Contacts of the helix formed by residues 180 - 190 (chain A) in PDB entry 1B70
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 SER 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A LEU* 3.8 16.2 - - - +
178A HIS* 3.3 26.2 + - - -
179A THR* 1.3 76.9 - - - +
181A PRO* 1.3 71.0 - - - +
183A GLN* 2.7 31.2 + - - +
184A VAL 3.8 0.2 + - - -
220A GLU* 2.6 30.4 + - - -
260A PHE* 3.7 12.3 - - - -
352A PHE 3.6 6.6 + - - -
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Residues in contact with PRO 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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128A GLU* 3.8 22.7 - - + +
132A PHE* 3.4 32.6 - - + +
133A ASN* 3.9 13.7 - - - +
137A LEU* 4.0 2.9 - - + -
176A ARG* 4.4 8.3 - - + +
178A HIS* 3.2 36.1 - - + +
179A THR* 4.0 1.8 - - - -
180A SER* 1.3 89.0 - - - +
182A MET* 1.3 62.2 + - - +
184A VAL* 2.8 18.3 + - + +
185A ARG* 3.2 14.2 + - - +
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Residues in contact with MET 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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122A VAL* 4.5 12.3 - - + -
123A GLU* 2.9 31.9 - - - +
124A GLY* 3.8 16.8 - - - +
125A PRO* 6.1 0.4 - - - +
176A ARG* 5.6 2.2 - - - +
179A THR* 3.0 15.6 + - - +
180A SER 2.9 0.2 + - - -
181A PRO* 1.3 77.9 - - - +
183A GLN* 1.3 63.7 + - - +
185A ARG* 3.9 24.9 - - + +
186A TYR* 2.9 39.1 + - + +
196A ILE* 5.6 0.4 - - - -
198A VAL* 3.6 38.6 - - + -
220A GLU* 6.0 0.2 - - + -
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Residues in contact with GLN 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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137A LEU* 4.7 6.9 - - + +
179A THR 4.2 0.4 + - - -
180A SER* 2.7 28.9 + - - +
182A MET* 1.3 72.8 - - - +
184A VAL* 1.3 63.8 + - + +
186A TYR* 3.8 3.5 - - - +
187A MET* 3.0 37.4 + - + +
196A ILE* 5.2 2.9 - - - -
198A VAL* 5.6 0.8 - - - +
220A GLU* 2.5 42.2 + - + +
222A LEU* 3.8 34.3 - - + +
260A PHE* 4.6 15.6 - - - +
261A VAL* 5.5 0.5 - - - +
286A VAL* 4.7 7.4 - - - +
290A VAL* 5.4 3.2 - - + +
314A ALA* 3.7 24.6 - - - +
352A PHE* 4.5 2.2 - - - -
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Residues in contact with VAL 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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131A PHE* 5.6 1.3 - - + -
132A PHE* 3.7 28.0 - - + +
136A ALA* 3.7 27.6 - - + -
137A LEU* 3.9 22.2 - - + -
181A PRO 2.8 11.8 + - - +
183A GLN* 1.3 72.7 - - + +
185A ARG* 1.3 69.2 + - - +
186A TYR 3.0 1.3 - - - -
187A MET* 2.8 20.4 + - - +
188A VAL* 2.9 23.8 + - + +
290A VAL* 4.6 12.8 - - + -
293A ALA* 6.1 0.9 - - + -
294A VAL* 4.5 11.9 - - + +
297A TYR* 6.4 0.9 - - + -
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Residues in contact with ARG 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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125A PRO* 3.8 22.7 - - - +
128A GLU* 2.8 41.6 + - - -
132A PHE* 4.0 25.4 - - + -
161A LEU* 4.1 9.9 - - - +
162A GLU 2.8 30.5 + - - -
163A GLY 3.5 18.6 + - - -
164A PRO* 3.4 24.4 - - + +
181A PRO 3.2 8.9 + - - +
182A MET* 3.9 30.3 - - + +
184A VAL* 1.3 75.4 - - - +
186A TYR* 1.3 62.8 + - - +
188A VAL 3.5 0.2 + - - -
189A ALA* 3.1 24.9 + - - +
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Residues in contact with TYR 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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120A GLN* 5.6 0.2 + - - -
122A VAL* 4.4 13.5 - - + -
182A MET* 2.9 28.7 + - + +
183A GLN 3.8 3.4 - - - +
184A VAL 2.8 3.2 + - - -
185A ARG* 1.3 74.8 - - - +
187A MET* 1.3 57.1 + - - +
189A ALA* 3.2 1.5 + - - -
190A HIS* 2.9 66.4 + + + +
194A PHE* 3.7 40.2 - + - +
196A ILE* 3.7 35.9 - - + +
485B ASN* 2.7 32.7 + - - +
488B VAL* 3.5 30.8 - - + +
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Residues in contact with MET 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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183A GLN* 3.0 39.0 + - + +
184A VAL* 2.8 14.0 + - - +
186A TYR* 1.3 73.8 - - - +
188A VAL* 1.3 64.7 + - - +
190A HIS 3.0 10.6 - - - +
194A PHE* 3.9 14.4 - - + -
222A LEU* 4.0 16.8 - - + -
224A VAL* 4.6 2.0 - - - -
286A VAL* 5.3 2.2 - - + -
290A VAL* 4.5 12.3 - - + -
291A PHE* 3.7 34.1 - - + -
294A VAL* 3.6 24.5 - - + -
298A ARG* 3.3 0.3 + - - -
307A TYR* 2.9 43.5 + - + +
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Residues in contact with VAL 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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132A PHE* 5.1 0.4 - - + -
164A PRO* 3.6 24.5 - - + -
165A LEU* 4.9 5.2 - - + +
184A VAL* 2.9 26.7 + - + +
185A ARG 3.8 7.2 - - - +
187A MET* 1.3 76.3 - - - +
189A ALA* 1.3 58.0 + - - +
294A VAL* 3.6 27.6 - - + +
297A TYR* 3.8 29.8 - - + -
298A ARG* 2.6 36.3 + - + +
301A LEU* 4.4 10.5 - - + -
303A LEU* 4.6 6.1 - - + +
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Residues in contact with ALA 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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164A PRO* 4.2 21.1 - - + +
165A LEU* 4.5 14.3 - - + +
185A ARG 3.1 15.9 + - - +
188A VAL* 1.3 81.3 - - - +
190A HIS* 1.3 83.4 + - + +
298A ARG* 4.6 0.9 - - - -
484B ASP* 4.6 1.7 - - - +
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Residues in contact with HIS 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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186A TYR* 2.9 64.1 + + + +
187A MET 3.0 5.8 + - - +
188A VAL 3.4 0.4 - - - -
189A ALA* 1.3 96.9 + - + +
191A THR* 1.3 64.5 + - - +
298A ARG* 3.3 13.9 + - - -
306A ALA* 4.6 0.2 - - - +
307A TYR* 2.9 19.4 + - - +
484B ASP* 3.2 36.1 + - + +
485B ASN* 3.5 14.4 - - - +
488B VAL* 4.1 9.4 - - + +
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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