Contacts of the helix formed by residues 173 - 183 (chain D) in PDB entry 3UNE
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 ALA 173 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D THR* 4.3 9.9 + - + -
172D SER* 1.3 81.4 + - - +
174D SER* 1.3 61.3 + - - +
175D GLU 3.4 2.5 - - - +
176D GLY* 4.1 6.7 - - - +
177D ALA* 3.3 24.3 + - - +
205D VAL* 3.8 35.4 - - + +
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Residues in contact with SER 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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32D LYS* 6.5 0.4 - - - -
36D THR* 5.4 0.4 - - - -
169D ALA* 2.8 32.9 + - - +
170D ILE* 3.9 3.2 - - - +
171D GLY 3.8 26.4 + - - +
172D SER 3.3 5.2 + - - -
173D ALA* 1.3 76.0 - - - +
175D GLU* 1.3 65.6 + - - +
178D GLN* 3.2 26.3 + - - +
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Residues in contact with GLU 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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173D ALA* 3.4 0.8 - - - +
174D SER* 1.3 80.1 - - - +
176D GLY* 1.3 61.0 + - - +
178D GLN* 4.2 3.6 - - - +
179D SER* 3.4 22.0 + - - -
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Residues in contact with GLY 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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173D ALA* 3.8 9.0 + - - +
174D SER 3.4 0.2 - - - -
175D GLU* 1.3 79.7 - - - +
177D ALA* 1.3 57.8 + - - +
179D SER* 2.8 19.0 + - - -
180D SER* 3.2 15.1 + - - -
205D VAL* 4.6 8.5 - - - -
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Residues in contact with ALA 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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36D THR* 4.8 4.3 - - - +
38D ILE* 4.5 10.1 - - + -
169D ALA* 3.8 17.9 - - + -
173D ALA 3.3 19.3 + - - +
176D GLY* 1.3 75.6 - - - +
178D GLN* 1.3 63.8 + - - +
179D SER 3.3 0.2 - - - -
180D SER* 3.3 4.2 + - - -
181D LEU* 3.1 27.4 + - - +
201D ILE* 3.9 22.6 - - + +
205D VAL* 4.0 11.3 - - + +
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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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167D ALA 3.2 21.4 + - - -
168D ARG* 3.6 9.4 - - - +
169D ALA* 3.0 31.2 + - - +
174D SER 3.2 18.6 + - - +
175D GLU* 4.2 4.7 - - - +
176D GLY 3.4 0.2 - - - -
177D ALA* 1.3 79.8 - - - +
179D SER* 1.3 60.7 + - - +
181D LEU* 3.2 11.2 + - - +
182D GLN* 3.1 39.2 + - - +
54E SER* 4.1 18.8 + - - -
56E LEU* 4.0 17.8 - - - +
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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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175D GLU 3.4 12.5 + - - -
176D GLY* 2.8 24.4 + - - -
178D GLN* 1.3 79.1 - - - +
180D SER* 1.3 61.0 + - - +
182D GLN* 3.5 26.6 + - - +
183D GLU* 3.8 17.5 + - - +
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Residues in contact with SER 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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176D GLY 3.2 12.0 + - - -
177D ALA 3.3 9.8 + - - -
178D GLN 3.2 0.6 - - - -
179D SER* 1.3 78.3 + - - +
181D LEU* 1.3 62.7 + - - +
182D GLN 3.6 0.2 + - - -
183D GLU* 3.7 8.2 + - - +
184D VAL* 3.4 25.5 - - - +
201D ILE* 3.8 28.1 - - - +
204D GLN* 4.1 16.2 + - - -
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Residues in contact with LEU 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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38D ILE* 3.9 24.9 - - + -
40D ILE* 3.8 33.7 - - + -
167D ALA* 4.2 20.0 - - + -
168D ARG 4.2 10.3 - - - -
169D ALA* 4.0 17.7 - - + -
177D ALA 3.1 19.1 + - - +
178D GLN* 3.2 15.4 + - - +
180D SER* 1.3 75.0 - - - +
182D GLN* 1.3 63.5 + - - +
183D GLU 3.3 0.2 - - - -
184D VAL* 4.8 2.5 - - + +
185D TYR* 3.2 32.0 + - + +
197D SER* 6.0 0.4 - - - -
201D ILE* 3.8 18.6 - - + -
56E LEU* 4.6 3.0 - - + +
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Residues in contact with GLN 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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178D GLN* 3.1 26.0 + - - +
179D SER* 3.7 21.3 - - - +
180D SER 3.3 0.6 - - - -
181D LEU* 1.3 79.1 - - - +
183D GLU* 1.3 62.3 + - + +
184D VAL 3.5 0.4 + - - -
185D TYR 4.6 7.2 - - - +
54E SER* 4.7 10.1 - - - +
55E GLU* 3.5 42.6 - - - +
56E LEU* 3.7 26.9 - - + +
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Residues in contact with GLU 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 SER 3.8 15.1 + - - +
180D SER* 3.7 8.1 + - - +
181D LEU 3.3 0.4 - - - -
182D GLN* 1.3 81.3 - - + +
184D VAL* 1.3 64.8 + - + +
185D TYR 5.2 0.9 - - - -
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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