Contacts of the helix formed by residues 180 - 193 (chain D) in PDB entry 2H5X
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 THR 180 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179D ALA* 1.3 75.8 - - - +
181D THR* 1.3 66.8 + - - +
182D SER* 4.1 8.1 - - - -
183D SER* 3.1 21.9 + - - -
184D ALA* 2.9 19.9 + - - +
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Residues in contact with THR 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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14C LEU* 3.8 21.9 - - + +
146D ALA 5.5 1.3 - - - -
147D VAL* 4.0 22.6 + - - +
150D PRO* 4.1 13.9 - - + +
151D VAL* 3.3 28.6 - - - +
179D ALA 3.5 2.3 + - - -
180D THR* 1.3 72.2 - - - +
182D SER* 1.3 67.5 + - - +
184D ALA* 4.6 1.6 - - - -
185D LEU* 3.1 18.9 + - - +
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Residues in contact with SER 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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12C VAL* 6.4 2.2 - - - -
13C ALA 5.9 1.8 - - - -
14C LEU* 3.9 19.5 - - - -
32C PRO* 5.1 4.5 - - - +
35C LEU* 6.1 3.4 - - - -
36C ALA* 5.0 8.4 - - - -
180D THR* 3.1 8.9 - - - -
181D THR* 1.3 81.9 - - - +
183D SER* 1.3 63.3 + - - +
185D LEU* 2.9 19.3 + - - +
186D ARG* 3.0 34.8 + - - +
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Residues in contact with SER 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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176D ASN* 5.1 2.3 + - - -
179D ALA* 4.2 10.6 - - - +
180D THR* 3.1 24.3 + - - -
182D SER* 1.3 81.6 + - - +
184D ALA* 1.3 61.9 + - - +
186D ARG* 3.6 29.6 + - - +
187D SER* 3.0 24.9 + - - -
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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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151D VAL* 4.0 15.2 - - + +
169D THR* 5.7 1.1 - - + -
172D VAL* 3.8 19.2 - - + +
173D LEU* 3.9 28.5 - - + -
179D ALA* 4.7 5.6 - - + +
180D THR 2.9 16.1 + - - +
181D THR* 3.8 5.8 - - - +
182D SER 3.2 0.2 - - - -
183D SER* 1.3 77.8 - - - +
185D LEU* 1.3 58.8 + - - +
187D SER* 3.5 1.9 + - - -
188D ALA* 2.9 30.3 + - - +
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Residues in contact with LEU 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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14C LEU* 4.1 21.8 - - + +
32C PRO* 3.3 32.5 - - + -
151D VAL* 3.9 13.0 - - + +
154D ALA* 4.0 26.5 - - + -
155D LEU* 3.6 32.8 - - + +
158D LEU* 5.2 2.7 - - + -
181D THR 3.1 14.0 + - - +
182D SER* 2.9 11.1 + - - +
184D ALA* 1.3 74.0 - - - +
186D ARG* 1.3 64.5 + - - +
188D ALA* 3.1 3.3 + - - +
189D LEU* 3.0 25.6 + - + +
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Residues in contact with ARG 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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32C PRO* 3.9 20.0 - - + -
33C ALA* 4.6 8.3 - - + +
36C ALA* 3.4 34.8 + - - +
182D SER* 3.0 22.1 + - - +
183D SER* 3.6 32.7 + - - +
185D LEU* 1.3 75.3 - - - +
187D SER* 1.3 64.1 + - - +
189D LEU* 3.0 22.9 + - + +
190D SER* 3.1 14.0 + - - -
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Residues in contact with SER 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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172D VAL* 3.4 23.8 - - - +
183D SER* 3.0 22.2 + - - -
184D ALA 3.5 4.3 - - - -
185D LEU 3.1 0.2 - - - -
186D ARG* 1.3 79.8 - - - +
188D ALA* 1.3 59.0 + - - +
190D SER* 2.9 25.1 + - - -
191D LEU* 3.4 10.6 + - - +
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Residues in contact with ALA 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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151D VAL* 4.9 0.4 - - + -
155D LEU* 4.2 22.7 - - + -
168D ALA* 4.4 12.5 - - + +
169D THR* 4.7 4.7 - - - +
172D VAL* 3.8 17.9 - - + +
184D ALA 2.9 19.6 + - - +
185D LEU* 3.1 6.5 + - - +
187D SER* 1.3 76.5 - - - +
189D LEU* 1.3 58.3 + - - +
191D LEU* 3.4 5.9 + - - +
192D LEU* 3.0 33.6 + - - +
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Residues in contact with LEU 189 (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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32C PRO* 3.7 34.5 - - + -
90C ALA 3.6 26.5 - - - +
91C VAL* 4.9 11.4 - - + +
155D LEU* 3.6 21.8 - - + -
158D LEU* 4.1 11.9 - - + -
160D PHE* 3.9 22.0 - - + -
185D LEU* 3.0 22.8 + - + +
186D ARG* 3.0 10.9 + - - +
188D ALA* 1.3 73.8 - - - +
190D SER* 1.3 67.0 + - - +
191D LEU 3.0 1.3 - - - -
192D LEU* 2.8 14.5 + - + +
193D GLY* 2.8 11.8 + - - -
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Residues in contact with SER 190 (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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91C VAL 5.8 1.6 - - - -
186D ARG 3.1 10.8 + - - -
187D SER* 2.9 16.4 + - - -
189D LEU* 1.3 75.8 - - - +
191D LEU* 1.3 70.8 + - - +
193D GLY* 3.3 11.5 + - - +
194D LYS* 3.3 10.0 + - - -
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Residues in contact with LEU 191 (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 ALA* 4.1 16.4 - - + +
171D THR* 4.2 19.1 - - + -
172D VAL* 3.9 26.5 - - + -
187D SER* 3.4 4.9 + - - +
188D ALA 3.4 10.5 + - - +
189D LEU 3.0 0.2 - - - -
190D SER* 1.3 90.2 + - - +
192D LEU* 1.3 58.7 + - - +
194D LYS* 2.8 28.5 + - + +
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Residues in contact with LEU 192 (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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91C VAL* 4.8 2.2 - - + -
111C ARG* 4.2 12.8 - - - +
155D LEU* 4.0 24.7 - - + -
160D PHE* 3.6 46.6 - - + -
164D GLN* 3.8 36.3 - - + +
165D ALA* 5.3 0.9 - - - -
168D ALA* 4.1 19.1 - - + -
188D ALA 3.0 17.2 + - - +
189D LEU* 2.8 9.2 + - + +
191D LEU* 1.3 78.1 - - - +
193D GLY* 1.3 56.0 + - - +
194D LYS* 2.9 28.6 - - - +
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Residues in contact with GLY 193 (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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91C VAL* 3.9 23.5 - - - +
92C HIS* 4.1 13.6 + - - -
111C ARG* 3.5 14.5 + - - -
189D LEU 2.8 13.5 + - - -
190D SER* 3.3 7.5 + - - -
192D LEU* 1.3 75.5 - - - +
194D LYS* 1.3 67.8 + - - +
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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