Contacts of the helix formed by residues 209 - 219 (chain C) in PDB entry 1AV1
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 PRO 209 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205C GLU* 2.9 23.8 - - - +
206C LYS* 2.9 25.6 - - + +
208C LYS* 1.4 81.3 - - + +
210C ALA* 1.3 60.9 + - - +
212C GLU* 3.0 27.0 + - + +
213C ASP 4.2 1.0 + - - -
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Residues in contact with ALA 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ARG* 4.4 0.7 + - - -
206C LYS* 3.6 34.1 - - - +
207C ALA 3.7 6.1 - - - +
208C LYS 3.3 0.4 - - - -
209C PRO* 1.3 81.2 - - + +
211C LEU* 1.3 63.6 + - + +
212C GLU 3.1 5.4 + - - -
213C ASP* 3.1 26.1 + - - +
52D SER* 5.9 4.1 - - - -
55D SER* 6.4 0.4 - - - -
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Residues in contact with LEU 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ARG* 2.5 68.6 + - + +
174B LEU* 4.3 34.5 - - + -
175B ALA* 5.3 7.0 - - + -
178B LEU* 5.6 0.2 - - + -
207C ALA* 2.8 32.3 + - + +
208C LYS* 3.5 11.4 - - - +
209C PRO 3.1 1.8 - - - -
210C ALA* 1.3 80.3 - - + +
212C GLU* 1.3 64.7 + - - +
215C ARG* 3.9 2.6 + - - +
52D SER* 4.9 11.9 - - - -
56D THR* 5.5 6.3 - - - +
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Residues in contact with GLU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ARG* 3.8 0.2 - - - -
208C LYS* 3.9 13.5 - - - +
209C PRO* 3.0 19.8 + - + +
211C LEU* 1.3 82.3 - - - +
213C ASP* 1.3 67.4 + - - +
214C LEU 3.7 0.2 - - - -
215C ARG* 3.5 28.6 + - - -
216C GLN* 3.2 52.2 + - - +
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Residues in contact with ASP 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ARG* 4.5 0.2 - - - +
209C PRO 4.2 0.6 + - - -
210C ALA* 3.1 18.6 + - - +
212C GLU* 1.3 76.5 - - - +
214C LEU* 1.3 61.9 + - + +
217C GLY* 2.7 35.5 + - - -
48D ASP* 3.7 30.2 - - - +
51D ASP* 4.9 6.1 - - - +
52D SER* 5.9 1.7 - - - -
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Residues in contact with LEU 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ARG* 2.7 23.2 - - - +
213C ASP* 1.3 78.9 - - + +
215C ARG* 1.3 61.8 + - - +
217C GLY* 3.0 9.6 + - - +
218C LEU* 3.2 21.9 - - + +
45D LYS 3.9 4.7 - - - +
46D LEU* 3.7 10.8 - - + +
48D ASP* 3.0 57.7 - - - +
49D ASN* 3.0 29.8 - - - +
52D SER* 3.3 24.2 - - - +
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Residues in contact with ARG 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ARG* 6.1 0.5 - - - +
164B ALA* 5.9 0.2 - - - -
167B SER* 3.1 32.6 + - - +
168B ASP* 3.7 22.3 + - - +
171B ARG* 2.6 48.9 - - + +
172B GLN* 5.5 6.5 - - - +
211C LEU 3.9 3.9 + - - +
212C GLU* 3.5 34.1 + - - +
213C ASP 3.6 0.2 - - - -
214C LEU* 1.3 71.7 - - - +
216C GLN* 1.3 75.8 + - - +
218C LEU* 4.1 9.0 - - - +
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Residues in contact with GLN 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ARG* 5.7 5.6 - - - +
212C GLU* 3.2 40.2 + - - +
213C ASP 4.7 0.2 - - - +
215C ARG* 1.3 98.2 - - - +
217C GLY* 1.3 50.5 + - - +
218C LEU 2.9 4.9 - - - -
219C LEU* 2.5 48.2 + - + +
220C PRO* 2.6 20.0 - - + +
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Residues in contact with GLY 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C ASP 2.7 22.1 + - - -
214C LEU* 3.0 5.6 + - - -
216C GLN* 1.3 74.1 - - - +
218C LEU* 1.3 54.6 + - - +
219C LEU 3.0 2.5 + - - -
220C PRO* 3.9 12.9 - - - -
221C VAL* 2.8 34.5 + - - +
45D LYS* 4.4 4.0 - - - +
48D ASP* 5.2 5.8 - - - -
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Residues in contact with LEU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B VAL* 4.0 11.8 - - - +
159B LEU* 4.6 14.2 - - + +
160B ARG* 4.7 13.3 - - + +
163B LEU* 3.9 38.4 - - + -
164B ALA 5.4 0.2 - - - +
167B SER* 3.9 19.5 - - - -
214C LEU* 3.2 23.8 - - + +
215C ARG 4.1 6.7 - - - +
216C GLN 2.7 0.8 + - - +
217C GLY* 1.3 80.5 - - - +
219C LEU* 1.3 57.6 + - - +
221C VAL* 4.0 11.0 - - - +
45D LYS* 4.5 18.1 - - + +
46D LEU* 3.4 31.0 - - + -
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Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B VAL* 3.8 27.5 - - + +
157B ASP* 4.2 14.8 - - - +
160B ARG* 3.2 50.7 - - + +
216C GLN* 2.5 42.7 + - + +
218C LEU* 1.3 72.7 - - - +
220C PRO* 1.4 59.3 - - + +
221C VAL* 3.0 9.6 + - - +
222C LEU* 4.3 2.9 + - - +
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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