Contacts of the helix formed by residues 205 - 215 (chain A) in PDB entry 4BOS
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 THR 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A GLU* 4.1 22.0 - - - +
202A LEU* 4.5 0.4 - - - -
204A LYS* 1.3 76.7 - - - +
206A ASN* 1.3 65.7 + - - +
207A GLN* 3.6 8.6 + - - +
208A GLU* 2.8 51.1 + - - +
209A TYR* 2.9 22.3 + - - +
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Residues in contact with ASN 206 (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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190A VAL* 2.9 29.4 + - - +
191A ALA* 3.2 24.5 - - - +
194A PRO* 3.5 23.4 - - + +
197A TYR* 3.3 23.8 + - - +
199A GLU 5.6 1.6 - - - +
202A LEU* 3.8 10.2 - - - +
204A LYS 3.8 1.0 + - - -
205A THR* 1.3 73.1 - - - +
207A GLN* 1.3 63.9 + - - +
209A TYR* 3.3 2.8 + - - +
210A CYS* 3.0 27.4 + - - -
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Residues in contact with GLN 207 (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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205A THR* 3.2 8.3 + - - +
206A ASN* 1.3 81.0 + - - +
208A GLU* 1.3 63.9 + - + +
210A CYS* 3.3 9.9 + - - +
211A ASP* 3.0 61.1 + - - +
214A LYS* 5.7 1.4 - - - +
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Residues in contact with GLU 208 (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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204A LYS* 3.5 12.5 - - + +
205A THR* 2.8 52.5 + - - +
207A GLN* 1.3 78.7 - - + +
209A TYR* 1.3 58.3 + - - +
211A ASP* 3.2 8.5 + - - +
212A TRP* 2.9 29.1 + - - +
219B TRP* 3.7 37.8 - - + -
266B ILE* 6.1 0.2 - - - -
1311B NO3 4.9 8.5 + - - -
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Residues in contact with TYR 209 (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 ILE* 4.8 0.2 - - + -
190A VAL* 4.2 22.0 - - + -
202A LEU* 3.8 50.0 - - + -
204A LYS* 3.6 16.2 - - + +
205A THR 2.9 12.8 + - - +
206A ASN 3.6 7.4 - - - +
208A GLU* 1.3 76.1 - - - +
210A CYS* 1.3 58.9 + - - +
212A TRP* 3.1 16.1 + + - +
213A ILE* 2.8 41.4 + - + +
223A ILE* 3.6 15.4 - - + +
224A GLU* 2.4 33.0 + - - -
74C ARG* 2.9 33.1 + - - -
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Residues in contact with CYS 210 (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 ALA* 3.3 39.0 - - + -
190A VAL* 3.8 10.1 - - - -
191A ALA* 3.7 12.6 - - - -
206A ASN* 3.0 34.1 + - - +
207A GLN* 3.7 13.2 - - - +
208A GLU 3.3 0.2 - - - -
209A TYR* 1.3 75.9 - - - +
211A ASP* 1.3 65.7 + - - +
213A ILE* 3.4 5.5 - - - +
214A LYS* 3.2 34.4 + - + +
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Residues in contact with ASP 211 (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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207A GLN* 3.0 48.2 + - - +
208A GLU* 3.8 4.9 - - - +
210A CYS* 1.3 75.8 - - - +
212A TRP* 1.3 63.4 + - - +
214A LYS* 3.4 29.3 + - - +
215A ARG* 3.6 14.6 + - - +
266B ILE* 3.7 21.5 - - + +
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Residues in contact with TRP 212 (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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204A LYS* 4.8 2.2 - - + -
208A GLU 2.9 17.1 + - - +
209A TYR* 3.4 22.0 - + - +
211A ASP* 1.3 78.1 - - - +
213A ILE* 1.3 82.4 + - + +
215A ARG* 3.1 21.3 + - - +
218A THR* 3.0 44.0 + - + +
219A TRP 4.0 6.7 - - - -
156B ALA 3.5 17.9 - - - -
157B ASP* 4.6 1.8 - - - -
158B ASN* 3.4 27.3 + - - -
219B TRP* 3.4 27.8 - + + -
266B ILE* 4.0 12.5 - - + +
1310B NO3 2.9 23.6 + - - -
74C ARG* 3.6 47.6 - - - -
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Residues in contact with ILE 213 (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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162A PHE* 4.1 8.7 - - + -
183A ARG* 2.8 55.0 + - + +
186A ILE* 4.0 20.0 - - + -
187A ALA* 4.2 5.4 - - + -
209A TYR* 2.8 26.2 + - + +
210A CYS* 3.4 15.9 - - - +
212A TRP* 1.3 89.2 - - + +
214A LYS* 1.3 60.4 + - - +
218A THR* 3.7 10.8 - - - +
219A TRP 4.7 1.3 - - - +
220A GLY* 4.6 5.8 - - - +
224A GLU* 3.8 37.0 - - + +
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Residues in contact with LYS 214 (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 PRO* 5.5 2.8 - - - +
183A ARG* 3.9 12.9 - - - +
184A ARG* 3.7 52.4 - - + +
187A ALA* 3.5 24.8 - - + +
207A GLN* 5.7 1.4 - - - +
210A CYS* 3.2 24.2 + - - +
211A ASP* 3.7 23.9 + - - +
212A TRP 3.1 1.4 - - - -
213A ILE* 1.3 73.7 - - - +
215A ARG* 1.3 67.5 + - - +
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Residues in contact with ARG 215 (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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183A ARG* 2.9 30.7 + - - -
211A ASP 3.6 9.4 + - - +
212A TRP* 3.1 19.8 + - - +
214A LYS* 1.3 79.6 - - - +
216A ASP* 1.3 60.0 + - - +
217A ASP* 2.8 44.7 + - - +
218A THR* 3.7 9.5 + - + +
156B ALA* 4.6 1.8 - - - +
264B ASP* 2.8 33.9 + - - -
266B ILE* 4.1 28.0 - - + +
267B HIS* 3.4 28.7 - - - +
1310B NO3 5.9 0.2 - - - -
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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