Contacts of the helix formed by residues 218 - 226 (chain B) in PDB entry 3V3Q
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 ALA 218 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205B LYS* 5.1 12.1 - - - +
208B VAL* 5.7 2.4 - - - +
216B GLN 3.7 1.6 + - - +
217B PRO* 1.3 83.3 - - - +
219B SER* 1.3 58.2 + - - +
221B LEU* 3.7 27.6 - - + +
222B SER* 3.5 20.6 + - - -
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Residues in contact with SER 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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217B PRO* 3.0 17.2 + - - -
218B ALA* 1.3 77.7 - - - +
220B CYS* 1.3 66.6 + - - +
221B LEU 3.1 1.1 - - - -
222B SER* 3.2 5.5 + - - -
223B ARG* 2.8 52.5 + - - +
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Residues in contact with CYS 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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208B VAL* 3.8 31.4 - - + -
215B PRO* 5.4 2.5 - - + -
217B PRO* 3.3 24.0 - - + +
219B SER* 1.3 77.0 - - - +
221B LEU* 1.3 57.7 + - - +
223B ARG* 3.2 7.6 + - - +
224B LEU* 2.9 51.1 + - - +
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Residues in contact with LEU 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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201B ALA 5.7 0.4 - - - +
204B LEU* 4.1 24.5 - - + -
205B LYS* 4.4 28.7 - - + +
208B VAL* 4.2 13.2 - - + -
218B ALA* 3.7 26.4 - - + +
219B SER 3.1 0.2 - - - -
220B CYS* 1.3 81.4 - - - +
222B SER* 1.3 65.1 + - - +
224B LEU* 3.3 9.5 + - + +
225B LEU* 3.0 55.1 + - + +
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Residues in contact with SER 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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218B ALA 3.5 14.1 + - - -
219B SER* 3.2 10.0 + - - -
221B LEU* 1.3 87.3 - - - +
223B ARG* 1.3 59.5 + - - +
225B LEU* 4.0 4.7 - - - +
226B GLY* 3.0 22.7 + - - -
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Residues in contact with ARG 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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165B LEU* 4.1 33.2 - - + +
219B SER* 2.8 39.0 + - - +
220B CYS* 3.6 6.7 - - - +
222B SER* 1.3 75.3 + - - +
224B LEU* 1.3 66.0 + - + +
226B GLY* 3.1 14.7 + - - -
227B LYS* 3.6 4.0 + - - +
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Residues in contact with LEU 224 (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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165B LEU* 4.2 20.6 - - + +
167B VAL* 4.4 27.8 - - + -
171B ALA* 4.3 12.3 - - + +
175B LEU* 4.0 23.2 - - + +
204B LEU* 4.1 31.0 - - + -
208B VAL* 4.2 15.5 - - + -
220B CYS* 2.9 47.2 + - - +
221B LEU* 3.9 5.6 - - - +
223B ARG* 1.3 72.5 - - + +
225B LEU* 1.3 60.0 + - + +
227B LYS* 2.9 26.7 + - - +
228B LEU 4.3 0.2 + - - -
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Residues in contact with LEU 225 (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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175B LEU* 3.6 23.8 - - + -
178B LEU* 4.3 9.2 - - + -
201B ALA* 6.1 4.0 - - + -
204B LEU* 3.8 18.8 - - + -
221B LEU* 3.0 45.9 + - + +
222B SER* 4.4 4.7 - - - +
224B LEU* 1.3 72.4 - - + +
226B GLY* 1.3 60.9 + - - +
227B LYS 3.0 5.8 + - - -
228B LEU* 3.2 29.7 + - + +
229B PRO* 3.6 7.8 - - - +
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Residues in contact with GLY 226 (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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222B SER 3.0 16.9 + - - -
223B ARG* 3.1 8.7 + - - -
225B LEU* 1.3 74.7 - - - +
227B LYS* 1.3 60.2 + - - +
228B LEU 3.3 0.2 - - - -
229B PRO* 3.5 13.3 - - - +
230B GLU* 3.5 21.4 - - - +
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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