Contacts of the strand formed by residues 234 - 238 (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 TRP 234 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ALA* 3.9 19.3 - - + -
63D GLU 3.2 18.0 + - - -
64D GLY 3.2 23.6 - - - -
65D LEU* 3.7 26.0 - - + +
172D ARG* 4.1 12.7 - - - +
197D PHE* 3.6 35.3 - - + -
198D ARG* 3.2 27.6 - - - -
199D HIS* 3.5 37.1 - + + -
212D ALA* 4.1 14.8 - - + -
213D VAL* 4.4 8.7 - - - -
214D VAL* 4.4 7.0 - - + -
230D THR* 3.7 17.2 + - + +
231D ASN* 4.6 4.0 + - - -
233D HIS* 1.3 86.2 - - + +
235D TYR* 1.3 63.9 + - - +
236D HIS* 4.2 6.6 + - - -
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Residues in contact with TYR 235 (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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170D GLU* 3.7 28.9 - - - +
171D HIS* 3.7 22.2 - - - +
172D ARG* 3.3 42.2 + - + -
197D PHE* 3.4 4.7 - - - -
198D ARG* 2.6 37.6 + - + +
199D HIS 4.9 0.2 - - - -
200D LYS* 3.4 34.5 - - + +
203D ARG* 3.3 40.3 + - - -
233D HIS 3.9 3.6 - - - -
234D TRP* 1.3 77.1 - - - +
236D HIS* 1.3 61.2 + - - +
263E A 4.9 0.9 - - - -
264E T 2.8 24.1 + - - -
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Residues in contact with HIS 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D ILE* 6.2 0.9 - - + -
170D GLU* 3.4 4.7 - - - -
171D HIS* 3.0 53.8 + + - +
173D ASP* 2.5 32.7 + - - -
195D PHE* 3.8 31.6 - + + -
196D VAL 3.0 12.3 - - - +
197D PHE* 3.9 11.1 - - + -
226D MET* 4.2 17.5 - - + +
230D THR* 6.0 0.2 - - - +
231D ASN* 3.5 26.6 + - - -
234D TRP 4.6 2.6 + - - -
235D TYR* 1.3 75.1 - - - +
237D SER* 1.3 63.1 + - - +
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Residues in contact with SER 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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168D ILE* 3.5 20.6 - - - -
169D CYS* 4.7 0.4 - - - -
170D GLU* 3.7 23.8 + - - +
195D PHE* 3.6 13.4 - - - -
196D VAL* 3.0 42.9 + - - +
198D ARG* 5.5 1.4 - - - +
236D HIS* 1.3 77.8 - - - +
238D LEU* 1.3 64.8 + - - +
239D PRO* 3.7 7.4 - - - +
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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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161D TYR* 3.6 26.2 - - + +
167D HIS* 3.0 21.7 - - - +
168D ILE* 3.2 25.0 + - + +
193D ARG* 3.8 39.3 - - + +
194D ASP 3.3 22.7 - - - +
195D PHE* 4.2 17.3 - - + -
237D SER* 1.3 75.5 - - - +
239D PRO* 1.3 69.0 - - - +
248D ARG* 3.4 39.7 - - - +
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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