Contacts of the helix formed by residues 186 - 192 (chain A) in PDB entry 3SPH
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 ARG 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A VAL* 3.4 25.3 + - + -
76A ASP* 3.7 17.0 + - - +
79A TRP* 5.3 1.8 - - - -
182A ALA 4.0 4.5 - - - +
183A LYS* 2.8 51.3 + - - +
184A MET 3.4 4.7 + - - +
185A ALA* 1.3 76.5 - - - +
187A PRO* 1.3 70.9 - - + +
188A LYS* 3.3 25.8 - - + +
189A LYS* 3.4 34.5 - - + +
190A ARG 4.7 0.2 + - - -
308A MET* 5.3 0.4 - - - -
400A PIO 2.9 44.3 + - - -
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Residues in contact with PRO 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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185A ALA 3.2 7.1 - - - +
186A ARG* 1.3 86.6 - - + +
188A LYS* 1.3 58.5 + - + +
189A LYS 3.0 6.1 - - - -
190A ARG* 3.1 18.7 + - + +
303A VAL* 4.3 10.1 - - + -
306A THR* 5.6 0.4 - - - +
308A MET* 3.6 52.0 - - + +
309A THR 3.8 15.7 - - - +
310A THR* 2.8 20.7 + - - -
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Residues in contact with LYS 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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76A ASP* 4.9 8.5 + - - +
186A ARG* 3.7 37.9 - - + +
187A PRO* 1.3 82.7 - - + +
189A LYS* 1.3 73.5 + - + +
190A ARG 3.2 0.2 - - - -
191A ALA* 3.3 19.3 + - - +
192A GLN* 4.5 5.2 + - - +
310A THR* 3.6 9.4 - - - +
311A GLN 6.1 0.7 - - - +
313A ARG* 6.3 0.9 - - - +
400A PIO 3.6 16.4 + - - -
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Residues in contact with LYS 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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184A MET 5.9 1.8 - - - +
186A ARG* 3.4 34.3 - - + +
187A PRO 3.0 0.4 - - - -
188A LYS* 1.3 90.1 - - + +
190A ARG* 1.3 63.1 + - - +
191A ALA 3.3 0.9 + - - -
192A GLN* 3.3 33.4 + - - +
193A THR* 4.5 1.7 + - - +
400A PIO 3.3 65.2 + - - -
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Residues in contact with ARG 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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187A PRO* 3.1 16.6 + - + +
189A LYS* 1.3 75.1 - - - +
191A ALA* 1.3 54.9 + - - +
192A GLN 2.9 9.3 + - - -
193A THR* 2.6 57.1 + - - -
194A LEU* 3.2 30.8 + - + +
217A ASN* 2.7 35.9 + - - +
219A ARG* 3.9 23.3 - - - +
221A SER* 3.5 19.0 + - - -
222A HIS 4.4 6.9 + - - -
223A LEU* 4.5 10.1 - - + +
303A VAL* 3.5 34.2 - - + +
310A THR* 4.2 11.0 - - + -
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Residues in contact with ALA 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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188A LYS* 3.3 16.3 + - - +
189A LYS 3.1 1.2 - - - -
190A ARG* 1.3 77.7 - - - +
192A GLN* 1.3 60.9 + - + +
193A THR 3.4 0.4 - - - -
194A LEU* 3.5 29.4 + - + +
310A THR* 3.8 15.4 + - - +
311A GLN 4.2 8.5 - - - +
312A ALA* 4.1 19.8 - - + +
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Residues in contact with GLN 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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188A LYS 4.5 4.8 + - - +
189A LYS* 3.3 35.1 - - - +
190A ARG 2.9 0.6 - - - -
191A ALA* 1.3 80.7 - - + +
193A THR* 1.3 61.5 + - + +
194A LEU 3.3 7.3 - - - +
218A LEU* 4.2 8.1 - - - +
400A PIO 3.9 19.5 + - - -
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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