Contacts of the strand formed by residues 177 - 184 (chain A) in PDB entry 3ADL
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 GLU 177 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LEU 3.6 1.3 + - - +
176A PRO* 1.3 74.1 - - - +
178A TYR* 1.3 63.2 + - - +
179A THR* 4.1 18.2 - - + +
195A THR 3.4 4.0 - - - +
196A CYS* 3.4 1.4 - - - -
197A ARG* 2.8 72.0 + - + +
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Residues in contact with TYR 178 (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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161A VAL* 3.9 17.6 + - + +
164A LEU* 3.4 22.9 - - - +
176A PRO* 3.9 22.5 - - + +
177A GLU* 1.3 76.0 - - - +
179A THR* 1.3 67.9 + - - +
194A MET* 4.0 18.6 - - + +
195A THR 3.2 4.3 - - - -
196A CYS* 3.7 31.9 - - + -
214A LYS* 3.5 57.4 - - + -
217A ALA* 4.5 0.2 - - + -
218A ALA* 3.4 13.2 - - + +
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Residues in contact with THR 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLU* 4.1 22.9 - - + -
178A TYR* 1.3 80.3 - - - +
180A VAL* 1.3 61.2 + - - +
181A THR* 3.3 11.5 + - - +
194A MET* 3.5 6.4 - - - -
195A THR* 2.8 38.0 + - - -
197A ARG* 3.3 30.2 + - - +
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Residues in contact with VAL 180 (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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179A THR* 1.3 72.7 - - - +
181A THR* 1.3 62.5 + - - +
182A GLN 3.8 15.7 - - - +
183A GLU* 4.0 23.6 - - + +
192A PHE* 4.6 7.0 - - + -
193A THR 3.5 13.0 - - - +
194A MET* 3.6 18.8 - - + -
210A LYS* 4.0 31.2 - - + +
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Residues in contact with THR 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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179A THR* 3.3 21.7 + - - +
180A VAL* 1.3 73.4 - - - +
182A GLN* 1.3 63.4 + - - +
193A THR* 3.0 19.6 + - - +
195A THR* 2.8 30.4 + - - +
197A ARG* 4.5 8.3 - - - +
204A ILE* 4.9 0.9 - - - +
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Residues in contact with GLN 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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180A VAL* 3.7 4.1 - - - +
181A THR* 1.3 81.7 + - - +
183A GLU* 1.3 78.9 + - - +
184A SER* 4.3 13.6 + - - +
191A GLU 4.6 0.4 - - - +
192A PHE* 3.5 1.4 - - - -
193A THR* 2.8 54.5 + - + +
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Residues in contact with GLU 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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180A VAL* 4.0 12.2 - - + +
182A GLN* 1.3 83.3 - - - +
184A SER* 1.3 62.0 + - - +
190A LYS* 2.4 39.3 + - - +
191A GLU 3.4 7.4 - - - +
192A PHE* 3.4 30.8 - - + -
210A LYS* 3.9 13.5 + - - -
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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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182A GLN* 4.3 16.3 + - - +
183A GLU* 1.3 74.8 - - - +
185A GLY* 1.3 70.0 + - - +
190A LYS* 3.5 8.9 - - - +
191A GLU* 3.0 42.2 + - - +
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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