Contacts of the strand formed by residues 177 - 183 (chain D) in PDB entry 1R4N
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 LEU 177 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141D ILE* 3.4 14.4 - - + +
143D CYS* 3.9 26.5 - - + -
154D ILE* 4.2 18.8 - - + -
155D ASN* 4.3 15.9 - - - +
158D LEU* 3.4 28.7 - - + -
175D VAL 3.3 2.3 + - - +
176D PRO* 1.3 71.3 - - - +
178D ILE* 1.3 68.5 + - - +
179D ASP* 3.8 3.0 + - + +
192D ILE* 3.1 60.5 + - + +
194D PRO* 5.0 1.1 - - + -
200D ILE* 4.4 8.1 - - + -
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Residues in contact with ILE 178 (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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140D ILE* 3.7 22.7 - - + -
141D ILE 2.8 9.9 + - - +
142D VAL* 3.1 12.1 - - + +
143D CYS 2.7 32.6 + - - +
176D PRO 4.2 3.1 - - - -
177D LEU* 1.3 78.5 - - - +
179D ASP* 1.3 54.6 + - - +
189D ALA* 5.8 0.2 - - + -
190D ARG 3.4 11.2 - - - +
191D VAL* 4.1 19.7 - - + -
303D CYS* 3.3 42.0 - - + -
306D GLU* 4.3 8.5 - - + -
307D VAL* 4.2 10.8 - - + -
310D ILE* 3.6 26.7 - - + -
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Residues in contact with ASP 179 (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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143D CYS* 3.6 18.7 - - + +
151D ARG* 2.6 41.5 + - - +
177D LEU* 3.8 7.2 + - + +
178D ILE* 1.3 73.4 - - - +
180D GLY* 1.3 68.5 + - - +
181D GLY 4.2 0.3 + - - -
188D ASN* 4.5 4.9 + - - -
189D ALA* 3.4 4.7 - - - -
190D ARG* 3.0 63.4 + - + +
192D ILE* 5.4 0.2 - - + -
200D ILE* 4.5 11.2 - - + -
207D TYR* 4.5 0.3 + - - -
303D CYS* 3.8 7.6 - - - -
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Residues in contact with GLY 180 (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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59D LEU* 3.8 16.4 - - - +
143D CYS 3.3 17.2 + - - +
144D GLY* 4.3 1.2 - - - -
151D ARG* 2.9 19.9 + - - -
179D ASP* 1.3 84.3 - - - +
181D GLY* 1.3 58.9 + - - -
188D ASN 3.5 3.8 - - - -
299D ILE* 3.9 13.7 - - - -
303D CYS* 4.0 5.2 - - - -
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Residues in contact with GLY 181 (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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59D LEU* 4.8 0.9 - - - -
151D ARG* 3.8 5.6 - - - -
180D GLY* 1.3 75.8 - - - -
182D THR* 1.3 64.6 + - - -
187D GLY* 3.2 4.0 - - - -
188D ASN* 2.7 50.8 + - - -
299D ILE* 3.4 9.0 - - - +
173J LEU* 4.1 5.2 - - - -
175J GLY 3.6 6.3 - - - -
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Residues in contact with THR 182 (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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59D LEU* 4.7 1.8 - - - +
181D GLY* 1.3 75.2 + - - -
183D GLU* 1.3 74.5 + - - +
184D GLY 4.5 4.5 - - - +
186D LYS 3.7 6.5 - - - -
187D GLY* 4.2 0.2 - - - -
289D ILE* 6.0 0.7 - - + -
291D ALA* 4.6 13.0 - - + -
292D VAL 5.9 0.4 - - - +
295D THR* 3.3 23.7 - - + +
296D ASN* 3.0 36.0 + - - +
299D ILE* 4.2 4.3 - - - +
173J LEU* 3.8 4.4 - - - +
175J GLY* 2.9 34.6 + - - -
176J GLY* 4.3 12.8 - - - +
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Residues in contact with GLU 183 (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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182D THR* 1.3 81.7 - - - +
184D GLY* 1.3 63.8 + - - +
185D PHE 3.3 0.3 + - - -
186D LYS* 3.0 26.4 + - + +
208D PRO* 5.7 5.7 - - - +
289D ILE* 3.4 28.0 - - + -
290D PRO* 5.7 1.3 - - + -
172J ALA 5.1 0.3 - - - +
173J LEU* 3.9 23.6 - - + +
174J ARG* 3.2 54.8 + - - +
175J GLY 4.9 0.2 - - - +
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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