Contacts of the strand formed by residues 158 - 164 (chain D) in PDB entry 3ARE
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 158 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D PRO* 4.5 1.3 - - + -
150D ALA* 5.8 0.7 - - + -
153D PHE* 3.6 46.7 - - + -
156D ASP 3.8 1.9 + - - -
157D HIS* 1.3 82.1 - - - +
159D GLU* 1.3 65.7 - - - +
160D LEU 4.1 0.6 + - - -
179D PRO* 5.7 3.4 - - + -
193D LEU* 4.1 23.8 - - + +
215D VAL* 3.8 26.2 - - + -
216D GLN 3.2 4.7 - - - +
217D PHE* 3.9 14.8 - - + -
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Residues in contact with GLU 159 (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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9D ARG* 5.4 2.8 - - - +
10D ASN* 3.6 14.9 + - - +
158D VAL* 1.3 76.6 - - - +
160D LEU* 1.3 61.2 + - - +
161D SER* 5.1 0.7 + - - -
214D GLN 3.5 1.9 - - - +
215D VAL* 3.5 2.7 - - - -
216D GLN* 2.8 49.5 + - + +
218D TYR* 2.8 37.7 + - + -
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Residues in contact with LEU 160 (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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148D CYS* 4.6 4.5 - - - -
150D ALA* 5.1 2.2 - - + -
158D VAL 4.1 1.2 - - - -
159D GLU* 1.3 73.3 - - - +
161D SER* 1.3 86.3 + - - +
162D TRP* 3.9 11.2 - - + +
175D THR* 4.1 17.6 + - + +
193D LEU* 4.0 30.8 - - + +
194D SER 4.9 0.7 - - - -
195D SER* 3.6 39.5 - - - +
213D CYS* 4.0 13.2 - - - -
214D GLN 3.3 9.2 - - - +
215D VAL* 4.0 20.4 - - + +
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Residues in contact with SER 161 (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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159D GLU 5.1 1.1 + - - -
160D LEU* 1.3 82.1 - - - +
162D TRP* 1.3 62.6 + - - +
163D TRP* 2.6 28.8 + - - -
168D GLU* 3.1 28.0 - - - -
213D CYS* 3.7 2.1 - - - -
214D GLN* 2.8 50.7 + - - +
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Residues in contact with TRP 162 (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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130D VAL* 4.7 8.1 - - + -
146D LEU* 3.6 45.5 - - + -
147D VAL 4.1 1.8 - - - -
148D CYS* 3.4 34.3 - - + -
160D LEU* 3.9 8.7 - - + +
161D SER* 1.3 73.6 - - - +
163D TRP* 1.3 62.5 + - - +
164D VAL* 4.0 0.9 - - + -
168D GLU* 3.4 8.4 - - - +
169D VAL* 3.0 47.3 + - + +
173D VAL* 3.4 28.5 - - + +
195D SER* 2.8 29.3 + - - -
196D ARG 3.6 5.7 + - - -
197D LEU* 3.6 28.9 - - + -
211D PHE* 5.3 2.7 - - + -
212D ARG 3.5 20.6 - - - -
213D CYS* 4.2 11.0 - - + -
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Residues in contact with TRP 163 (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 SER* 2.6 35.6 + - - -
162D TRP* 1.3 77.5 - - - +
164D VAL* 1.3 63.3 + - - +
165D ASN 3.8 1.1 + - - -
166D GLY* 3.6 29.0 + - - +
167D LYS* 3.4 4.9 - - - +
168D GLU* 3.7 38.8 - - + -
210D HIS* 3.7 4.7 - - - +
211D PHE 3.7 0.2 - - - -
212D ARG* 2.7 67.4 + - + +
214D GLN* 3.5 31.6 + - + -
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Residues in contact with VAL 164 (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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162D TRP* 4.0 0.8 + - + -
163D TRP* 1.3 72.3 - - - +
165D ASN* 1.3 77.1 - - + +
166D GLY 3.3 1.1 - - - -
167D LYS* 2.9 22.1 + - - +
169D VAL* 3.7 28.1 - - + +
197D LEU* 3.7 30.3 - - + -
199D VAL* 5.6 2.2 - - + -
203D PHE* 3.7 35.7 - - + -
210D HIS 3.3 9.2 - - - +
211D PHE* 4.0 11.9 - - + -
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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