Contacts of the helix formed by residues 177 - 191 (chain A) in PDB entry 1BRW
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 ILE 177 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A THR* 6.1 0.4 - - - +
176A SER* 1.3 68.4 - - - +
178A PRO* 1.3 70.8 - - + +
180A ILE* 3.1 3.3 + - - +
181A ALA* 2.8 29.8 + - - +
208A MET* 3.6 26.2 - - + +
213A GLU* 3.5 27.6 - - + +
216A ARG* 3.7 45.8 - - + +
217A LEU* 3.9 24.2 - - + +
220A VAL* 4.5 11.7 - - + -
6002A MES 5.0 3.4 + - - +
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Residues in contact with PRO 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 4.1 9.6 - - + -
49A GLY* 4.2 4.0 - - - -
50A MET* 3.7 55.9 - - + +
55A THR* 3.7 17.2 - - + +
58A LEU* 4.3 1.8 - - - +
176A SER* 3.3 12.3 - - - +
177A ILE* 1.3 97.6 - - + +
179A LEU* 1.3 58.7 + - + +
182A SER* 3.0 32.3 + - - -
6002A MES 4.3 9.4 - - - +
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA* 4.4 24.7 - - + +
45A ILE* 4.2 21.8 - - + -
58A LEU* 4.0 21.3 - - + -
164A LEU* 4.5 17.9 - - + +
168A ARG* 3.5 33.4 + - + +
173A THR 3.5 22.7 - - - +
176A SER* 3.2 23.8 + - - +
178A PRO* 1.3 74.7 - - - +
180A ILE* 1.3 59.4 + - - +
182A SER* 3.6 4.7 + - - +
183A SER* 3.1 26.3 + - - -
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Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 5.2 5.4 - - + +
168A ARG* 3.8 6.5 - - - +
174A VAL 3.6 13.7 - - - +
175A ASN* 4.0 0.7 - - - +
176A SER 2.9 27.9 + - - +
177A ILE 3.8 2.7 - - - +
179A LEU* 1.3 74.9 - - - +
181A ALA* 1.3 67.4 + - - +
183A SER* 3.3 3.2 + - - -
184A ILE* 3.1 42.9 + - + +
207A PHE* 3.6 42.0 - - + -
208A MET* 3.9 17.3 - - + -
217A LEU* 4.1 21.1 - - + -
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 4.0 10.5 - - + -
59A THR* 4.7 0.7 - - - -
177A ILE 2.8 16.9 + - - +
178A PRO 4.0 2.9 - - - +
180A ILE* 1.3 78.1 - - - +
182A SER* 1.3 57.7 + - - +
183A SER 3.3 0.2 + - - -
184A ILE* 3.9 0.5 - - - +
185A MET* 3.0 36.6 + - - +
217A LEU* 4.0 3.3 - - + +
220A VAL* 3.9 20.4 - - + -
221A MET* 3.8 28.5 - - + -
224A ILE* 4.5 2.9 - - + -
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 4.2 3.4 - - - -
58A LEU* 3.5 18.3 - - - +
59A THR* 3.3 24.5 + - - +
62A MET* 3.1 27.4 - - - +
164A LEU* 5.8 0.7 - - - +
178A PRO 3.0 18.0 + - - -
179A LEU* 3.6 7.4 + - - +
181A ALA* 1.3 79.9 - - - +
183A SER* 1.3 60.4 + - - +
186A SER* 3.0 31.9 + - - -
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Residues in contact with SER 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A MET* 4.7 2.5 - - - -
161A ASP* 2.9 27.8 + - - +
165A TYR* 5.2 3.8 - - - +
168A ARG* 3.9 12.8 + - - -
179A LEU 3.1 19.2 + - - -
180A ILE* 3.3 6.4 + - - -
181A ALA 3.2 0.4 - - - -
182A SER* 1.3 81.0 + - - +
184A ILE* 1.3 63.5 + - - +
186A SER* 3.0 16.3 + - - -
187A LYS* 3.4 27.1 + - - +
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A HIS* 3.9 29.8 - - + +
83A SER 4.3 0.9 - - - +
84A THR* 4.0 39.0 - - + +
180A ILE* 3.1 28.5 + - + +
181A ALA 4.1 2.0 - - - +
183A SER* 1.3 80.3 - - - +
185A MET* 1.3 62.6 + - - +
187A LYS* 3.3 13.7 + - - +
188A LYS* 3.2 26.4 + - + +
198A LEU* 4.4 15.7 - - + -
221A MET* 4.1 17.9 - - + -
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Residues in contact with MET 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR* 4.0 5.2 - - + -
181A ALA 3.0 19.7 + - - +
184A ILE* 1.3 74.9 - - - +
186A SER* 1.3 67.1 + - - +
188A LYS* 4.4 7.2 - - - +
189A ILE* 3.0 33.4 + - + +
196A ILE* 4.4 15.0 - - + -
198A LEU* 4.2 19.1 - - - -
221A MET* 3.3 48.0 - - + +
224A ILE* 3.8 23.6 - - + -
225A GLY* 3.8 21.5 - - - +
232A THR* 4.1 14.4 - - + +
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Residues in contact with SER 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR* 3.6 20.3 - - - +
62A MET* 4.0 14.1 - - - +
63A VAL* 3.7 15.0 - - - +
158A THR* 3.6 12.0 - - - +
161A ASP* 4.1 9.2 - - - +
182A SER 3.0 22.7 + - - -
183A SER* 3.0 10.0 + - - -
185A MET* 1.3 76.7 - - - +
187A LYS* 1.3 63.7 + - - +
190A ALA* 3.2 30.0 + - - +
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Residues in contact with LYS 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A HIS* 5.3 7.6 - - - -
109A MET* 5.7 0.3 - - - +
153A GLN* 3.3 42.6 - - + +
157A LEU* 4.8 6.0 - - + +
158A THR* 3.8 15.7 - - - +
161A ASP* 3.2 26.0 + - - +
183A SER* 3.4 26.0 + - - +
184A ILE* 3.3 13.5 + - - +
185A MET 3.1 0.6 - - - -
186A SER* 1.3 79.8 + - - +
188A LYS* 1.3 68.0 + - - +
190A ALA* 3.6 3.8 + - - +
191A ALA* 3.0 28.8 + - - +
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Residues in contact with LYS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP* 3.0 42.2 + - - +
81A LYS 3.7 1.2 + - - -
82A HIS* 3.2 44.0 - - + -
109A MET* 3.6 18.4 + - - +
184A ILE* 3.2 26.9 + - + +
185A MET* 3.3 8.7 + - - +
187A LYS* 1.3 80.9 - - - +
189A ILE* 1.3 66.1 + - + +
191A ALA* 3.3 13.4 + - - +
192A GLY* 3.6 7.3 + - - -
193A ALA 4.4 5.7 + - - +
196A ILE* 3.8 40.4 - - + +
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Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR* 4.4 4.5 - - + -
60A MET* 4.1 12.3 - - + -
63A VAL* 4.2 19.1 - - + -
68A MET* 3.8 7.3 - - + +
185A MET* 3.0 31.1 + - + +
186A SER 4.2 2.2 - - - +
188A LYS* 1.3 76.7 - - - +
190A ALA* 1.3 63.0 + - - +
191A ALA 3.4 0.5 + - - -
192A GLY* 3.4 7.4 + - - -
196A ILE* 5.0 2.2 - - + -
224A ILE* 4.0 26.0 - - + +
225A GLY* 4.9 0.7 - - - -
228A VAL* 3.7 27.8 - - + -
230A ARG* 2.9 52.5 + - + +
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Residues in contact with ALA 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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63A VAL* 4.7 7.8 - - + +
67A GLU 4.0 15.0 - - - +
68A MET* 3.8 11.6 - - - +
69A LEU* 2.9 29.6 + - - +
157A LEU* 3.9 15.7 - - + +
158A THR* 4.0 16.6 - - + -
186A SER 3.2 20.2 + - - +
187A LYS 4.0 3.6 - - - +
189A ILE* 1.3 77.0 - - - +
191A ALA* 1.3 58.5 + - - +
192A GLY 3.2 0.6 + - - -
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Residues in contact with ALA 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.4 19.9 - - - +
71A LEU* 3.5 15.2 - - - +
80A ASP* 4.2 15.5 - - - +
107A ALA 5.9 0.9 - - - +
109A MET* 4.4 22.0 - - + -
139A PHE* 5.3 2.7 - - + -
157A LEU* 4.1 8.7 - - + -
187A LYS 3.0 18.7 + - - +
188A LYS* 3.6 11.0 - - - +
189A ILE 3.2 0.8 - - - -
190A ALA* 1.3 78.3 - - - +
192A GLY* 1.3 56.8 + - - +
193A ALA 3.6 1.1 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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