Contacts of the helix formed by residues 261 - 270 (chain B) in PDB entry 6QPA
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 261 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B THR* 3.1 8.9 + - - -
259B TRP* 3.2 3.1 - - - +
260B GLU* 1.3 83.1 - - - +
262B PRO* 1.3 76.9 - - - +
263B GLU* 3.2 13.6 + - - +
264B HIS* 2.7 36.3 + - - -
265B ALA* 3.0 22.0 + - - +
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Residues in contact with PRO 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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51B THR* 5.6 5.6 - - - +
65B VAL* 3.7 25.6 - - + +
66B ASP* 6.4 0.7 - - + -
159B THR* 3.0 18.1 - - + +
261B SER* 1.3 89.6 - - - +
263B GLU* 1.3 69.3 + - - +
265B ALA 3.2 0.7 + - - -
266B HIS* 2.8 30.8 + - - +
298B PHE* 3.5 17.3 - - + -
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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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65B VAL* 5.5 2.8 - - + +
261B SER* 3.2 16.0 + - - +
262B PRO* 1.3 90.5 - - - +
264B HIS* 1.3 59.1 + - + +
266B HIS* 3.8 5.4 - - - +
267B GLN* 2.9 36.5 + - - +
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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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191B PRO* 4.0 32.1 - - + +
192B GLY* 4.2 6.7 - - - -
259B TRP* 3.5 11.5 - - + -
260B GLU* 3.4 37.0 + - + +
261B SER* 2.7 35.8 + - - +
263B GLU* 1.3 79.6 - - + +
265B ALA* 1.3 53.9 + - - +
267B GLN* 4.9 2.7 - - - -
268B GLY* 2.6 34.9 + - - +
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Residues in contact with ALA 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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159B THR* 4.1 3.1 - - + -
161B VAL* 3.8 10.1 - - + -
259B TRP* 3.3 38.4 - - + +
261B SER 3.0 12.9 + - - +
262B PRO 3.6 7.2 - - - +
264B HIS* 1.3 74.0 - - - +
266B HIS* 1.3 65.3 + - - +
269B LEU* 3.0 30.3 + - - +
298B PHE* 3.7 17.7 - - + -
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Residues in contact with HIS 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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54B HIS* 3.0 55.5 + + - -
55B PRO* 4.0 12.5 - - + +
56B MET 5.4 0.2 + - - -
57B ALA 5.8 1.6 + - - -
65B VAL* 3.5 30.2 - - + +
262B PRO 2.8 20.7 + - - +
263B GLU* 3.8 7.4 + - - +
264B HIS 3.3 0.2 - - - -
265B ALA* 1.3 75.6 - - - +
267B GLN* 1.3 65.3 + - - +
270B GLY* 3.3 7.8 + - - -
298B PHE* 3.8 2.2 - - + -
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Residues in contact with GLN 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* 2.9 18.8 + - - +
264B HIS* 4.3 2.7 - - - +
266B HIS* 1.3 81.9 - - - +
268B GLY* 1.3 63.0 + - - +
270B GLY* 3.3 9.1 + - - -
271B HIS* 3.0 28.5 + - + -
274B VAL* 5.7 0.3 - - - +
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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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186B MET* 3.9 8.1 - - - +
190B VAL* 3.6 16.9 - - - +
259B TRP* 3.5 20.9 - - - -
264B HIS 2.6 24.9 + - - -
267B GLN* 1.3 73.2 - - - +
269B LEU* 1.3 60.7 + - - +
271B HIS* 3.1 22.3 + - - +
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Residues in contact with LEU 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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54B HIS* 3.6 29.2 - - + -
161B VAL* 3.7 25.4 - - + -
186B MET* 4.3 11.9 - - + -
257B ILE* 3.8 29.2 - - + -
259B TRP* 4.0 7.5 - - + +
265B ALA 3.0 18.8 + - - +
268B GLY* 1.3 74.9 - - - +
270B GLY* 1.3 61.8 + - - +
271B HIS 3.1 1.2 + - - -
272B VAL* 3.2 29.0 + - + +
273B MET* 5.5 0.2 - - - +
296B TYR* 3.9 32.1 - - + -
298B PHE* 4.2 5.8 - - + -
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Residues in contact with GLY 270 (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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54B HIS* 4.1 5.1 + - - -
266B HIS 3.3 11.7 + - - -
267B GLN* 3.3 6.9 + - - -
268B GLY 3.2 1.8 - - - -
269B LEU* 1.3 77.6 - - - +
271B HIS* 1.3 56.6 + - - +
272B VAL 3.1 0.4 - - - -
273B MET* 2.8 38.4 + - - +
274B VAL* 3.1 19.8 + - - +
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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