Contacts of the helix formed by residues 173 - 184 (chain H) in PDB entry 6BCH
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 ASP 173 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18H SER* 5.5 0.2 - - - -
20H TRP* 3.7 35.6 - - + +
171H ILE* 3.3 6.3 + - - +
172H PRO* 1.3 83.8 - - - +
174H SER* 1.3 69.8 + - - +
175H ASN* 2.7 43.9 + - - +
176H TRP* 3.0 18.4 + - + +
177H VAL* 3.4 8.5 + - - +
225H TYR* 4.0 5.1 - - - -
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Residues in contact with SER 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173H ASP* 1.3 78.5 + - - +
175H ASN* 1.3 60.6 + - - +
177H VAL* 3.1 9.2 + - - +
178H ALA* 2.9 23.2 + - - +
225H TYR* 3.3 23.0 + - - -
264H PHE* 3.8 13.0 - - - -
268H ASN* 2.7 35.6 + - - +
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Residues in contact with ASN 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H SER* 3.6 24.9 + - - +
20H TRP* 4.4 0.2 - - + -
21H THR* 3.2 32.7 + - - +
173H ASP* 2.7 24.3 + - - +
174H SER* 1.3 73.9 + - - +
176H TRP* 1.3 62.9 + - - +
178H ALA* 3.2 6.5 + - - +
179H GLY 2.9 18.5 + - - -
267H LYS 5.2 0.7 - - - +
268H ASN* 3.6 21.3 - - - +
269H HIS 5.2 0.9 + - - -
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Residues in contact with TRP 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H TRP* 3.2 36.9 + + + +
23H THR* 4.0 3.9 - - + +
24H GLY* 3.4 24.1 - - - +
27H ASP* 2.9 33.7 + - - -
105H ILE* 3.7 22.4 - - + +
106H THR* 4.3 3.1 - - + -
171H ILE* 4.2 13.0 - - + -
172H PRO* 4.0 19.5 - - + -
173H ASP* 3.0 14.7 + - - +
175H ASN* 1.3 78.2 - - - +
177H VAL* 1.3 69.4 - - + +
179H GLY 3.2 1.4 + - - -
180H PHE* 2.9 64.1 + + + +
218H LEU* 4.5 17.3 - - + -
222H LEU* 4.3 18.4 - - + -
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Residues in contact with VAL 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H ILE* 3.6 30.1 - - + -
173H ASP 3.7 6.1 - - - +
174H SER 3.1 9.9 - - - +
176H TRP* 1.3 86.1 - - + +
178H ALA* 1.3 48.8 + - - +
180H PHE* 3.8 2.4 - - + +
181H THR* 2.7 51.3 + - + +
209H ILE* 6.1 0.2 - - + -
222H LEU* 4.3 18.8 - - + -
225H TYR* 4.0 15.9 - - + -
226H LEU* 4.7 11.0 - - + -
264H PHE* 3.5 22.7 - - + -
265H PHE* 4.6 1.1 - - + -
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Residues in contact with ALA 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H THR* 4.9 4.5 - - + +
174H SER 2.9 12.0 + - - +
175H ASN* 3.2 14.1 + - + +
177H VAL* 1.3 77.2 - - - +
179H GLY* 1.3 55.9 + - - +
181H THR* 2.9 19.0 + - - -
182H ALA* 2.9 19.6 + - - +
264H PHE* 4.8 0.2 - - - -
265H PHE* 4.5 5.6 - - - -
268H ASN* 3.8 21.8 - - + +
269H HIS 3.6 23.1 - - - +
270H ILE* 4.1 3.3 - - - +
271H ILE* 6.1 0.2 - - - -
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Residues in contact with GLY 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H THR* 3.6 31.8 - - - +
25H PHE* 3.3 18.8 - - - -
175H ASN 2.9 11.9 + - - -
176H TRP 3.7 1.3 - - - -
178H ALA* 1.3 72.8 - - - +
180H PHE* 1.3 64.7 + - - +
182H ALA* 3.1 9.8 + - - +
183H GLY 3.0 17.7 + - - -
271H ILE* 5.3 0.2 - - - -
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Residues in contact with PHE 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H GLY 3.6 20.4 - - - +
27H ASP* 4.1 0.9 - - + -
28H ALA* 4.1 10.8 - - + -
106H THR* 3.7 27.1 - - + -
176H TRP* 2.9 48.7 + + + +
177H VAL* 3.8 4.0 - - - +
179H GLY* 1.3 74.6 - - - +
181H THR* 1.3 59.1 + - + +
183H GLY* 3.1 1.6 + - - +
184H GLU* 2.9 47.5 + - + +
209H ILE* 3.9 33.7 - - + -
211H GLN* 4.3 16.8 - - + -
218H LEU* 5.3 4.7 - - + -
219H MET* 5.3 7.9 - - - -
222H LEU* 5.3 10.1 - - + -
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Residues in contact with THR 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177H VAL* 2.7 32.1 + - + +
178H ALA 2.9 12.3 + - - -
180H PHE* 1.3 76.0 - - + +
182H ALA* 1.3 61.9 + - - +
185H GLY* 2.8 34.1 + - - +
187H PHE* 5.3 3.2 - - - -
207H PHE* 4.0 8.3 - - + -
209H ILE* 3.7 28.0 - - + -
226H LEU* 6.0 0.4 - - + -
265H PHE* 3.1 40.0 - - + -
270H ILE* 3.3 9.9 - - - +
274H LYS* 6.0 0.7 - - - +
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Residues in contact with ALA 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H PHE* 3.8 12.0 - - + -
178H ALA 2.9 19.9 + - - +
179H GLY 3.1 8.7 + - - +
181H THR* 1.3 78.9 + - - +
183H GLY* 1.3 57.5 + - - +
185H GLY 5.6 0.2 - - - +
270H ILE* 4.2 10.5 - - + +
271H ILE* 3.7 44.9 - - + +
274H LYS* 4.9 10.7 - - - +
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Residues in contact with GLY 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H PHE* 3.8 12.3 - - - -
28H ALA* 3.7 14.6 - - - -
29H ASP* 4.0 10.6 - - - +
179H GLY 3.0 9.9 + - - -
180H PHE 3.1 2.9 + - - -
181H THR 3.1 0.2 - - - -
182H ALA* 1.3 80.6 - - - +
184H GLU* 1.3 69.7 + - - +
185H GLY 3.6 2.3 + - - +
16J G 3.6 12.5 + - - +
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Residues in contact with GLU 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H ALA* 3.2 40.8 - - + +
29H ASP* 3.7 0.2 - - - +
180H PHE* 2.9 31.3 + - + +
183H GLY* 1.3 72.7 - - - +
185H GLY* 1.3 63.9 + - - +
186H SER* 5.1 0.7 - - - -
209H ILE* 4.0 13.3 - - + -
210H THR* 3.8 27.9 + - - +
211H GLN* 3.1 24.2 + - - +
15J C 4.0 7.9 - - - +
16J G 3.2 37.8 + - - +
17K A 3.5 9.1 + - - -
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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