Contacts of the helix formed by residues 186 - 193 (chain A) in PDB entry 3BMW
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 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A PHE 3.4 4.2 - - - -
185A SER* 1.3 83.6 + - - +
187A TYR* 1.3 64.4 + - - +
188A GLU* 3.6 8.5 + - - +
189A ASP* 3.1 24.4 + - - +
190A GLY* 3.1 19.9 + - - -
625A GLN* 4.3 11.8 + - - -
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Residues in contact with TYR 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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186A SER* 1.3 72.3 - - - +
188A GLU* 1.3 63.3 + - - +
190A GLY* 3.3 3.5 + - - -
191A ILE* 3.2 37.4 + - + +
233A LYS* 3.8 15.7 - - + +
235A MET 4.6 2.6 + - - -
237A PHE* 3.8 17.0 + - + +
259A TRP* 3.4 40.2 - + - -
267A ASP* 6.0 0.4 - - - -
269A ASN* 3.5 39.7 + - + +
272A TYR* 6.1 0.7 - - - -
273A PHE* 4.8 1.6 - - - +
623A PHE* 3.8 18.2 - + + -
635A TYR* 4.3 5.8 - - - -
706A GOL 3.1 31.5 + - - -
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Residues in contact with GLU 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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186A SER* 3.3 8.1 + - - +
187A TYR* 1.3 79.8 - - - +
189A ASP* 1.3 63.8 + - - +
191A ILE 3.1 9.9 + - - -
192A TYR* 3.2 16.7 + - + +
623A PHE* 3.4 49.0 - - + +
624A ASN* 3.2 15.4 + - - +
625A GLN* 2.9 29.9 + - - +
626A VAL* 2.8 25.4 + - + +
634A TYR* 2.6 25.7 + - - +
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Residues in contact with ASP 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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181A GLY 5.0 0.2 - - - +
182A THR* 2.6 29.5 + - - -
183A ASP* 3.1 28.2 + - - +
184A PHE 3.9 0.2 + - - -
185A SER* 4.1 4.0 + - - +
186A SER* 3.1 28.8 + - - +
188A GLU* 1.3 76.8 - - - +
190A GLY* 1.3 60.3 + - - +
193A ARG* 3.0 58.4 + - - +
625A GLN* 5.3 3.7 + - - +
626A VAL* 4.8 4.0 - - + -
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Residues in contact with GLY 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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182A THR* 3.3 17.7 + - - -
184A PHE* 5.3 2.7 - - - -
186A SER 3.1 14.5 + - - -
187A TYR 3.3 4.2 + - - -
188A GLU 3.2 0.2 - - - -
189A ASP* 1.3 75.8 - - - +
191A ILE* 1.3 60.6 + - - +
193A ARG 4.1 7.5 - - - +
233A LYS 4.4 2.0 - - - -
234A HIS* 2.8 39.5 + - - +
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Residues in contact with ILE 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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177A HIS* 4.3 3.1 + - + -
187A TYR* 3.3 33.2 - - + +
188A GLU 3.1 1.6 + - - +
190A GLY* 1.3 80.0 - - - +
192A TYR* 1.3 84.9 + - + +
193A ARG 3.5 1.1 - - - -
200A ASP* 3.2 3.8 - - - +
233A LYS 3.6 15.3 - - - +
234A HIS 3.1 3.9 - - - +
235A MET 3.8 11.0 - - - +
236A PRO* 3.6 29.8 - - + -
623A PHE* 3.8 15.7 - - + -
698A CA 2.5 26.0 - - - -
706A GOL 3.5 25.1 - - - +
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Residues in contact with TYR 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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177A HIS* 3.3 47.5 - + - +
179A TYR* 3.3 10.2 - - + +
188A GLU* 3.2 17.8 + - + +
191A ILE* 1.3 96.3 - - + +
193A ARG* 1.3 62.8 + - - +
200A ASP* 4.1 1.8 - - - -
236A PRO* 3.9 3.8 - - + +
587A ARG* 3.6 21.5 - - - -
623A PHE* 3.6 24.0 - + - -
626A VAL* 3.7 21.1 - - + -
627A VAL* 3.6 18.6 - - + -
634A TYR* 3.7 19.2 - + - -
636A ASP* 2.7 23.8 + - - -
706A GOL 2.8 18.0 + - - -
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Residues in contact with ARG 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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177A HIS* 5.4 0.2 - - - -
179A TYR* 2.6 49.4 + - + +
180A GLY 3.6 8.7 - - - +
181A GLY 3.6 14.6 - - - -
182A THR* 3.6 10.6 - - - +
189A ASP* 3.0 44.3 + - - +
190A GLY 4.1 12.5 - - - +
191A ILE 4.1 0.2 - - - +
192A TYR* 1.3 82.2 - - - +
194A ASN* 1.3 66.7 + - - +
195A LEU 3.6 2.1 + - - -
200A ASP* 3.8 11.4 - - - +
625A GLN* 5.1 7.3 + - - +
626A VAL* 3.6 29.2 - - + +
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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