Contacts of the helix formed by residues 169 - 177 (chain D) in PDB entry 4YP8
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 SER 169 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167D SER 4.7 2.9 + - - -
168D PHE* 1.3 75.4 - - - +
170D PHE* 1.3 55.3 + - - +
171D TYR* 3.2 28.5 - - - -
172D GLU* 2.6 51.6 + - - +
173D LEU* 3.3 4.2 + - - +
252D SER* 4.0 0.4 - - - -
254D ASP* 3.4 14.6 + - - -
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Residues in contact with PHE 170 (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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169D SER* 1.3 69.1 - - - +
171D TYR* 1.4 54.3 + - - +
172D GLU 3.4 0.2 - - - -
173D LEU* 3.4 5.9 + - + +
174D LYS* 3.1 56.3 + - + +
180D PHE* 3.7 30.7 - + - -
252D SER* 3.3 16.2 + - - +
254D ASP* 2.9 17.6 + - - +
255D GLY* 3.9 20.2 - - - -
256D ASP* 4.5 11.9 - - + -
257D ASP* 3.8 43.1 - - + -
259D CYS* 4.0 17.3 - - - -
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Residues in contact with TYR 171 (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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169D SER* 2.9 33.8 + - - -
170D PHE* 1.4 72.5 - - - +
172D GLU* 1.4 82.0 + - + +
174D LYS* 3.3 16.5 + - + +
175D ASN* 3.1 38.6 + - - +
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Residues in contact with GLU 172 (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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166D HIS* 4.9 7.8 + - - -
167D SER 4.4 2.1 - - - +
168D PHE* 3.5 16.3 - - + -
169D SER* 2.6 48.5 + - - +
171D TYR* 1.4 98.7 + - + +
173D LEU* 1.3 58.3 + - + +
175D ASN* 3.0 16.0 + - - +
176D VAL* 2.9 33.9 + - + +
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Residues in contact with LEU 173 (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 PHE* 3.7 38.6 - - + -
169D SER 3.3 4.1 + - - +
170D PHE* 3.9 9.0 - - - +
171D TYR 3.4 0.2 - - - -
172D GLU* 1.3 77.0 - - - +
174D LYS* 1.4 50.7 + - - +
176D VAL* 3.5 18.7 - - + +
177D THR* 2.7 39.7 + - - +
180D PHE* 4.2 13.3 - - + -
205D VAL* 5.1 1.1 - - + -
212D VAL* 4.2 7.2 - - + -
252D SER* 3.5 31.2 - - - +
259D CYS* 3.7 17.0 - - + -
261D VAL* 3.8 26.2 - - + -
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Residues in contact with LYS 174 (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 PHE* 3.1 48.0 + - + +
171D TYR* 3.4 14.6 - - + +
172D GLU 3.2 0.2 - - - -
173D LEU* 1.4 74.6 - - - +
175D ASN* 1.4 64.2 + - - +
177D THR* 3.9 4.7 - - - -
178D ASN 3.3 1.7 + - - -
179D ASN* 2.4 59.4 + - + +
180D PHE* 3.8 17.7 - - + -
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Residues in contact with ASN 175 (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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171D TYR* 3.1 30.8 + - - +
172D GLU* 3.0 15.4 + - - +
174D LYS* 1.4 79.5 - - - +
176D VAL* 1.4 63.2 + - + +
178D ASN* 3.6 12.2 + - - +
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Residues in contact with VAL 176 (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 PHE* 6.2 0.7 - - + -
172D GLU* 2.9 19.0 + - + +
173D LEU* 3.5 33.0 - - + +
175D ASN* 1.4 79.9 - - + +
177D THR* 1.3 67.8 + - + +
178D ASN* 3.3 1.9 + - - +
190D ASN* 4.2 2.9 + - - -
202D LYS 4.0 0.9 - - - +
203D GLY* 3.3 16.3 - - - -
204D TYR* 3.3 40.8 + - - +
205D VAL* 3.9 20.0 - - + -
212D VAL* 4.5 3.6 - - + -
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Residues in contact with THR 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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173D LEU 2.7 22.4 + - - +
174D LYS* 3.8 2.1 + - - -
175D ASN 3.5 0.2 - - - -
176D VAL* 1.3 77.3 - - + +
178D ASN* 1.4 67.4 + - - +
180D PHE* 3.1 39.2 + - + -
181D ASP 3.2 9.2 + - - -
190D ASN* 3.3 11.0 - - - +
201D TYR* 4.1 10.8 - - + -
202D LYS 3.7 18.8 - - - +
203D GLY* 4.3 0.4 - - - -
212D VAL* 3.7 35.9 - - + -
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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