Contacts of the strand formed by residues 176 - 183 (chain D) in PDB entry 2PI8
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 ASN 176 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166D TYR* 4.1 0.7 - - - -
167D ILE 2.8 37.8 + - - +
169D PHE* 4.4 15.0 - - + -
174D PRO 3.4 4.6 + - - +
175D LEU* 1.3 70.5 - - - +
177D PHE* 1.3 61.4 + - - +
178D PHE* 3.4 22.2 + - + -
238D PRO* 3.2 19.8 - - - +
239D GLN 3.0 12.3 + - - -
240D SER* 3.0 32.4 + - - +
241D PHE 3.9 4.3 - - - +
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Residues in contact with PHE 177 (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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103D THR* 4.1 2.7 - - + -
164D SER* 3.5 35.9 - - - -
165D GLY 4.0 12.8 - - - -
166D TYR* 3.7 30.1 - + + -
175D LEU 3.6 3.6 + - - -
176D ASN* 1.3 71.8 + - - +
178D PHE* 1.3 60.3 + - - +
179D SER* 3.3 24.6 + - - -
239D GLN* 2.8 49.7 + - + +
240D SER 3.9 0.4 - - - +
241D PHE 3.9 4.0 - - - +
242D ALA* 3.7 13.0 - - + +
243D PRO 4.1 9.0 - - - -
244D VAL* 3.9 27.4 - - + -
245D LYS* 3.9 25.8 - - + -
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Residues in contact with PHE 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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120D ILE* 3.8 26.5 - - + -
147D LEU* 3.7 39.3 - - + -
148D ALA* 4.8 2.7 - - + -
159D MSE 5.1 3.4 - - - -
164D SER* 3.2 26.9 - - - -
165D GLY 3.0 17.3 + - - +
167D ILE* 3.7 33.9 - - + -
169D PHE* 4.6 9.9 - + - -
176D ASN* 3.5 35.7 - - + -
177D PHE* 1.3 72.0 - - - +
179D SER* 1.3 63.5 + - - +
236D PHE* 3.3 18.6 - + + -
237D LYS 3.8 4.3 - - - -
238D PRO* 3.8 15.5 - - + -
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Residues in contact with SER 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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164D SER* 4.1 2.9 - - - -
177D PHE* 3.3 26.7 + - - -
178D PHE* 1.3 73.3 - - - +
180D TYR* 1.3 59.9 + - - +
181D ALA 3.1 4.2 + - - -
236D PHE* 3.1 7.9 - - - -
237D LYS* 2.9 46.2 + - - +
239D GLN* 3.0 22.8 + - - -
245D LYS 5.5 1.8 - - - -
5H NAG 4.1 10.1 - - - -
6H NAG 3.8 6.3 - - - +
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Residues in contact with TYR 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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163D GLY* 3.2 33.8 + - - +
164D SER* 4.3 1.8 - - - -
179D SER* 1.3 69.8 - - - +
181D ALA* 1.3 60.2 + - - +
182D GLY* 4.0 18.6 - - - -
183D LYS* 3.5 26.9 - - + +
234D VAL* 3.7 31.2 - - + -
235D PHE 4.2 2.5 - - - -
236D PHE* 4.6 0.7 - - - -
3H NAG 4.4 8.3 - - - -
4H NAG 3.8 43.6 + - - +
5H NAG 2.8 55.8 + - - +
6H NAG 3.5 3.2 - - - +
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Residues in contact with ALA 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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123D MSE 3.6 33.2 - - + +
179D SER 3.1 1.8 + - - -
180D TYR* 1.3 76.5 - - - +
182D GLY* 1.3 57.7 + - - +
235D PHE 2.9 14.7 + - - +
236D PHE 3.6 19.5 - - - +
237D LYS* 3.7 15.7 - - + -
5H NAG 5.4 0.2 + - - -
6H NAG 3.4 21.8 - - + +
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Residues in contact with GLY 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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123D MSE 3.9 14.1 - - - +
180D TYR* 3.7 15.5 - - - -
181D ALA* 1.3 79.1 - - - +
183D LYS* 1.3 62.2 + - - +
234D VAL* 3.5 9.2 - - - +
235D PHE* 2.9 29.2 + - - +
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Residues in contact with LYS 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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123D MSE 4.7 0.4 - - - -
129D ARG* 4.2 13.5 - - - +
180D TYR* 3.5 19.7 + - + +
182D GLY* 1.3 75.2 - - - +
184D ASN* 1.3 85.9 + - - +
186D HIS 2.7 31.5 + - - +
187D ALA* 4.8 1.6 - - - +
188D TYR* 5.7 3.4 - - + +
232D SER* 3.1 17.1 + - - +
233D PHE 3.2 19.1 - - - +
234D VAL* 4.2 9.4 - - + -
235D PHE* 3.7 13.2 - - - -
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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