Contacts of the helix formed by residues 216 - 228 (chain A) in PDB entry 1VGU
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 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LYS* 4.0 2.7 - - - -
214A VAL* 4.2 0.7 - - - +
215A THR* 1.3 77.4 - - - +
217A PRO* 1.3 81.4 - - + +
218A GLU* 2.7 45.1 + - + +
219A ASP* 2.7 45.1 + - - +
220A LEU* 3.7 6.5 - - - +
138B ARG* 4.6 12.3 - - - +
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Residues in contact with PRO 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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27A LYS* 3.7 17.0 - - - +
216A ARG* 1.3 95.8 - - + +
218A GLU* 1.3 60.9 + - - +
220A LEU* 3.1 32.4 + - + +
221A ALA* 4.3 1.4 + - - +
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Residues in contact with GLU 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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216A ARG* 2.7 54.3 + - + +
217A PRO* 1.3 75.7 - - + +
219A ASP* 1.3 68.0 + - - +
220A LEU 3.3 0.5 + - - -
221A ALA* 3.6 7.6 + - - +
222A LEU* 3.6 17.7 + - - +
138B ARG* 5.7 2.5 + - - -
209B ALA* 5.8 4.0 - - - +
226B TYR* 5.9 2.9 - - - -
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Residues in contact with ASP 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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212A ILE* 3.9 7.1 - - + +
213A LYS 3.6 3.3 - - - +
214A VAL* 3.5 22.5 - - + +
215A THR* 2.6 30.1 + - - -
216A ARG* 2.7 28.8 + - - +
218A GLU* 1.3 83.7 - - - +
220A LEU* 1.3 58.0 + - - +
222A LEU* 3.7 8.8 - - - +
223A ALA* 2.8 32.9 + - - +
138B ARG* 3.4 23.0 + - - -
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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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27A LYS* 4.8 2.9 - - + -
30A LEU* 4.2 30.5 - - + -
31A SER 5.0 3.8 - - - +
32A ILE* 3.5 19.1 - - + +
37A ILE* 4.0 26.2 - - + -
214A VAL* 4.1 9.4 - - + -
216A ARG 3.7 4.9 - - - +
217A PRO* 3.1 33.6 + - + +
219A ASP* 1.3 76.9 - - - +
221A ALA* 1.3 58.6 + - - +
223A ALA* 3.0 6.9 + - - +
224A GLU* 2.8 30.6 + - - +
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Residues in contact with ALA 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 PRO 4.3 1.4 + - - +
218A GLU* 3.6 9.5 + - - +
219A ASP 3.5 0.2 - - - -
220A LEU* 1.3 77.2 - - - +
222A LEU* 1.3 52.6 + - - +
224A GLU* 3.1 12.5 + - - +
225A PHE* 2.6 36.6 + - - +
225B PHE* 4.0 20.2 - - + -
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Residues in contact with LEU 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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212A ILE* 4.3 14.6 - - + -
218A GLU 3.6 10.7 + - - +
219A ASP* 3.4 12.3 + - - +
220A LEU 3.2 0.2 - - - -
221A ALA* 1.3 75.9 - - - +
223A ALA* 1.3 67.5 + - - +
225A PHE* 3.1 7.6 + - + +
226A TYR* 3.0 63.6 + - + +
222B LEU* 3.8 9.0 - - + -
225B PHE* 4.2 10.2 - - + -
226B TYR* 2.8 36.3 - - + +
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Residues in contact with ALA 223 (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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32A ILE* 3.7 13.2 - - + -
110A PRO* 4.1 12.8 - - + -
111A CYS* 3.6 7.2 - - - -
212A ILE* 3.9 10.7 - - + +
214A VAL* 3.4 24.5 - - + -
219A ASP 2.8 22.1 + - - +
220A LEU 3.5 3.6 - - - +
222A LEU* 1.3 72.4 - - - +
224A GLU* 1.3 57.8 + - - +
226A TYR* 3.4 0.6 + - - -
227A LEU* 2.9 32.7 + - - +
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Residues in contact with GLU 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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32A ILE* 3.7 29.5 - - + +
220A LEU 2.8 13.1 + - - +
221A ALA* 3.4 13.9 - - - +
223A ALA* 1.3 76.7 - - - +
225A PHE* 1.3 69.9 + - - +
227A LEU* 3.3 3.4 + - - +
228A THR* 3.3 31.1 + - - -
225B PHE* 6.4 0.2 - - + -
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Residues in contact with PHE 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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221A ALA 2.6 19.3 + - - +
222A LEU* 3.1 12.8 + - + +
224A GLU* 1.3 79.8 - - + +
226A TYR* 1.3 100.8 + + - +
228A THR* 3.5 21.9 - - + +
221B ALA* 3.8 34.3 - - + -
222B LEU* 3.8 16.2 - - + -
225B PHE* 3.9 37.5 - + + -
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Residues in contact with TYR 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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111A CYS* 3.7 19.4 - - + +
113A HIS* 5.2 8.0 - - - -
209A ALA 4.9 0.6 - - - -
210A ASP* 3.2 55.3 - - + +
212A ILE* 4.1 14.6 - - + -
222A LEU* 3.0 33.3 + - + +
225A PHE* 1.3 105.8 - + - +
227A LEU* 1.3 62.1 + - - +
228A THR 2.9 12.9 + - - +
229A ARG 4.2 7.8 - - - +
222B LEU* 3.1 28.0 - - + +
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Residues in contact with LEU 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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32A ILE* 3.4 39.7 - - + -
40A HIS* 3.8 31.2 - - + +
110A PRO* 3.5 31.2 - - + +
111A CYS* 3.8 15.5 - - - -
223A ALA 2.9 25.2 + - - +
224A GLU* 3.3 5.8 + - - +
226A TYR* 1.3 75.8 - - - +
228A THR* 1.3 56.8 + - - +
229A ARG* 3.0 12.0 + - - -
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Residues in contact with THR 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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224A GLU* 3.3 25.8 + - - -
225A PHE* 3.5 20.5 - - + +
226A TYR 2.9 2.6 - - - +
227A LEU* 1.3 73.6 - - - +
229A ARG* 1.3 87.3 + - + +
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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