Contacts of the helix formed by residues 182 - 193 (chain A) in PDB entry 1BQ4
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 GLY 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ARG* 3.4 41.5 - - - +
8A HIS* 5.7 1.0 + - - -
86A GLU* 3.7 6.5 + - - -
181A HIS* 1.3 73.6 - - - +
183A ASN* 1.3 59.3 + - - +
185A LEU* 3.8 2.7 - - - +
186A ARG* 2.8 33.9 + - - +
205A ILE* 5.0 7.0 + - - +
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Residues in contact with ASN 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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7A ARG* 6.1 0.4 - - - +
86A GLU* 2.9 29.4 + - - +
87A ARG* 3.8 33.1 - - + +
151A LEU* 3.2 17.6 - - + +
154A VAL* 4.6 3.7 - - + +
182A GLY* 1.3 70.3 - - - -
184A SER* 1.3 56.8 + - - +
185A LEU 3.1 1.6 - - - -
186A ARG* 2.4 41.7 + - - -
187A GLY* 2.6 30.1 + - - -
302A BHC 3.1 33.3 + - - +
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Residues in contact with SER 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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84A LEU* 2.8 32.7 + - - -
85A ASN 3.1 13.5 + - - -
86A GLU* 4.2 1.8 + - - +
154A VAL* 4.2 9.6 - - - +
158A LEU* 3.5 26.2 - - - +
180A ALA* 3.3 5.5 - - - +
181A HIS 3.0 22.6 + - - -
183A ASN* 1.3 78.3 - - - +
185A LEU* 1.3 58.5 + - - +
187A GLY* 3.4 1.1 + - - -
188A LEU* 3.0 22.2 + - - +
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Residues in contact with LEU 185 (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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5A LEU* 3.8 42.2 - - + -
6A VAL 4.0 30.1 - - - +
7A ARG* 4.0 12.8 - - + +
84A LEU* 5.6 1.8 - - + -
178A ILE* 4.5 15.7 - - + -
180A ALA* 4.3 11.0 - - + +
181A HIS 3.0 19.4 + - - +
182A GLY* 4.1 2.2 - - - +
184A SER* 1.3 78.3 + - - +
186A ARG* 1.3 59.6 + - - +
187A GLY 3.2 0.2 - - - -
188A LEU* 3.7 7.5 - - + +
189A VAL* 2.8 39.8 + - - +
205A ILE* 3.9 19.5 - - + -
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Residues in contact with ARG 186 (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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87A ARG* 4.7 2.4 - - - +
113A ARG 4.5 3.8 + - - -
114A ARG* 3.5 47.1 + - - +
115A SER 5.7 1.0 + - - -
116A PHE* 6.2 0.4 - - - +
151A LEU* 3.8 38.6 - - + +
182A GLY 2.8 21.4 + - - +
183A ASN* 2.4 44.2 + - - +
185A LEU* 1.3 75.6 - - - +
187A GLY* 1.3 64.4 + - - +
189A VAL* 3.2 2.4 + - - +
190A LYS* 3.1 22.3 + - - +
200A ILE* 3.8 14.0 + - + +
201A ALA* 3.2 33.5 - - - +
203A LEU* 3.8 37.4 + - + +
204A ASN* 5.3 2.2 - - - +
205A ILE* 4.3 5.3 - - + +
302A BHC 4.5 0.8 + - - -
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Residues in contact with GLY 187 (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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151A LEU* 3.6 3.8 - - - +
154A VAL* 5.9 0.7 - - - -
155A ILE* 3.6 38.5 - - - +
158A LEU* 5.5 2.2 - - - -
183A ASN 2.6 21.7 + - - -
184A SER* 3.6 2.9 - - - -
186A ARG* 1.3 76.0 - - - +
188A LEU* 1.3 61.3 + - - +
190A LYS* 3.3 14.7 - - - +
191A HIS* 3.3 7.6 + - - +
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Residues in contact with LEU 188 (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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3A LEU* 4.7 1.6 - - + -
5A LEU* 4.1 15.5 - - + -
84A LEU* 5.8 2.0 - - + -
155A ILE* 6.0 0.2 - - - -
158A LEU* 4.3 20.9 - - + +
162A TRP* 4.0 35.0 - - + -
166A ILE* 5.7 1.1 - - + -
178A ILE* 3.7 29.6 - - + -
184A SER 3.0 16.6 + - - +
185A LEU* 3.5 9.4 + - + +
186A ARG 3.3 0.2 - - - -
187A GLY* 1.3 73.8 - - - +
189A VAL* 1.3 60.7 + - - +
191A HIS* 3.4 13.0 + - + -
192A LEU* 3.0 47.2 + - + +
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Residues in contact with VAL 189 (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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5A LEU* 3.9 21.3 - - + -
185A LEU 2.8 25.5 + - - +
186A ARG 3.2 2.7 + - - +
188A LEU* 1.3 73.4 - - - +
190A LYS* 1.3 53.6 + - - +
192A LEU* 3.8 4.9 - - + +
193A GLU* 2.7 59.6 + - - +
195A ILE* 4.4 3.1 - - + -
203A LEU* 4.2 24.0 - - + -
205A ILE* 3.8 17.9 - - + -
211A LEU* 4.1 5.2 - - + -
213A PHE* 4.0 13.5 - - + -
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Residues in contact with LYS 190 (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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116A PHE* 3.5 29.4 - - + -
155A ILE* 3.6 21.8 - - + -
186A ARG 3.1 10.7 + - - +
187A GLY 3.3 9.9 - - - +
189A VAL* 1.3 75.8 - - - +
191A HIS* 1.3 55.6 + - - +
194A GLY* 2.8 33.1 + - - -
195A ILE* 2.7 49.3 + - + +
197A ASP* 3.1 28.7 + - - +
200A ILE* 3.5 36.2 - - + +
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Residues in contact with HIS 191 (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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155A ILE* 5.0 5.1 - - + +
159A LEU* 3.1 46.0 - - + +
162A TRP* 3.5 26.3 + + - -
163A GLN* 5.3 3.1 - - - -
187A GLY 3.3 9.3 + - - +
188A LEU* 3.7 16.8 - - + +
190A LYS* 1.3 81.1 - - - +
192A LEU* 1.3 65.9 + - + +
194A GLY* 3.9 5.4 + - - -
141C ASP* 4.2 10.3 + - - -
143C ASN* 5.6 9.4 + - + -
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Residues in contact with LEU 192 (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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3A LEU* 3.9 25.6 - - + -
5A LEU* 5.4 0.9 - - + -
162A TRP* 3.4 34.3 - - + +
188A LEU* 3.0 33.3 + - + +
189A VAL* 3.8 3.1 - - - +
191A HIS* 1.3 81.1 - - + +
193A GLU* 1.3 61.8 + - - +
194A GLY 3.8 0.2 + - - -
213A PHE* 3.9 35.0 - - + -
215A LEU* 4.0 6.7 - - + -
219A LEU 3.7 17.3 - - - +
220A LYS* 5.2 1.9 - - - +
221A PRO* 3.5 22.3 - - + +
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Residues in contact with GLU 193 (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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189A VAL* 2.7 29.5 + - - +
192A LEU* 1.3 75.0 - - - +
194A GLY* 1.3 62.9 + - - +
195A ILE* 3.6 27.0 - - + +
203A LEU* 5.5 1.9 - - - +
213A PHE* 3.0 32.3 - - + -
221A PRO* 4.9 8.0 - - + +
224A PRO* 5.9 0.8 - - - +
225A SER* 3.9 11.4 + - - -
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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