.9 + - - +
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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