Contacts of the helix formed by residues 162 - 171 (chain D) in PDB entry 3SPD
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 162 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161D LYS* 1.3 82.1 - - - +
163D SER* 1.3 64.2 + - - +
164D ALA* 3.3 11.9 + - - +
165D HIS* 3.0 57.7 + - - +
166D TYR 3.5 1.4 + - - -
211D PHE* 3.3 21.1 - - - -
9G T 5.7 9.2 - - + -
1H G 4.5 7.5 + - - +
3H C 5.3 0.2 + - - -
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Residues in contact with SER 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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162D ASN* 1.3 71.5 - - - +
164D ALA* 1.3 67.7 + - - +
166D TYR* 3.0 4.1 + - - +
167D ILE* 2.8 28.3 + - - +
198D LEU* 3.5 36.0 - - - +
209D ARG* 3.8 32.2 + - - -
211D PHE* 3.6 17.5 - - - +
9G T 4.5 5.2 + - - -
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Residues in contact with ALA 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 ASN* 3.3 6.9 + - - +
163D SER* 1.3 77.3 - - - +
165D HIS* 1.3 64.2 + - - +
167D ILE* 4.5 1.3 - - - +
168D SER* 2.9 27.0 + - - -
194D PHE* 3.5 22.8 + - + +
209D ARG* 5.5 0.4 - - - +
1H G 3.3 49.9 + - + +
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Residues in contact with HIS 165 (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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67D LYS* 3.5 19.5 - - + +
159D SER 3.5 16.6 + - - -
160D LEU* 3.9 16.2 - - + -
161D LYS* 3.1 28.3 + - + -
162D ASN* 3.0 39.9 + - - +
164D ALA* 1.3 75.6 - - - +
166D TYR* 1.3 60.8 + - - +
168D SER* 2.6 21.9 + - - -
169D PHE* 3.3 13.5 - + - -
1H G 3.3 24.0 + - - -
2H T 5.2 0.7 - - - -
3H C 2.8 31.6 + - - -
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Residues in contact with TYR 166 (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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155D HIS* 4.2 14.4 - + + -
160D LEU* 4.1 11.7 - - + -
162D ASN 3.5 6.2 + - - +
163D SER* 3.0 8.5 + - - +
165D HIS* 1.3 78.1 - - - +
167D ILE* 1.3 66.4 + - + +
169D PHE* 3.1 11.9 + - - +
170D THR* 2.8 48.0 + - + +
198D LEU* 4.1 9.9 - - + -
199D LYS 2.8 33.5 + - - -
200D CYS* 3.4 4.0 - - - -
201D TRP* 2.8 28.9 + + - +
211D PHE* 4.6 4.9 - - + -
214D LEU* 3.6 30.9 - - + +
218D LEU* 3.9 29.6 - - + -
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Residues in contact with ILE 167 (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 SER 2.8 23.6 + - - +
164D ALA 4.0 2.9 - - - +
166D TYR* 1.3 77.6 - - + +
168D SER* 1.3 61.9 + - - +
169D PHE 3.1 1.2 + - - -
170D THR* 3.8 6.7 - - - -
171D SER* 2.8 47.2 + - - +
193D LEU* 3.8 25.8 - - + +
194D PHE* 3.6 40.2 - - + +
196D GLU* 4.1 6.5 - - + +
197D ASP 5.6 1.8 - - - +
198D LEU* 4.1 16.4 - - + -
209D ARG* 3.8 14.6 - - - +
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Residues in contact with SER 168 (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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138D HIS* 3.2 32.6 + - - -
164D ALA 2.9 16.1 + - - -
165D HIS* 2.6 21.1 + - - -
167D ILE* 1.3 77.0 - - - +
169D PHE* 1.3 69.8 + - - +
173D PHE* 3.5 20.7 - - - -
174D PHE* 3.5 12.1 + - - +
194D PHE* 4.0 2.7 - - - -
1H G 3.8 22.4 + - - -
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Residues in contact with PHE 169 (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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67D LYS* 3.6 32.8 - - + -
71D HIS* 3.7 18.4 - + - -
134D LYS* 2.9 20.9 + - - +
138D HIS* 3.3 26.5 - + - -
149D HIS* 3.5 25.6 - + - -
151D MET* 3.3 22.0 - - - -
155D HIS* 3.3 26.7 - + + +
165D HIS* 3.3 10.8 - - - -
166D TYR 3.1 3.8 + - - +
167D ILE 3.1 0.4 - - - -
168D SER* 1.3 100.5 + - - +
170D THR* 1.3 58.0 + - - +
171D SER 3.7 1.1 - - - -
174D PHE* 3.6 31.8 - + - +
176D LYS* 5.8 0.5 + - - -
1H G 5.9 0.4 - - - -
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Residues in contact with THR 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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134D LYS* 3.9 4.3 - - - +
155D HIS* 3.6 27.1 - - + +
166D TYR* 2.8 53.6 + - + +
167D ILE* 3.3 4.2 + - - -
169D PHE* 1.3 83.3 - - - +
171D SER* 1.3 61.2 + - - +
199D LYS* 5.8 3.6 - - - -
201D TRP* 4.3 16.1 - - + +
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Residues in contact with SER 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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167D ILE* 2.8 32.1 + - - +
170D THR* 1.3 80.2 - - - +
172D PRO* 1.3 71.3 - - - +
173D PHE* 3.0 18.8 + - - +
174D PHE* 2.9 25.3 + - - +
193D LEU* 3.5 13.9 - - - +
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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