Contacts of the helix formed by residues 211 - 223 (chain A) in PDB entry 3C9S
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 GLY 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A ILE* 3.5 9.9 - - - +
209A SER 3.4 2.8 - - - -
210A ASP* 1.3 81.1 - - - +
212A LEU* 1.3 59.4 + - - +
213A VAL 3.5 1.8 - - - -
214A ALA* 3.6 3.7 + - - -
215A ASP* 2.9 32.0 + - - +
256A LEU 4.1 2.7 - - - -
257A PHE* 4.2 4.7 - - - -
258A GLY 3.3 21.5 - - - -
259A GLY* 4.0 1.0 - - - -
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Residues in contact with LEU 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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153A VAL* 4.3 0.7 - - + -
157A LEU* 3.8 22.9 - - + -
208A ILE* 3.5 21.9 - - + +
211A GLY* 1.3 70.3 - - - +
213A VAL* 1.3 56.5 + - - +
215A ASP* 3.7 1.2 - - - +
216A ALA* 2.7 38.6 + - + +
229A ILE* 4.1 16.8 - - + -
234A LEU* 4.0 15.7 - - + -
255A ALA 3.7 15.3 + - - +
256A LEU* 3.4 22.8 + - + +
258A GLY 4.5 0.8 + - - -
265A LEU* 4.2 22.0 - - + -
282A ILE* 4.0 29.6 - - + -
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Residues in contact with VAL 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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212A LEU* 1.3 79.6 - - + +
214A ALA* 1.3 62.9 + - - +
216A ALA* 3.2 6.4 + - - +
217A ASN* 2.7 33.4 + - - +
229A ILE* 5.6 1.6 - - + -
256A LEU* 3.1 40.6 + - + +
257A PHE* 4.1 18.8 - - + -
291A VAL* 5.0 4.9 - - + -
293A VAL* 4.6 10.1 - - + -
298A VAL* 3.6 41.3 - - + +
299A GLU 3.7 13.2 - - - +
300A PRO* 4.6 0.9 - - + -
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Residues in contact with ALA 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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210A ASP* 4.3 24.5 - - + +
211A GLY 3.6 7.4 + - - +
212A LEU 3.3 0.6 - - - -
213A VAL* 1.3 80.7 - - - +
215A ASP* 1.3 60.8 + - - +
217A ASN* 3.5 9.5 + - - +
218A HIS* 3.0 23.8 + - + -
256A LEU 4.9 0.2 + - - -
257A PHE* 5.8 1.3 - - + -
300A PRO* 3.8 26.8 - - + +
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Residues in contact with ASP 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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206A MET* 3.2 44.3 - - + +
207A ASP 4.1 4.3 - - - +
208A ILE* 3.4 6.6 - - + -
209A SER* 2.8 31.9 + - - -
210A ASP* 2.9 26.9 + - - +
211A GLY 2.9 19.3 + - - +
212A LEU 4.1 1.1 - - - +
214A ALA* 1.3 72.6 - - - +
216A ALA* 1.3 63.3 + - - +
217A ASN 3.1 2.5 - - - -
218A HIS* 3.2 10.0 + - - -
219A LEU 3.2 8.3 + - - -
265A LEU* 4.3 5.4 - - + -
900B ACP 5.0 4.3 + - - +
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Residues in contact with ALA 216 (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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212A LEU* 2.7 25.5 + - + +
213A VAL* 3.6 5.2 - - - +
215A ASP* 1.3 73.2 - - - +
217A ASN* 1.3 57.2 + - - +
219A LEU* 3.3 2.4 + - - -
220A ALA* 2.8 30.1 + - - +
227A ILE* 3.4 13.0 - - + +
229A ILE* 4.5 11.9 - - + -
265A LEU* 3.8 19.7 - - + +
291A VAL* 3.6 19.1 - - + -
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Residues in contact with ASN 217 (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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213A VAL* 2.7 28.5 + - - +
214A ALA 3.6 10.1 - - - +
215A ASP 3.1 0.6 - - - -
216A ALA* 1.3 76.3 - - - +
218A HIS* 1.3 56.2 + - - +
220A ALA* 3.9 1.6 - - - +
221A GLN* 2.7 40.5 + - - +
290A GLY* 4.8 5.1 - - - -
291A VAL* 3.2 29.0 - - - +
298A VAL 3.5 18.4 + - - +
299A GLU* 4.3 2.0 - - - +
300A PRO* 3.7 28.6 - - + +
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Residues in contact with HIS 218 (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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9A PHE* 3.1 51.9 - + - -
142A ARG* 4.0 30.3 - - - +
206A MET* 4.3 6.1 - - + -
210A ASP* 5.6 3.1 - - - -
214A ALA* 3.0 29.3 + - + -
215A ASP* 3.2 16.0 + - - +
217A ASN* 1.3 76.4 - - + +
219A LEU* 1.3 62.0 + - - +
221A GLN* 4.3 14.1 + - - +
222A ARG* 2.9 38.5 + - + +
300A PRO* 5.7 6.5 - - + -
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Residues in contact with LEU 219 (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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142A ARG* 3.1 43.2 - - + +
145A ALA* 5.4 3.4 - - + -
151A VAL* 5.9 2.5 - - + -
204A ALA* 3.8 24.5 - - + +
205A SER 4.5 4.3 - - - +
206A MET* 3.9 10.0 - - + -
215A ASP 3.2 9.9 + - - +
216A ALA* 3.6 8.5 - - - +
218A HIS* 1.3 80.7 - - - +
220A ALA* 1.3 63.2 + - - +
223A SER* 3.0 30.1 + - - +
225A VAL* 6.5 0.2 - - + -
227A ILE* 4.3 13.0 - - + -
265A LEU* 4.0 36.6 - - + +
266A PHE* 5.1 4.3 - - - -
267A THR* 5.3 4.5 - - - -
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Residues in contact with ALA 220 (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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216A ALA 2.8 19.3 + - - +
217A ASN* 3.9 3.6 - - - +
219A LEU* 1.3 75.6 - - - +
221A GLN* 1.3 57.1 + - - +
224A GLY* 3.0 8.1 + - - -
225A VAL* 2.9 49.9 + - - +
227A ILE* 3.8 17.0 - - + +
290A GLY* 3.9 20.4 - - - +
291A VAL* 4.0 5.8 - - + -
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Residues in contact with GLN 221 (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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217A ASN* 2.7 25.5 + - - +
218A HIS* 3.7 17.1 + - - +
220A ALA* 1.3 74.0 - - - +
222A ARG* 1.3 67.4 + - + +
224A GLY* 3.2 12.2 + - - -
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Residues in contact with ARG 222 (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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16A LYS* 4.6 12.9 - - - +
23A VAL 5.6 0.6 + - - -
24A ILE 5.0 2.2 + - - -
25A GLY* 3.6 31.3 + - - -
26A ASP* 3.2 35.3 + - - -
142A ARG* 3.8 30.0 - - - +
143A ASP* 3.0 39.7 + - + +
218A HIS* 2.9 22.6 + - + +
221A GLN* 1.3 78.7 - - + +
223A SER* 1.3 58.1 + - - +
224A GLY 3.2 1.4 + - - -
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Residues in contact with SER 223 (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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142A ARG 2.8 19.1 + - - -
143A ASP* 3.1 9.6 - - - +
145A ALA* 3.0 47.6 + - - +
219A LEU* 3.0 16.3 + - - +
222A ARG* 1.3 74.9 - - - +
224A GLY* 1.3 65.3 + - - +
225A VAL* 3.2 16.7 - - - +
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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