Contacts of the helix formed by residues 257 - 268 (chain B) in PDB entry 2QNJ
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 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255B GLY 3.9 3.9 - - - -
256B GLN* 1.3 81.6 - - - +
258B LEU* 1.3 65.2 + - - +
259B LYS* 3.6 14.1 + - - +
260B GLU* 3.1 31.3 + - - +
261B LEU* 3.2 20.0 + - - +
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Residues in contact with LEU 258 (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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216B PRO* 4.0 31.6 - - + -
224B PHE* 4.7 15.7 - - + -
257B ASN* 1.3 72.9 - - - +
259B LYS* 1.3 66.9 + - - +
261B LEU* 3.3 13.4 + - + +
262B ARG* 2.9 27.4 + - + +
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Residues in contact with LYS 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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257B ASN* 3.6 15.1 + - - +
258B LEU* 1.3 81.2 - - - +
260B GLU* 1.3 59.1 + - + +
262B ARG* 3.4 10.9 + - - +
263B GLU* 2.8 65.2 + - - +
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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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254B ASP 4.4 1.8 - - - -
255B GLY* 3.9 2.8 - - - -
256B GLN* 3.6 36.7 + - - +
257B ASN* 3.1 20.4 + - - +
259B LYS* 1.3 79.5 - - + +
261B LEU* 1.3 63.4 + - - +
263B GLU* 3.4 18.3 - - - +
264B ARG* 2.5 64.7 + - - +
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Residues in contact with LEU 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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216B PRO* 3.6 35.0 - - + +
217B PRO* 4.1 12.8 - - + -
224B PHE* 3.9 21.5 - - + -
253B PHE* 3.3 33.9 - - + +
254B ASP* 3.9 12.3 - - - +
255B GLY* 4.1 5.0 - - - -
257B ASN 3.2 10.8 + - - +
258B LEU* 3.7 12.3 - - + +
260B GLU* 1.3 76.9 - - - +
262B ARG* 1.3 59.5 + - - +
264B ARG* 3.4 2.4 + - - +
265B VAL* 2.9 46.7 + - + +
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Residues in contact with ARG 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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224B PHE* 3.7 61.9 + - + -
258B LEU* 2.9 18.2 + - + +
259B LYS* 3.5 9.8 + - - +
261B LEU* 1.3 74.9 - - - +
263B GLU* 1.3 68.6 + - - +
265B VAL* 3.1 1.0 + - - +
266B LEU* 2.8 44.6 + - + +
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Residues in contact with GLU 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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259B LYS* 2.8 37.8 + - - +
260B GLU* 3.4 22.9 - - - +
262B ARG* 1.3 81.8 - - - +
264B ARG* 1.3 63.1 - - + +
266B LEU* 3.9 6.5 - - - +
267B ARG* 3.2 22.6 + - - +
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Residues in contact with ARG 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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253B PHE* 3.9 22.4 - - + +
254B ASP* 3.1 34.4 + - - +
255B GLY* 3.9 0.4 - - - -
260B GLU* 2.5 47.6 + - - +
261B LEU 3.8 5.8 - - - +
262B ARG 3.2 0.4 - - - -
263B GLU* 1.3 80.5 - - + +
265B VAL* 1.3 59.5 + - - +
267B ARG* 3.1 16.1 + - - +
268B GLY* 2.8 27.2 + - - -
269B LYS 4.0 7.0 + - - +
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Residues in contact with VAL 265 (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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216B PRO 5.0 1.6 - - - +
217B PRO 5.3 1.3 - - - +
219B ALA 4.2 11.7 - - - +
221B PRO* 3.6 33.9 - - + +
224B PHE* 3.7 18.2 - - + -
237B TRP* 4.4 6.7 - - + -
253B PHE* 3.6 35.4 - - + -
261B LEU* 2.9 35.8 + - + +
262B ARG 3.7 2.5 - - - +
264B ARG* 1.3 73.5 - - - +
266B LEU* 1.3 66.2 + - - +
268B GLY* 3.0 14.0 + - - -
290B LEU* 3.7 7.1 - - - +
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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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221B PRO* 3.5 31.6 - - + +
224B PHE* 3.6 20.9 - - + +
225B GLN* 3.9 22.6 + - + +
262B ARG* 2.8 48.9 + - + +
263B GLU* 3.9 6.3 - - - +
265B VAL* 1.3 76.1 - - - +
267B ARG* 1.3 56.3 + - - +
290B LEU* 3.2 23.9 - - - +
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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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263B GLU 3.2 14.5 + - - +
264B ARG* 3.1 14.1 + - - +
265B VAL 3.1 0.6 - - - -
266B LEU* 1.3 79.7 - - - +
268B GLY* 1.3 63.1 + - - +
269B LYS* 3.4 23.0 + - + +
290B LEU* 4.1 10.1 - - - +
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Residues in contact with GLY 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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237B TRP* 4.9 2.9 - - - -
253B PHE* 3.9 15.9 - - - -
264B ARG 2.8 10.5 + - - -
265B VAL 3.0 12.5 + - - -
266B LEU 3.3 0.2 - - - -
267B ARG* 1.3 77.5 - - - +
269B LYS* 1.3 57.2 + - - -
270B TYR* 3.8 15.1 - - - -
288B LEU* 5.2 5.0 - - - +
290B LEU* 3.8 13.0 - - - -
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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