Contacts of the strand formed by residues 182 - 188 (chain A) in PDB entry 3DB3
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 VAL 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A GLU* 5.8 4.9 - - + -
132A LEU 5.5 0.7 - - - -
133A GLY* 4.5 12.6 - - - +
134A LEU* 4.3 15.5 - - + -
159A VAL* 3.2 34.8 - - + -
160A THR 3.2 10.8 - - - +
161A ARG* 4.8 5.4 - - + +
162A LYS 4.6 0.9 - - - +
180A GLU* 3.5 18.8 - - - +
181A ASP* 1.3 81.0 - - - +
183A ILE* 1.3 72.3 + - - +
184A TYR* 4.1 12.6 - - + +
200A ASN* 4.5 1.2 + - - -
201A SER* 3.5 24.4 + - - -
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Residues in contact with ILE 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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159A VAL* 3.6 3.6 - - - -
160A THR* 2.9 43.3 + - - +
162A LYS* 3.6 31.4 - - + +
181A ASP 5.1 0.2 - - - +
182A VAL* 1.3 79.3 - - - +
184A TYR* 1.3 70.3 + - - +
185A HIS* 3.9 16.9 - - - +
198A GLN* 4.1 26.0 - - + +
199A MSE 3.4 12.6 - - - +
200A ASN* 4.3 19.5 - - + +
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Residues in contact with TYR 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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134A LEU* 2.5 40.1 + - + +
135A TYR* 3.0 44.7 + + + -
156A VAL* 4.1 19.1 - - + -
158A ARG 3.9 0.7 - - - -
159A VAL* 3.8 18.8 - - + -
182A VAL* 4.1 9.5 - - + +
183A ILE* 1.3 73.5 - - - +
185A HIS* 1.3 62.3 + - - +
186A VAL* 3.9 10.1 - - + -
197A VAL 3.4 0.9 - - - +
198A GLN* 3.4 2.6 - - - -
199A MSE 2.6 51.4 + - + +
201A SER* 3.7 32.8 - - - -
204A VAL* 3.7 23.1 - - + -
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Residues in contact with HIS 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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127A TRP* 4.1 17.9 + - + -
156A VAL* 3.6 2.4 - - - -
157A VAL* 2.7 33.7 + - + -
158A ARG* 2.8 48.6 + - + +
160A THR* 2.9 36.6 + - + +
183A ILE* 3.9 9.8 - - + +
184A TYR* 1.3 72.3 - - - +
186A VAL* 1.3 55.1 + - - +
196A VAL* 3.8 20.3 - - + +
197A VAL 3.5 2.7 - - - -
198A GLN* 3.3 42.8 - - + +
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Residues in contact with VAL 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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141A VAL* 4.5 11.4 - - + -
143A ALA* 4.0 13.7 - - + -
154A ALA* 3.7 21.1 - - + -
155A GLN 3.4 12.1 - - - +
156A VAL* 4.2 13.0 - - + -
157A VAL* 4.1 2.2 - - - -
184A TYR* 4.3 11.4 - - + -
185A HIS* 1.3 77.1 - - - +
187A LYS* 1.3 64.8 + - - +
188A TYR* 4.7 8.9 - - + +
195A GLY 3.9 0.7 - - - +
196A VAL* 3.4 5.2 - - - +
197A VAL* 2.8 34.1 + - + +
199A MSE 3.8 25.8 - - + -
204A VAL* 4.7 3.4 - - + -
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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
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138A ASN* 5.9 0.4 + - - -
154A ALA* 3.2 5.1 - - - +
155A GLN* 2.8 69.1 + - + +
157A VAL* 3.7 29.6 - - + +
186A VAL* 1.3 76.3 - - - +
188A TYR* 1.3 64.4 + - - +
189A ASP* 5.6 1.1 - - - +
192A PRO* 6.2 2.7 - - + -
195A GLY 3.9 14.1 - - - +
196A VAL* 4.6 6.1 - - + -
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Residues in contact with TYR 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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143A ALA* 4.0 19.3 - - + -
145A ASP* 4.0 27.4 + - - -
152A PHE* 3.7 32.5 - + + -
153A GLU 3.8 2.7 - - - +
154A ALA* 4.0 9.4 - - + -
186A VAL* 4.8 6.5 - - + -
187A LYS* 1.3 79.2 - - - +
189A ASP* 1.3 66.6 + - - +
191A TYR* 3.6 36.7 + - + +
192A PRO* 4.1 4.5 - - - +
194A ASN* 4.3 17.5 - - + -
195A GLY 4.6 3.6 + - - -
197A VAL* 4.4 25.7 - - + +
199A MSE 4.3 13.3 - - - -
9B M3L 3.8 27.6 - - - -
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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