Contacts of the helix formed by residues 170 - 179 (chain D) in PDB entry 1YAA
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 170 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D LEU* 2.9 27.2 + - + +
169D ASP* 1.3 72.1 - - - +
171D ASN* 1.3 69.0 + - - +
173D PHE* 3.1 9.4 + - + +
174D LEU* 2.9 41.7 + - + +
204D GLN* 3.9 34.1 - - + +
207D GLN* 3.6 31.9 - - + +
208D ILE* 4.4 20.6 - - + -
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Residues in contact with ASN 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 ASP* 3.3 7.5 + - - +
170D LEU* 1.3 81.3 - - - +
172D GLY* 1.3 57.5 + - - +
174D LEU* 4.1 5.7 - - - +
175D ASN* 3.1 28.9 + - - +
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Residues in contact with GLY 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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159D PRO* 3.6 23.4 - - - +
169D ASP* 3.1 19.0 + - - -
171D ASN* 1.3 74.2 - - - +
173D PHE* 1.3 65.9 + - - +
175D ASN* 3.9 5.6 + - - +
176D ALA* 3.0 26.7 + - - +
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Residues in contact with PHE 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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158D TYR* 3.5 38.4 - + - -
159D PRO* 3.6 14.5 + - - +
160D TYR* 4.0 27.6 - + - -
168D LEU* 4.3 8.3 - - + -
169D ASP 3.1 13.5 + - - +
170D LEU* 3.1 16.7 + - + +
172D GLY* 1.3 79.1 - - - +
174D LEU* 1.3 62.8 + - + +
176D ALA* 3.3 3.0 + - - +
177D ILE* 3.2 42.2 + - + +
186D PHE* 4.9 1.8 - + - -
188D LEU* 3.7 24.2 - - + -
200D PRO* 5.0 1.3 - - + -
205D TRP* 5.8 1.3 - + - -
208D ILE* 3.9 32.5 - - + -
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Residues in contact with LEU 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 LEU* 2.9 39.7 + - + +
171D ASN* 4.2 5.8 - - - +
173D PHE* 1.3 79.2 - - + +
175D ASN* 1.3 56.9 - - - +
177D ILE* 3.3 8.1 + - + +
178D GLN* 2.8 37.6 + - - +
207D GLN* 3.8 52.7 - - + +
208D ILE* 4.1 11.9 - - + +
211D ALA* 4.2 9.9 - - + -
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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 ASN 3.1 19.6 + - - +
172D GLY* 3.9 6.4 + - - +
173D PHE 3.4 0.2 - - - -
174D LEU* 1.3 72.7 - - - +
176D ALA* 1.3 64.7 + - - +
178D GLN* 3.1 6.2 + - - +
179D LYS* 2.8 57.3 + - - +
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Residues in contact with ALA 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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134D TYR* 4.3 10.0 + - + -
156D THR 4.6 4.3 - - - +
158D TYR* 3.7 26.2 - - + -
159D PRO* 3.8 9.2 - - + -
172D GLY 3.0 18.6 + - - +
173D PHE 3.6 4.3 - - - +
175D ASN* 1.3 78.8 - - - +
177D ILE* 1.3 57.1 + - - +
179D LYS* 3.8 5.3 - - - +
180D ALA* 3.0 30.0 + - - +
186D PHE* 4.7 2.0 - - - -
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Residues in contact with ILE 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 PHE* 3.2 40.8 + - + +
174D LEU* 3.4 12.6 - - + +
175D ASN 3.1 0.2 - - - -
176D ALA* 1.3 77.9 - - + +
178D GLN* 1.3 63.6 + - - +
179D LYS 3.4 0.5 + - - -
180D ALA 3.5 4.0 + - - -
186D PHE* 3.8 24.9 - - + -
208D ILE* 4.2 13.2 - - + +
211D ALA* 3.8 29.8 - - + +
212D ILE* 4.0 19.3 - - + -
215D LYS* 3.4 3.3 - - + +
217D HIS* 2.9 43.9 + - + -
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Residues in contact with GLN 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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174D LEU* 2.8 35.9 + - - +
175D ASN* 3.1 8.9 + - - +
177D ILE* 1.3 76.0 - - - +
179D LYS* 1.3 66.8 + - + +
211D ALA* 3.7 23.4 + - - +
214D SER* 3.7 20.8 + - - -
215D LYS* 3.0 33.9 + - + +
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Residues in contact with LYS 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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134D TYR* 5.2 0.2 - - - -
175D ASN* 2.8 41.1 + - - +
176D ALA* 4.0 5.4 - - - +
177D ILE 3.2 0.2 - - - -
178D GLN* 1.3 85.2 - - + +
180D ALA* 1.3 61.2 + - - +
181D PRO* 3.7 3.6 - - - +
215D LYS* 4.2 1.5 + - - -
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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