Contacts of the helix formed by residues 212 - 228 (chain A) in PDB entry 2V40
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 ASP 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A GLU 4.2 1.2 + - - -
211A ILE* 1.3 72.4 - - - +
213A ILE* 1.3 58.0 + - - +
214A GLU* 3.9 3.5 + - - +
215A GLY* 2.9 34.0 + - - -
216A GLU* 2.9 32.1 + - + +
219A LYS* 5.7 2.8 + - - -
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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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195A PHE* 3.6 20.1 - - + -
196A LYS* 3.8 34.1 - - + -
199A ALA* 3.8 19.3 - - + -
200A ASN* 3.5 30.5 - - - +
203A LYS* 3.5 23.3 - - - +
211A ILE* 3.4 20.2 + - + +
212A ASP* 1.3 71.1 + - - +
214A GLU* 1.3 66.6 + - + +
216A GLU* 5.9 0.2 - - - -
217A LEU* 3.1 25.5 + - + +
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Residues in contact with GLU 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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196A LYS* 3.4 31.2 + - - -
212A ASP* 3.5 3.5 + - - +
213A ILE* 1.3 78.4 - - + +
215A GLY* 1.3 57.0 + - - +
217A LEU* 3.5 10.7 + - - +
218A GLN* 3.0 31.9 + - - +
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Residues in contact with GLY 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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212A ASP* 2.9 29.1 + - - -
214A GLU* 1.3 73.8 - - - +
216A GLU* 1.3 65.5 + - - +
218A GLN* 3.4 5.0 + - - +
219A LYS* 3.1 36.4 + - - +
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Residues in contact with GLU 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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102A HIS* 5.5 0.2 - - - -
104A PRO* 5.9 1.4 - - - +
137A PHE* 3.4 14.8 - - - +
138A ASP* 2.8 59.5 + - + +
139A PHE* 3.8 11.4 + - - +
195A PHE* 3.6 27.9 - - + -
211A ILE* 5.6 1.9 - - - +
212A ASP* 2.9 20.9 + - + +
215A GLY* 1.3 75.5 - - - +
217A LEU* 1.3 57.9 + - - +
219A LYS* 3.2 9.4 + - - +
220A LEU* 2.9 38.5 + - + +
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Residues in contact with LEU 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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188A PHE* 3.8 11.9 - - + -
191A PHE* 3.8 26.0 - - + -
192A SER* 3.9 26.7 - - - +
195A PHE* 3.7 30.1 - - + -
196A LYS* 3.8 30.5 - - + +
213A ILE 3.1 18.3 + - - +
214A GLU* 3.8 14.6 - - - +
216A GLU* 1.3 77.6 - - - +
218A GLN* 1.3 56.6 + - - +
220A LEU* 3.4 9.3 + - + +
221A LYS* 3.1 29.5 + - - +
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Residues in contact with GLN 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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214A GLU* 3.0 21.4 + - - +
215A GLY* 3.8 6.5 - - - +
216A GLU 3.2 0.2 - - - -
217A LEU* 1.3 72.6 - - - +
219A LYS* 1.3 66.3 + - + +
221A LYS* 3.1 56.6 + - - +
222A GLY* 3.5 4.3 + - - -
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Residues in contact with LYS 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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104A PRO* 6.0 1.1 - - + -
138A ASP* 5.7 3.4 - - - +
212A ASP* 5.7 2.6 + - - -
215A GLY* 3.1 23.7 + - - +
216A GLU* 3.6 10.1 - - - +
218A GLN* 1.3 75.9 - - + +
220A LEU* 1.3 53.0 + - - +
222A GLY* 3.2 4.3 + - - -
223A TYR* 2.8 53.9 + - + +
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Residues in contact with LEU 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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103A LEU* 3.8 36.1 - - + -
104A PRO* 5.3 4.0 - - + -
135A ILE* 5.2 0.4 - - + -
137A PHE* 3.8 31.6 - - + -
184A LEU* 4.4 12.9 - - + +
188A PHE* 4.5 5.2 - - + -
191A PHE* 3.9 16.8 - - + -
195A PHE* 4.1 5.2 - - + -
216A GLU* 2.9 34.6 + - + +
217A LEU* 3.5 12.8 - - - +
218A GLN 3.3 0.2 - - - -
219A LYS* 1.3 73.7 - - + +
221A LYS* 1.3 55.0 + - - +
223A TYR* 4.0 8.5 - - + -
224A MET* 2.6 39.2 + - - +
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Residues in contact with LYS 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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188A PHE* 3.6 38.9 - - + -
217A LEU* 3.1 14.7 + - - +
218A GLN* 3.1 44.0 + - - +
219A LYS 3.3 0.2 - - - -
220A LEU* 1.3 76.1 - - - +
222A GLY* 1.3 60.4 + - - +
224A MET* 3.9 10.9 - - + +
225A GLU* 3.4 26.5 + - - +
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Residues in contact with GLY 222 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A GLN 3.5 4.6 + - - -
219A LYS* 3.2 7.8 + - - -
221A LYS* 1.3 76.0 - - - +
223A TYR* 1.3 67.0 + - - +
225A GLU* 3.5 11.9 + - - +
226A LYS* 3.4 23.9 + - - +
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Residues in contact with TYR 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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103A LEU* 4.3 16.8 - - + -
104A PRO* 3.6 48.5 + - + +
107A PHE* 3.4 42.9 - + + +
184A LEU* 5.3 0.2 - - - -
219A LYS* 2.8 45.6 + - + +
220A LEU* 3.7 12.3 - - + +
222A GLY* 1.3 74.5 - - - +
224A MET* 1.3 61.4 + - - +
226A LYS* 3.4 17.6 + - - -
227A ILE* 3.1 28.5 + - - +
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Residues in contact with MET 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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184A LEU* 3.4 44.0 - - + +
185A VAL* 4.3 5.4 - - + -
188A PHE* 4.8 16.6 - - + -
220A LEU 2.6 21.4 + - - +
221A LYS* 3.9 10.5 - - + +
223A TYR* 1.3 73.6 - - - +
225A GLU* 1.3 86.1 + - + +
227A ILE* 3.3 10.3 - - - +
228A LYS* 3.0 59.8 + - - +
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Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A LYS 3.4 18.2 + - - +
222A GLY* 4.0 6.5 - - - +
223A TYR 3.4 0.8 - - - -
224A MET* 1.3 98.2 - - + +
226A LYS* 1.3 62.5 + - + +
228A LYS* 4.1 10.8 + - - +
229A PRO* 3.9 12.8 - - - +
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Residues in contact with LYS 226 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A PHE* 3.5 34.3 - - + -
111A GLU* 2.8 29.8 + - - +
124A GLU* 5.9 2.3 - - - +
222A GLY 3.4 15.5 - - - +
223A TYR* 3.4 27.4 + - - +
224A MET 3.4 0.4 - - - -
225A GLU* 1.3 77.7 - - + +
227A ILE* 1.3 62.5 + - - +
229A PRO* 3.4 11.3 - - - +
230A MET* 4.1 10.9 - - - +
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Residues in contact with ILE 227 (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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103A LEU* 4.0 16.2 - - + -
106A LEU* 4.9 1.1 - - + -
107A PHE* 3.1 37.2 - - + -
129A ILE* 4.5 7.4 - - + -
181A MET* 3.6 20.2 - - + -
184A LEU* 3.9 11.0 - - + -
185A VAL* 3.4 27.8 - - + -
223A TYR 3.1 15.8 + - - +
224A MET* 3.3 10.8 - - - +
226A LYS* 1.3 80.5 - - - +
228A LYS* 1.3 67.9 + - - +
229A PRO 3.4 0.4 - - - -
230A MET* 2.9 31.5 + - + +
231A VAL* 3.4 14.1 + - + +
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Residues in contact with LYS 228 (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 LEU 5.4 0.2 + - - -
185A VAL* 3.3 39.9 + - + -
186A SER 4.8 4.4 + - - -
224A MET* 3.0 43.7 + - - +
225A GLU* 4.3 13.1 + - - +
227A ILE* 1.3 80.6 - - - +
229A PRO* 1.4 69.2 - - + +
230A MET 3.1 0.9 + - - -
231A VAL* 3.2 19.8 + - - +
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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