Contacts of the helix formed by residues 173 - 184 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A SER* 5.6 0.2 - - - -
20A TRP* 3.8 34.9 - - + +
171A ILE* 3.3 5.4 + - - +
172A PRO* 1.3 83.8 - - - +
174A SER* 1.3 69.2 + - - +
175A ASN* 2.7 44.5 + - - +
176A TRP* 3.0 18.6 + - - +
177A VAL* 3.4 8.0 + - - +
225A TYR* 4.0 5.4 - - - -
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Residues in contact with SER 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ASP* 1.3 78.7 + - - +
175A ASN* 1.3 61.9 + - - +
177A VAL* 3.1 9.1 + - - +
178A ALA* 2.9 23.4 + - - +
225A TYR* 3.3 23.8 + - - -
264A PHE* 3.8 12.7 - - - -
268A ASN* 2.7 35.3 + - - +
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Residues in contact with ASN 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER* 3.7 25.1 + - - +
20A TRP* 4.5 0.2 - - + -
21A THR* 3.2 32.5 + - - +
173A ASP* 2.7 24.0 + - - +
174A SER* 1.3 72.5 + - - +
176A TRP* 1.3 63.5 + - - +
178A ALA* 3.5 6.3 - - - +
179A GLY 2.9 18.7 + - - -
267A LYS 5.2 0.9 - - - +
268A ASN* 3.6 21.4 - - - +
269A HIS 5.2 1.0 + - - -
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Residues in contact with TRP 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TRP* 3.3 30.0 + + + +
23A THR* 4.0 9.6 - - + +
24A GLY* 3.4 25.1 - - - -
27A ASP* 2.8 35.0 + - - -
105A ILE* 3.8 19.5 - - + +
106A THR* 4.3 3.8 - - + -
171A ILE* 4.3 13.0 - - + -
172A PRO* 4.0 19.7 - - + -
173A ASP* 3.0 15.4 + - - +
175A ASN* 1.3 77.4 - - - +
177A VAL* 1.3 69.6 + - + +
179A GLY 3.2 1.4 + - - -
180A PHE* 2.9 66.5 + + + +
218A LEU* 4.4 17.3 - - + -
222A LEU* 4.3 18.2 - - + -
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Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ILE* 3.6 30.5 - - + -
173A ASP 3.7 5.4 - - - +
174A SER 3.1 10.5 + - - +
176A TRP* 1.3 87.3 - - + +
178A ALA* 1.3 48.3 + - - +
180A PHE* 3.8 1.2 - - + +
181A THR* 2.7 50.2 + - + +
209A ILE* 6.0 0.2 - - + -
222A LEU* 4.3 17.3 - - + -
225A TYR* 4.0 18.2 - - + -
226A LEU* 4.7 10.1 - - + -
264A PHE* 3.5 24.0 - - + -
265A PHE* 4.7 0.9 - - + -
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Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A THR* 4.9 4.3 - - + +
174A SER 2.9 12.2 + - - +
175A ASN* 3.2 14.1 + - + +
177A VAL* 1.3 77.0 - - - +
179A GLY* 1.3 58.8 + - - +
181A THR* 2.9 18.2 + - - -
182A ALA* 2.9 18.5 + - - +
264A PHE* 4.8 0.4 - - - -
265A PHE* 4.5 5.4 - - - -
268A ASN* 3.8 21.8 - - + +
269A HIS 3.5 24.5 - - - +
270A ILE* 4.1 3.5 - - - +
271A ILE* 6.2 0.2 - - - -
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Residues in contact with GLY 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A THR* 3.6 31.7 - - - +
25A PHE* 3.3 19.1 - - - -
175A ASN 2.9 10.9 + - - -
176A TRP 3.7 1.3 - - - -
178A ALA* 1.3 73.8 - - - +
180A PHE* 1.3 64.9 + - - +
182A ALA* 3.1 9.3 + - - +
183A GLY 3.0 17.8 + - - -
271A ILE* 5.4 0.2 - - - -
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Residues in contact with PHE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLY 3.5 20.7 - - - +
27A ASP* 4.1 0.9 - - + -
28A ALA* 4.0 12.8 - - + -
106A THR* 3.7 24.7 - - + -
176A TRP* 2.9 49.0 + + + +
177A VAL* 3.8 3.6 - - + +
179A GLY* 1.3 75.9 - - - +
181A THR* 1.3 59.6 + - + +
183A GLY* 3.1 1.9 + - - -
184A GLU* 2.9 47.2 + - + +
209A ILE* 3.9 32.5 - - + -
211A GLN* 4.2 20.2 - - + -
218A LEU* 5.3 4.5 - - + -
219A MET* 5.3 8.1 - - - -
222A LEU* 5.3 10.1 - - + -
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A VAL* 2.7 34.4 + - + +
178A ALA 2.9 11.8 + - - -
180A PHE* 1.3 74.9 - - + +
182A ALA* 1.3 62.5 + - - +
185A GLY* 2.8 32.9 + - - +
187A PHE* 5.3 2.9 - - - -
207A PHE* 3.9 8.3 - - + -
209A ILE* 3.7 28.3 - - + -
226A LEU* 6.0 0.4 - - + -
265A PHE* 3.2 39.5 - - + -
270A ILE* 3.4 8.4 - - - +
274A LYS* 5.9 1.2 - - - +
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PHE* 3.8 11.4 - - + -
178A ALA 2.9 18.4 + - - +
179A GLY* 3.1 8.9 + - - +
181A THR* 1.3 79.5 + - - +
183A GLY* 1.3 57.6 + - - +
185A GLY 5.6 0.3 - - - +
270A ILE* 4.2 11.0 - - + +
271A ILE* 3.7 44.5 - - + +
274A LYS* 4.7 12.1 - - - +
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Residues in contact with GLY 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PHE* 3.9 12.3 - - - -
28A ALA* 3.9 15.0 - - - -
29A ASP* 4.0 12.1 - - - +
179A GLY 3.0 10.3 + - - -
180A PHE 3.1 3.1 + - - -
181A THR 3.1 0.2 - - - -
182A ALA* 1.3 80.5 - - - +
184A GLU* 1.3 67.4 + - - +
185A GLY 3.6 2.1 + - - +
16C G 3.8 12.8 + - - +
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Residues in contact with GLU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA* 3.1 41.5 - - + +
29A ASP* 3.4 8.1 - - - +
180A PHE* 2.9 29.1 + - + +
183A GLY* 1.3 72.1 - - - -
185A GLY* 1.3 64.3 + - - +
186A SER* 5.1 0.7 - - - -
208A GLN 4.1 0.2 - - - +
209A ILE* 4.0 13.1 - - + -
210A THR* 3.7 29.5 + - - +
211A GLN* 3.0 22.3 + - - +
15C C 4.3 7.0 + - - +
16C G 3.3 37.2 + - - +
17X A 4.1 6.7 + - - -
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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