Contacts of the helix formed by residues 245 - 253 (chain D) in PDB entry 6Q2J
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 TRP 245 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240D PHE* 4.5 14.0 - + - -
241D GLN* 3.2 10.4 + - - +
244D CYS* 1.3 85.9 - - + +
246D GLN* 1.3 53.9 + - - +
247D ARG 3.4 2.9 - - - -
248D VAL* 3.5 19.0 + - + +
249D THR* 2.7 34.6 + - - -
267D LEU* 3.6 24.0 - - + -
268D THR 3.5 24.9 - - - -
269D CYS* 3.4 32.1 - - + -
309D HIS* 4.1 17.9 - + - -
310D MET* 3.8 53.9 + - + +
315D SER* 4.5 12.1 - - - -
316D CYS* 3.8 23.1 - - - -
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Residues in contact with GLN 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D SER 3.6 22.1 + - - +
243D LYS* 3.5 23.2 + - - +
244D CYS 3.4 5.1 + - - +
245D TRP* 1.3 72.0 - - - +
247D ARG* 1.3 62.1 + - + +
249D THR* 3.4 8.2 - - - -
250D ARG* 2.9 52.8 + - - +
268D THR 5.5 1.0 + - - -
270D SER* 4.4 13.8 + - - +
272D SER* 5.6 2.0 + - - -
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Residues in contact with ARG 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D TRP 3.4 0.6 - - - -
246D GLN* 1.3 76.6 - - + +
248D VAL* 1.3 62.4 + - + +
250D ARG* 3.4 11.8 + - + +
251D LYS* 3.0 40.9 + - + +
262D LEU* 5.6 1.3 - - + -
266D ASP* 3.8 22.0 - - - +
268D THR* 3.5 41.4 + - - +
169F GLU* 4.4 17.7 + - - -
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Residues in contact with VAL 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D GLN* 3.6 21.3 - - - +
245D TRP* 3.5 20.8 + - + +
246D GLN 3.4 0.2 - - - -
247D ARG* 1.3 77.6 - - + +
249D THR* 1.3 58.1 + - - +
251D LYS* 4.8 1.3 - - - -
252D CYS* 2.9 26.8 + - + +
253D HIS 3.4 5.3 + - - -
259D ILE* 3.7 29.8 - - + -
262D LEU* 3.7 20.6 - - + -
267D LEU* 3.7 30.5 - - + -
306D ILE* 6.2 0.7 - - + -
310D MET* 4.7 8.5 - - - -
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Residues in contact with THR 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D GLN* 2.4 36.5 + - - +
242D SER* 3.5 28.5 - - - +
245D TRP 2.7 11.1 + - - -
246D GLN* 3.4 12.8 - - + -
247D ARG 3.2 0.2 - - - -
248D VAL* 1.3 75.9 - - - +
250D ARG* 1.3 60.7 + - + +
253D HIS* 2.9 57.1 + - + +
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Residues in contact with ARG 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D GLN* 2.9 42.0 + - - +
247D ARG* 3.7 14.5 - - - +
249D THR* 1.3 75.5 - - + +
251D LYS* 1.3 68.6 + - + +
253D HIS* 4.2 13.4 + - + -
117F PRO* 6.4 0.2 - - - +
119F LEU* 3.7 48.0 - - + +
120F THR* 3.9 2.4 + - - -
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Residues in contact with LYS 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D ARG* 3.0 24.5 + - + +
248D VAL* 4.3 1.3 - - - +
249D THR 4.2 0.2 - - - -
250D ARG* 1.3 91.8 - - + +
252D CYS* 1.3 72.1 + - - +
253D HIS* 4.8 3.9 - - - -
258D CYS* 3.8 1.7 - - - -
262D LEU* 5.5 7.6 - - + +
37F TRP* 3.9 26.9 - - + -
75F THR* 5.1 1.2 + - - -
119F LEU* 4.4 4.7 - - - +
120F THR* 2.9 38.3 + - - +
148F SER* 3.5 31.1 + - - +
150F PHE* 6.3 2.0 - - - -
169F GLU* 4.5 15.8 + - - -
170F THR* 5.4 3.8 + - - -
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Residues in contact with CYS 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D VAL* 2.9 11.3 + - + +
249D THR 3.6 0.2 + - - -
251D LYS* 1.3 86.7 - - - +
253D HIS* 1.3 63.4 + - - +
254D GLU 2.9 19.3 + - - +
255D ASP* 4.0 14.2 - - + +
258D CYS* 2.0 63.5 - - + -
259D ILE* 4.0 11.4 - - + -
262D LEU* 4.9 8.1 - - - -
37F TRP* 5.4 0.4 - - - -
75F THR* 3.3 15.8 - - - +
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Residues in contact with HIS 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D ARG* 5.4 4.9 - - - +
241D GLN* 4.2 16.5 - - - +
242D SER* 5.6 1.0 + - - -
248D VAL* 3.4 4.3 + - - -
249D THR* 2.9 49.0 + - + +
250D ARG* 4.2 12.3 + - + -
251D LYS 4.8 1.8 - - - -
252D CYS* 1.3 77.6 - - - +
254D GLU* 1.3 66.6 + - - +
75F THR* 3.5 34.9 + - + -
76F TYR* 4.5 7.8 + - + +
116F PHE* 4.8 25.3 - + + +
117F PRO* 4.7 17.6 + - + -
120F THR* 6.4 0.4 - - - -
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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