Contacts of the helix formed by residues 215 - 223 (chain B) in PDB entry 1VLP
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 ASN 215 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU 4.0 0.2 - - - +
11B ASP* 3.0 24.3 + - - +
12B THR 3.3 12.6 - - - +
179B THR* 2.9 33.9 + - - +
182B ARG* 3.8 0.2 - - - +
188B GLN* 3.7 13.0 + - - +
213B THR* 3.1 18.1 + - - +
214B SER* 1.3 75.6 + - - +
216B ILE* 1.3 58.5 + - - +
217B LEU* 3.2 13.0 + - - +
218B PHE* 2.9 39.1 + - + -
219B ALA* 2.9 25.5 + - - +
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Residues in contact with ILE 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 3.4 25.6 - - + +
12B THR* 3.1 19.6 + - + +
14B MSE 3.7 33.2 - - + +
17B ILE* 3.5 32.8 - - + -
72B TYR* 3.7 27.7 - - + -
73B LEU* 4.2 14.4 - - + -
77B ILE* 5.4 2.0 - - + -
214B SER 3.3 0.4 + - - -
215B ASN* 1.3 71.6 - - - +
217B LEU* 1.3 63.5 + - - +
219B ALA* 3.2 7.2 + - - +
220B LYS* 3.0 22.1 + - - +
226B PRO* 4.4 8.5 - - + -
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LYS* 5.5 7.0 - - + +
8B SER* 4.1 27.1 - - - +
10B LEU* 3.0 27.8 + - + +
11B ASP* 3.9 24.7 - - + +
69B GLU* 5.2 2.2 - - + +
185B LEU* 5.6 7.6 - - + -
215B ASN* 3.2 9.4 + - - +
216B ILE* 1.3 73.7 - - - +
218B PHE* 1.3 64.9 + - + +
220B LYS* 3.3 13.7 + - + +
221B LYS* 2.9 32.8 + - + +
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Residues in contact with PHE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ASP* 4.9 0.7 - - - -
182B ARG* 4.3 1.6 - - - -
185B LEU* 3.5 30.1 - - + -
188B GLN* 3.3 34.1 - - + -
189B ASP* 3.4 44.9 - - + -
192B MSE 4.0 15.1 - - + +
213B THR* 4.0 9.6 - - + -
215B ASN* 2.9 37.5 + - + +
217B LEU* 1.3 81.5 - - + +
219B ALA* 1.3 63.8 + - - +
221B LYS* 4.2 11.0 - - + -
222B TYR* 3.0 47.8 + + - +
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Residues in contact with ALA 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B TYR* 3.5 11.3 + - - +
213B THR* 3.4 15.6 - - + +
215B ASN 2.9 12.9 + - - +
216B ILE 3.2 7.2 + - - +
218B PHE* 1.3 75.1 - - - +
220B LYS* 1.3 57.0 + - - +
223B GLY* 2.9 26.3 + - - -
224B VAL* 3.0 31.1 + - - +
225B LYS 3.9 0.2 - - - -
226B PRO* 3.6 21.1 - - + -
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Residues in contact with LYS 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 4.0 17.3 - - + -
68B GLU* 2.7 43.6 + - - -
69B GLU* 4.8 4.7 - - + +
72B TYR* 3.5 53.0 + - + -
216B ILE 3.0 13.1 + - - +
217B LEU* 3.4 16.4 - - + +
218B PHE 3.2 0.2 - - - -
219B ALA* 1.3 78.8 - - - +
221B LYS* 1.3 62.2 + - - +
223B GLY* 3.6 6.8 + - - -
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Residues in contact with LYS 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B ASP* 2.8 31.4 + - - +
217B LEU* 2.9 20.5 + - + +
218B PHE* 3.8 14.0 - - + +
219B ALA 3.3 0.4 - - - -
220B LYS* 1.3 79.8 - - - +
222B TYR* 1.3 86.5 + - + +
223B GLY 3.7 0.3 + - - -
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Residues in contact with TYR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B ASP* 2.5 31.3 + - - -
192B MSE 3.7 24.2 - - + -
193B GLN* 3.2 36.7 + - + +
196B MSE 3.3 42.3 - - + +
218B PHE* 3.0 27.0 + + - +
221B LYS* 1.3 102.8 + - + +
223B GLY* 1.3 60.8 + - - +
224B VAL* 3.4 7.7 + - + +
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Residues in contact with GLY 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B ALA 2.9 7.7 + - - -
220B LYS* 3.6 5.4 + - - -
221B LYS 3.5 3.4 + - - -
222B TYR* 1.3 79.8 - - - +
224B VAL* 1.3 61.9 + - - +
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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