Contacts of the helix formed by residues 178 - 188 (chain D) in PDB entry 3P05
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 178 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176D GLN 3.5 4.0 + - - -
177D ALA* 1.3 73.3 - - - +
179D GLN* 1.3 66.5 + - - +
180D GLU* 3.7 8.7 + - - +
181D VAL* 2.9 43.7 + - - +
182D LYS* 3.0 10.2 + - - +
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Residues in contact with GLN 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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177D ALA 3.8 1.3 + - - +
178D SER* 1.3 73.4 - - - +
180D GLU* 1.3 60.5 + - - +
182D LYS* 4.3 11.4 - - - +
183D ASN* 3.0 58.6 + - - +
67E GLN* 4.2 18.3 + - - +
70E LYS* 4.2 21.4 + - - +
74E ASN* 5.6 4.4 - - - +
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Residues in contact with GLU 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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178D SER* 3.1 9.1 + - - +
179D GLN* 1.3 77.1 - - - +
181D VAL* 1.3 57.4 + - + +
183D ASN* 3.2 10.2 + - - +
184D ALA* 2.9 29.7 + - - +
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Residues in contact with VAL 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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172D LEU* 5.2 6.1 - - + -
177D ALA* 4.0 18.6 - - + -
178D SER* 2.9 32.8 + - - +
180D GLU* 1.3 73.2 - - + +
182D LYS* 1.3 59.3 + - - +
184D ALA* 3.4 6.7 + - - +
185D ALA* 2.8 30.4 + - + +
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Residues in contact with LYS 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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169D TYR* 5.1 7.4 - - + -
172D LEU* 3.9 24.5 - - + +
177D ALA* 4.4 9.3 - - + +
178D SER 3.0 14.6 + - - +
179D GLN* 3.8 20.9 - - - +
181D VAL* 1.3 78.8 - - - +
183D ASN* 1.3 57.6 + - - +
185D ALA* 3.3 2.4 + - - +
186D THR* 2.8 33.8 + - - -
67E GLN* 6.0 2.2 - - - +
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Residues in contact with ASN 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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179D GLN* 3.0 50.6 + - - +
180D GLU* 3.2 7.5 + - - +
182D LYS* 1.3 77.2 - - - +
184D ALA* 1.3 56.1 - - - +
186D THR* 3.2 8.0 + - - -
187D GLU* 2.9 30.9 + - - +
67E GLN* 5.1 3.8 + - - -
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Residues in contact with ALA 184 (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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180D GLU 2.9 19.1 + - - +
181D VAL* 3.6 8.5 - - + +
182D LYS 3.4 0.2 - - - -
183D ASN* 1.3 72.6 - - - +
185D ALA* 1.3 56.7 + - - +
187D GLU* 3.6 4.7 + - - +
188D THR* 2.8 37.3 + - - +
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Residues in contact with ALA 185 (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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150D ILE* 5.7 0.4 - - + -
168D PHE* 3.3 10.8 - - + -
172D LEU* 4.0 26.0 - - + -
181D VAL* 2.8 21.8 + - + +
182D LYS 3.7 4.5 - - - +
184D ALA* 1.3 70.6 - - - +
186D THR* 1.3 62.2 + - - +
189D LEU* 2.9 45.5 + - + +
190D LEU 3.3 6.8 + - - -
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Residues in contact with THR 186 (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* 4.3 2.5 - - - -
169D TYR* 2.5 35.3 + - - +
182D LYS 2.8 19.1 + - - -
183D ASN* 3.5 10.6 + - - -
185D ALA* 1.3 79.3 - - - +
187D GLU* 1.3 67.8 - - - +
188D THR 3.2 0.2 + - - -
190D LEU* 3.2 37.7 + - + +
191D VAL* 4.5 3.1 + - - +
211D LEU* 5.8 4.9 - - + -
214D MET* 5.9 4.5 - - - -
67E GLN* 5.5 1.2 + - - -
71E GLU* 5.7 4.7 - - - +
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Residues in contact with GLU 187 (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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183D ASN 2.9 17.1 + - - +
184D ALA* 3.9 5.4 - - - +
186D THR* 1.3 81.2 - - - +
188D THR* 1.3 63.6 + - - +
191D VAL* 5.3 6.6 - - - +
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Residues in contact with THR 188 (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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184D ALA* 2.8 19.6 + - - +
185D ALA* 4.7 0.2 - - - -
187D GLU* 1.3 82.3 - - - +
189D LEU* 1.3 84.1 + - + +
190D LEU 3.4 1.3 + - - -
191D VAL* 4.2 2.6 + - - +
192D GLN* 3.6 19.8 + - + +
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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