Contacts of the helix formed by residues 290 - 303 (chain B) in PDB entry 6UQY
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 THR 290 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B SER* 3.4 2.2 - - - -
75B ASN* 3.4 12.1 - - - +
264B CYS* 4.8 0.4 - - + -
278B PRO 3.9 13.9 - - - +
281B TYR* 2.8 33.4 + - + +
282B TYR 3.0 8.7 + - - +
283B PHE 3.4 27.4 - - - +
284B TRP* 3.5 13.2 - - + +
289B PRO* 1.3 75.9 - - - +
291B ARG* 1.3 65.1 + - - +
292B ARG* 3.4 12.2 + - - +
293B VAL* 3.1 9.4 + - - -
294B HIS* 3.0 21.4 + - - -
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Residues in contact with ARG 291 (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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74B SER* 3.4 4.1 + - - -
75B ASN* 2.7 45.0 + - - +
76B GLY* 3.6 25.4 - - - -
77B PRO* 4.4 10.5 - - + +
278B PRO* 5.3 6.8 - - - +
279B ASP* 2.9 38.0 + - - +
290B THR* 1.3 73.2 - - - +
292B ARG* 1.3 59.5 + - - +
294B HIS* 3.4 7.9 + - - +
295B GLN* 2.9 29.7 + - - +
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Residues in contact with ARG 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B TYR* 3.0 33.7 + - - +
257B LEU* 4.2 12.1 - - + -
279B ASP* 3.6 43.6 + - - +
281B TYR 4.8 1.1 - - - +
290B THR* 3.1 10.3 + - - +
291B ARG* 1.3 83.4 - - - +
293B VAL* 1.3 62.2 + - - +
295B GLN* 3.2 22.4 + - - +
296B LEU* 3.1 57.4 + - + +
299B GLU* 5.1 2.4 + - - -
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B HIS* 5.5 3.4 - - + -
244B PHE* 4.0 8.0 - - + -
248B LEU* 4.4 8.3 - - + -
257B LEU* 4.5 12.6 - - + -
281B TYR 4.3 1.3 - - - +
282B TYR* 3.5 65.1 - - + +
289B PRO* 3.7 21.3 - - + -
290B THR* 3.1 10.7 + - - +
292B ARG* 1.3 73.8 - - + +
294B HIS* 1.3 60.9 + - - +
296B LEU* 3.3 7.2 + - - +
297B ALA* 2.8 29.3 + - + +
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Residues in contact with HIS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER 4.9 1.6 + - - -
39B TYR* 3.3 34.1 - - + -
73B TRP 5.3 0.6 + - - -
74B SER* 3.7 15.1 - - - -
77B PRO 3.4 20.2 - - - +
78B THR* 3.6 16.9 - - - +
79B ALA* 3.1 32.1 + - + +
82B VAL* 4.1 2.1 - - - +
143B PHE* 5.8 1.1 - + - -
288B ASN* 5.5 0.4 - - - +
289B PRO* 3.6 38.4 + - + +
290B THR 3.0 21.5 + - - +
291B ARG 3.7 2.5 - - - +
293B VAL* 1.3 79.3 - - - +
295B GLN* 1.3 56.6 + - - +
297B ALA* 4.3 4.0 - - - +
298B GLY* 2.8 25.8 + - - -
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Residues in contact with GLN 295 (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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82B VAL* 3.6 17.6 - - + +
85B ARG* 2.4 34.9 + - - +
86B GLN* 4.6 6.3 - - - +
291B ARG 2.9 18.4 + - - +
292B ARG* 3.5 22.4 - - - +
293B VAL 3.2 0.2 - - - -
294B HIS* 1.3 73.2 - - - +
296B LEU* 1.3 65.5 - - - +
298B GLY 3.3 1.0 + - - -
299B GLU* 2.6 64.9 + - - +
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Residues in contact with LEU 296 (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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244B PHE* 3.6 15.7 - - + -
248B LEU* 3.9 22.2 - - + -
255B TYR* 3.9 36.6 - - + +
257B LEU* 5.0 3.4 - - + -
292B ARG* 3.1 59.2 + - + +
293B VAL* 3.3 7.2 + - - +
295B GLN* 1.3 77.9 - - - +
297B ALA* 1.3 55.1 + - - +
299B GLU* 3.4 18.6 + - - +
300B ALA* 2.9 28.9 + - - +
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Residues in contact with ALA 297 (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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79B ALA* 3.9 13.9 - - + -
239B PHE* 5.0 0.7 - - + -
241B HIS* 4.2 14.6 - - + +
244B PHE* 3.4 26.4 - - + -
293B VAL* 2.8 18.1 + - + +
294B HIS* 3.7 5.8 - - - +
296B LEU* 1.3 73.4 - - - +
298B GLY* 1.4 62.0 + - - +
300B ALA* 3.1 2.7 + - - +
301B MET* 2.9 39.0 + - + +
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Residues in contact with GLY 298 (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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79B ALA* 3.5 26.3 - - - +
82B VAL* 3.9 11.4 - - - -
83B LEU* 4.0 6.7 - - - -
86B GLN* 4.8 0.2 - - - -
294B HIS 2.8 18.3 + - - -
295B GLN 3.8 1.3 - - - -
297B ALA* 1.4 72.1 - - - +
299B GLU* 1.3 61.3 + - - +
301B MET* 3.3 7.5 + - - +
302B ALA* 3.0 24.3 + - - +
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Residues in contact with GLU 299 (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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82B VAL* 4.4 0.7 - - + -
86B GLN* 4.1 27.2 + - - +
292B ARG* 5.1 3.0 + - - -
295B GLN* 2.6 55.7 + - - +
296B LEU* 3.7 20.5 - - - +
298B GLY* 1.3 76.1 - - - +
300B ALA* 1.3 62.9 + - - +
302B ALA* 3.2 11.5 + - - +
303B ALA* 3.4 12.1 + - - +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B PHE* 3.7 26.7 - - + -
244B PHE* 3.9 13.9 - - + -
296B LEU 2.9 18.3 + - - +
297B ALA 3.5 4.5 - - - +
299B GLU* 1.3 78.3 - - - +
301B MET* 1.3 60.9 + - - +
303B ALA* 3.2 20.8 + - - +
304B ARG* 4.7 2.1 + - - +
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Residues in contact with MET 301 (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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79B ALA* 3.8 29.8 - - + +
83B LEU* 3.8 12.4 - - + +
141B PHE* 3.8 25.4 - - + -
143B PHE* 4.2 7.2 - - + -
188B LEU* 4.3 10.6 - - + +
190B VAL* 4.0 15.3 - - + -
239B PHE* 3.8 44.9 - - + -
241B HIS* 4.2 13.5 - - + -
297B ALA* 2.9 20.3 + - + +
298B GLY* 3.7 7.4 - - - +
300B ALA* 1.3 77.4 - - - +
302B ALA* 1.3 61.0 + - - +
303B ALA 3.1 1.5 + - - -
304B ARG* 3.8 5.9 + - - +
305B TYR* 3.8 19.4 - - - -
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 3.5 17.7 - - + +
86B GLN* 3.7 30.1 - - + +
87B LEU* 3.9 10.0 - - + +
298B GLY 3.0 16.5 + - - +
299B GLU 3.6 6.3 - - - +
300B ALA 3.2 0.4 - - - -
301B MET* 1.3 76.3 - - - +
303B ALA* 1.3 62.4 + - - +
304B ARG 3.2 0.2 - - - -
305B TYR* 3.0 26.6 + - - +
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Residues in contact with ALA 303 (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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25B LEU* 3.4 17.5 - - - +
299B GLU 3.4 8.2 + - - +
300B ALA* 3.2 16.3 + - - +
301B MET 3.1 2.2 - - - -
302B ALA* 1.3 77.5 - - - +
304B ARG* 1.3 63.0 + - + +
305B TYR 3.3 1.2 - - - +
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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