Contacts of the strand formed by residues 179 - 184 (chain N) in PDB entry 1A14
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 179 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134N LEU* 3.9 2.8 - - - +
177N GLY 3.6 1.3 - - - -
178N TRP* 1.3 103.3 + - - +
180N SER* 1.3 63.2 + - - +
193N CYS* 3.5 1.6 - - - +
194N ILE* 2.8 37.2 + - - +
224N ARG* 3.5 4.5 - - - +
225N THR* 2.9 27.5 + - - -
227N GLU* 2.7 23.4 + - - -
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Residues in contact with SER 180 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121N TYR* 3.3 11.8 + - - -
134N LEU* 4.2 10.6 - - - +
158N LEU* 3.0 36.6 - - - +
179N SER* 1.3 78.1 + - - +
181N THR* 1.3 58.7 + - - +
192N ILE 2.9 18.6 - - - -
193N CYS* 4.2 2.2 - - - -
225N THR* 3.3 10.4 - - - +
227N GLU* 2.8 38.2 + - - -
228N SER 4.0 0.2 + - - -
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Residues in contact with THR 181 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121N TYR* 3.4 6.9 + - - -
158N LEU* 4.2 1.6 - - - +
180N SER* 1.3 75.5 - - - +
182N SER* 1.3 72.0 + - - +
192N ILE* 2.8 58.8 + - + +
225N THR* 3.4 24.5 - - + +
226N GLN* 4.2 7.8 + - - +
228N SER 2.8 21.8 + - - -
229N GLU 3.8 0.7 - - - -
230N CYS* 3.6 19.6 + - - +
239N VAL* 4.0 6.3 - - + -
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Residues in contact with SER 182 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121N TYR* 3.6 15.4 + - - -
132N TYR* 4.4 7.3 - - - -
158N LEU* 4.6 1.8 - - - -
181N THR* 1.3 81.9 + - - +
183N CYS* 1.3 58.8 + - - +
189N ARG* 3.1 26.5 + - - -
190N MET 2.9 14.2 + - - -
191N SER* 2.8 25.7 + - - +
192N ILE* 5.9 0.2 - - - -
228N SER 3.9 1.2 + - - -
229N GLU* 3.0 28.6 - - - +
230N CYS* 3.1 6.1 + - - -
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Residues in contact with CYS 183 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123N SER* 4.4 2.2 - - - -
182N SER* 1.3 74.0 + - - +
184N HIS* 1.3 66.3 + - - +
185N ASP* 3.9 0.5 + - - +
189N ARG* 3.4 10.7 - - - +
190N MET* 2.8 44.8 + - - +
229N GLU* 4.9 2.0 - - + +
230N CYS* 2.0 62.8 - - - +
231N VAL* 4.9 0.4 - - - -
232N CYS* 3.5 23.9 - - - -
237N CYS* 4.1 0.4 - - - -
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Residues in contact with HIS 184 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82N ARG* 4.9 2.9 + - - -
123N SER* 5.1 0.2 + - - -
124N CYS 3.3 19.7 + - - +
125N ASP* 3.0 27.9 - - - -
126N PRO* 3.1 36.2 - - + +
183N CYS* 1.3 77.4 - - - +
185N ASP* 1.3 59.2 + - - +
186N GLY 3.1 16.2 + - - -
187N LYS 3.5 10.2 + - - -
188N THR* 2.9 44.2 + - - -
189N ARG* 3.3 16.1 - - + +
232N CYS* 4.0 10.7 + - - +
412N TRP* 3.5 18.1 + - - -
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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
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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