Contacts of the helix formed by residues 212 - 226 (chain A) in PDB entry 3V9G
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 PHE 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A GLN* 4.3 0.2 - - - -
153A LYS* 3.7 14.4 - - - -
160A ILE* 5.5 7.4 - - + -
161A ASP* 3.4 30.7 - - + +
165A GLU* 3.6 17.5 - - - +
209A PRO* 3.9 11.0 + - - +
210A PHE 3.3 3.8 - - - -
211A ASN* 1.3 105.6 + - + +
213A THR* 1.3 63.2 + - - +
215A ILE* 3.5 43.5 + - + +
216A GLY 3.9 4.0 + - - -
238A ALA* 5.7 0.7 - - - +
343A TYR* 5.8 0.7 - + - -
347A LYS* 4.0 40.4 - - + -
348A CYS* 5.4 1.3 - - - -
349A SER* 5.8 1.6 - - - -
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Residues in contact with THR 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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143A ILE* 3.6 28.5 - - + -
147A THR* 3.2 16.8 + - - +
151A GLN* 3.1 24.8 + - - +
161A ASP* 3.1 10.1 + - - -
162A ALA* 3.9 10.8 - - + -
166A LEU* 4.7 1.1 - - + -
212A PHE* 1.3 70.9 - - - +
214A ALA* 1.3 63.7 + - - +
215A ILE 3.3 0.5 + - - -
216A GLY* 3.5 9.0 + - - -
217A GLY* 3.5 8.3 + - - -
232A TRP* 5.8 0.7 - - - -
238A ALA* 5.5 1.7 - - - +
241A ALA* 3.8 11.1 - - + +
242A SER* 4.9 7.9 + - - +
245A VAL* 3.7 20.3 - - + +
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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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161A ASP* 2.9 20.5 + - - +
165A GLU* 3.5 23.6 - - + +
166A LEU* 3.5 41.5 - - - +
169A PHE* 4.0 3.3 - - + -
212A PHE* 4.9 0.2 - - + -
213A THR* 1.3 78.4 - - - +
215A ILE* 1.3 57.0 + - - +
217A GLY* 3.2 2.8 + - - -
218A ASN* 3.0 27.9 + - - +
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Residues in contact with ILE 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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165A GLU* 5.2 6.1 - - - +
169A PHE* 5.2 7.6 - - + -
209A PRO* 3.7 27.6 - - + -
211A ASN* 4.8 3.4 - - - +
212A PHE* 3.5 40.5 + - + +
213A THR 3.2 1.0 - - - -
214A ALA* 1.3 75.5 - - - +
216A GLY* 1.3 61.0 + - - +
218A ASN* 3.8 4.1 - - - +
219A LEU* 2.8 50.9 + - + +
285A THR* 3.8 21.1 - - + +
348A CYS* 5.6 4.5 - - - -
520A PHE* 6.5 1.1 - - + -
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Residues in contact with GLY 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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208A SER* 3.5 28.5 - - - -
212A PHE 3.9 4.6 + - - -
213A THR 3.5 5.8 + - - -
214A ALA 3.4 0.6 - - - -
215A ILE* 1.3 79.9 - - - +
217A GLY* 1.3 63.1 + - - +
219A LEU* 3.9 0.7 - - - +
220A ALA* 3.2 20.8 + - - +
232A TRP* 3.6 21.9 - - - -
242A SER* 5.8 1.3 - - - -
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Residues in contact with GLY 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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166A LEU* 3.9 15.0 - - - -
170A PHE* 3.8 13.3 - - - -
213A THR 3.5 6.7 + - - -
214A ALA 3.2 7.2 + - - -
215A ILE 3.2 0.4 - - - -
216A GLY* 1.3 77.0 - - - +
218A ASN* 1.3 56.2 + - - +
220A ALA* 4.6 0.6 - - - +
221A GLY* 2.8 28.1 + - - -
232A TRP* 4.3 4.6 - - - -
245A VAL* 4.4 16.6 - - - +
249A LEU* 5.4 2.7 - - - +
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Residues in contact with ASN 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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166A LEU* 4.7 0.2 - - - +
169A PHE* 3.5 43.5 - - + +
170A PHE* 5.2 1.9 - - - -
173A ASN* 2.9 28.5 + - - -
214A ALA 3.0 8.1 + - - +
215A ILE* 4.0 3.8 - - - +
216A GLY 3.2 0.2 - - - -
217A GLY* 1.3 77.3 - - - +
219A LEU* 1.3 68.1 + - + +
220A ALA 3.2 0.4 - - - -
221A GLY 4.2 0.2 - - - +
222A ALA* 3.0 33.8 + - - +
223A PRO* 3.6 0.2 - - - +
283A ASN* 4.2 1.0 + - - -
532A PRO* 3.8 13.0 - - - +
537A TYR* 3.5 20.8 + - - -
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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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206A ALA* 3.7 18.1 - - + +
207A ILE 3.3 27.8 - - - +
208A SER* 3.6 19.7 - - - -
215A ILE* 2.8 29.5 + - + +
216A GLY* 3.3 4.5 + - - +
218A ASN* 1.3 79.3 - - + +
220A ALA* 1.3 57.0 + - - +
223A PRO* 3.1 13.2 - - - +
232A TRP* 5.6 0.2 - - - +
283A ASN* 2.8 48.8 + - - +
284A PHE 4.7 0.9 - - - +
285A THR* 3.5 28.3 - - - +
537A TYR* 4.2 6.3 - - - +
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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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206A ALA* 3.9 5.8 - - + -
216A GLY 3.2 11.7 + - - +
217A GLY* 4.6 0.4 - - - +
218A ASN 3.2 0.2 - - - -
219A LEU* 1.3 78.0 - - - +
221A GLY* 1.3 64.2 + - - +
222A ALA 3.6 0.2 - - - -
223A PRO* 3.6 1.5 - - - +
224A ALA* 3.3 24.4 + - - +
230A VAL* 3.7 21.7 - - + +
232A TRP* 4.0 31.6 - - + -
259A ILE* 3.8 15.2 - - + +
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Residues in contact with GLY 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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128A PHE* 3.6 26.1 - - - -
170A PHE* 4.7 3.6 - - - -
217A GLY 2.8 21.6 + - - -
218A ASN* 4.6 0.2 - - - -
220A ALA* 1.3 77.7 - - - +
222A ALA* 1.3 59.5 + - - +
224A ALA* 3.3 1.2 + - - -
225A LEU* 2.8 31.8 + - - +
249A LEU* 5.4 1.8 - - - -
259A ILE* 4.7 3.4 - - - -
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Residues in contact with ALA 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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173A ASN* 3.9 11.0 - - - +
218A ASN* 3.0 29.7 + - - +
221A GLY* 1.3 75.8 - - - +
223A PRO* 1.3 68.3 - - + +
225A LEU* 3.4 9.4 + - - +
226A MET* 3.2 27.1 + - - +
537A TYR* 3.6 28.3 - - + -
538A ILE* 4.8 3.8 - - + -
541A TRP* 4.6 4.7 - - + -
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Residues in contact with PRO 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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204A VAL* 4.3 13.9 - - + -
218A ASN 3.6 0.9 - - - +
219A LEU 3.1 28.7 - - - +
220A ALA* 3.6 5.4 - - - +
222A ALA* 1.3 95.9 - - + +
224A ALA* 1.3 60.6 + - - +
226A MET 3.1 7.6 + - - -
228A ASN* 3.0 40.6 + - + +
230A VAL* 4.1 12.8 - - + -
283A ASN* 3.7 12.3 - - - +
541A TRP* 4.0 24.4 - - + -
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Residues in contact with ALA 224 (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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116A TRP* 2.9 29.0 + - + -
128A PHE* 4.1 9.4 - - + -
220A ALA 3.3 19.1 + - - +
221A GLY 3.3 4.6 + - - +
223A PRO* 1.3 77.4 - - - +
225A LEU* 1.3 63.2 + - - +
227A GLY 3.1 4.0 + - - -
228A ASN 3.5 15.9 - - - +
230A VAL* 4.1 3.0 - - + +
254A LEU* 4.9 0.7 - - + -
258A ILE* 4.2 8.5 - - + -
259A ILE* 3.9 24.2 - - + -
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Residues in contact with LEU 225 (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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116A TRP* 4.9 1.1 - - - -
121A ILE* 3.5 16.4 - - + +
124A ARG* 2.8 24.1 + - - +
125A ALA* 3.7 36.3 - - + +
128A PHE* 3.8 25.7 - - + -
170A PHE 5.7 0.2 - - - +
173A ASN* 3.3 44.9 - - + +
174A ALA* 4.0 3.6 - - + +
177A ALA* 3.9 8.7 - - + -
221A GLY 2.8 17.9 + - - +
222A ALA* 3.5 6.1 - - - +
223A PRO 3.3 0.2 - - - -
224A ALA* 1.3 76.6 - - - +
226A MET* 1.3 63.5 + - - +
227A GLY 3.2 0.4 - - - -
538A ILE* 4.8 2.7 - - + -
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Residues in contact with MET 226 (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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121A ILE* 4.6 3.6 - - + -
124A ARG* 3.6 12.2 + - - +
177A ALA* 3.6 29.6 - - + +
180A LEU* 4.0 17.9 - - + -
197A TYR* 4.5 8.8 - - + +
198A ARG 4.3 2.4 - - - +
199A GLY* 3.5 20.8 + - - -
222A ALA 3.2 13.2 + - - +
223A PRO 3.1 7.8 + - - +
225A LEU* 1.3 79.4 - - - +
227A GLY* 1.3 57.3 + - - +
228A ASN* 3.5 2.5 - - - -
538A ILE* 3.9 51.6 - - + +
541A TRP* 3.7 21.0 - - + +
542A THR* 4.3 12.5 - - - -
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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