Contacts of the helix formed by residues 258 - 269 (chain B) in PDB entry 2VJD
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 SER 258 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255B ASN* 4.3 1.0 + - - -
256B LEU 3.2 3.9 - - - -
257B ASN* 1.3 81.7 - - - +
259B ASP* 1.3 65.0 + - - +
260B GLU* 3.5 15.5 + - - +
261B GLU* 2.7 38.1 + - - +
262B LEU* 2.9 26.9 + - - +
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Residues in contact with ASP 259 (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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158B LEU* 4.0 13.7 - - + +
159B HIS 4.9 0.2 - - - +
160B GLY* 5.5 0.3 - - - -
161B SER* 4.5 16.6 + - - -
242B ARG* 2.8 43.6 + - - -
258B SER* 1.3 74.0 - - - +
260B GLU* 1.3 63.3 + - - +
262B LEU* 4.3 7.0 - - - +
263B ILE* 2.8 54.0 + - + +
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Residues in contact with GLU 260 (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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161B SER* 6.5 0.2 - - - -
163B GLU* 6.3 4.5 - - + -
258B SER* 3.5 20.6 - - - +
259B ASP* 1.3 83.0 + - - +
261B GLU* 1.3 59.5 + - + +
263B ILE* 3.8 5.6 - - - +
264B HIS* 2.8 30.5 + - - +
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Residues in contact with GLU 261 (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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255B ASN* 3.0 50.7 + - + +
257B ASN* 3.8 11.8 + - - +
258B SER* 2.7 26.4 + - - +
260B GLU* 1.3 75.3 - - + +
262B LEU* 1.3 61.6 + - - +
264B HIS* 3.6 6.8 + - - +
265B CYS* 2.8 30.0 + - - +
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Residues in contact with LEU 262 (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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158B LEU* 3.9 22.7 - - + -
245B ALA 4.0 14.6 - - - +
246B VAL* 4.2 21.3 - - + -
249B GLY* 3.7 30.3 - - - +
254B CYS* 4.1 5.2 - - + -
255B ASN 3.4 11.8 + - - +
256B LEU* 4.0 15.7 - - + -
258B SER 2.9 18.0 + - - +
259B ASP* 3.6 6.5 - - - +
261B GLU* 1.3 76.9 - - - +
263B ILE* 1.3 58.1 + - - +
265B CYS* 3.1 6.5 + - - +
266B LEU* 2.9 46.6 + - + +
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Residues in contact with ILE 263 (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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45B PHE* 4.3 11.0 - - + -
156B LEU* 5.2 3.1 - - + -
158B LEU* 3.7 23.3 - - + -
161B SER* 3.5 25.6 - - - +
163B GLU* 3.9 9.4 - - + -
164B ALA* 3.7 20.4 - - + -
259B ASP* 2.8 28.7 + - + +
260B GLU* 3.9 4.7 - - - +
262B LEU* 1.3 68.7 - - + +
264B HIS* 1.3 67.1 + - - +
266B LEU* 3.3 7.6 + - - +
267B ARG* 3.0 64.6 + - + +
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Residues in contact with HIS 264 (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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260B GLU 2.8 19.6 + - - +
261B GLU* 3.6 8.0 + - - +
262B LEU 3.2 0.2 - - - -
263B ILE* 1.3 76.2 - - - +
265B CYS* 1.3 66.3 + - - +
267B ARG* 3.3 19.4 + - + +
268B GLU* 3.3 47.5 + - + +
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Residues in contact with CYS 265 (chain B).
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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253B ASN 4.7 2.0 - - - -
254B CYS* 2.0 55.9 - - + -
255B ASN* 4.2 5.4 - - + +
261B GLU 2.8 14.3 + - - +
262B LEU* 3.2 7.9 - - - +
264B HIS* 1.3 81.7 + - - +
266B LEU* 1.3 62.4 + - - +
268B GLU* 3.1 19.3 + - - +
269B LYS* 3.4 25.6 - - - +
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Residues in contact with LEU 266 (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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44B ARG* 2.8 21.3 + - - -
45B PHE* 3.8 16.9 - - + -
156B LEU* 4.2 26.2 - - + -
158B LEU* 5.9 0.2 - - + -
245B ALA 4.6 4.7 - - - +
248B LEU* 4.4 18.6 - - + -
249B GLY* 4.3 7.4 - - - -
252B LEU* 3.8 29.8 - - + -
254B CYS* 3.8 12.3 - - - -
262B LEU* 2.9 40.5 + - + +
263B ILE* 3.3 4.5 + - - +
265B CYS* 1.3 74.8 - - - +
267B ARG* 1.3 58.1 + - - +
269B LYS* 3.6 11.5 + - + +
274B LEU* 4.1 6.4 - - + +
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Residues in contact with ARG 267 (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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41B GLY* 4.2 23.7 - - - +
42B ASN* 3.6 13.3 + - - +
44B ARG* 3.3 34.2 + - + +
45B PHE* 4.2 10.1 - - + -
46B ARG* 3.1 26.1 - - - +
163B GLU* 2.8 54.5 + - - +
263B ILE* 3.0 39.1 + - + +
264B HIS* 3.7 11.1 - - + +
265B CYS 3.1 0.2 - - - -
266B LEU* 1.3 76.6 - - - +
268B GLU* 1.3 65.6 + - + +
269B LYS 3.2 2.7 + - - +
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Residues in contact with GLU 268 (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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264B HIS* 3.3 43.7 + - + +
265B CYS* 3.1 10.4 + - - +
267B ARG* 1.3 78.3 - - - +
269B LYS* 1.3 66.2 + - + +
270B LYS* 3.9 2.6 + - - +
273B GLU* 5.2 0.2 - - - +
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Residues in contact with LYS 269 (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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44B ARG* 2.9 26.5 + - - -
252B LEU* 3.7 33.2 + - + +
253B ASN 5.5 0.6 + - - -
254B CYS* 4.3 2.2 - - - -
265B CYS* 3.4 35.3 - - - +
266B LEU* 3.7 10.3 - - + +
267B ARG 3.2 2.0 - - - +
268B GLU* 1.3 84.2 - - - +
270B LYS* 1.3 61.3 + - - +
273B GLU* 4.0 23.8 + - + +
274B LEU* 3.4 26.2 - - + -
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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