Contacts of the helix formed by residues 355 - 364 (chain G) in PDB entry 5UQ9
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 TYR 355 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339G PHE* 3.7 37.8 - + + -
342G LEU* 4.3 8.2 + - + -
343G ARG* 3.2 70.2 + - + +
346G ALA* 4.4 8.5 - - - +
353G LEU* 3.4 30.5 - - + -
354G ASN* 1.3 80.4 - - - +
356G GLY* 1.3 62.4 + - - +
357G GLY 3.4 0.9 - - - -
358G ILE* 3.3 24.3 + - + +
359G ALA* 3.2 18.0 + - - +
380G PHE* 4.8 5.2 - - + -
384G PRO 5.0 11.0 - - - +
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Residues in contact with GLY 356 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354G ASN* 2.5 15.1 + - - -
355G TYR* 1.3 70.6 - - - +
357G GLY* 1.3 62.2 + - - +
359G ALA* 3.2 15.4 + - - +
360G LEU 3.3 8.5 + - - -
377G LYS* 3.7 16.1 + - - +
380G PHE* 3.3 39.0 - - - -
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Residues in contact with GLY 357 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172G ASP* 5.2 11.2 - - - -
173G TRP 5.9 1.6 - - - -
354G ASN* 2.9 19.7 + - - -
355G TYR 3.4 0.2 - - - -
356G GLY* 1.3 73.9 - - - +
358G ILE* 1.3 64.9 + - - +
360G LEU* 3.1 9.1 + - - +
361G MET* 2.8 37.6 + - - +
377G LYS* 4.7 3.1 - - - -
380G PHE* 4.8 0.4 - - - -
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Residues in contact with ILE 358 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G VAL* 4.7 13.9 - - + -
183G VAL* 3.7 32.3 - - + -
339G PHE* 4.4 3.4 - - + -
342G LEU* 3.9 18.6 - - + -
353G LEU* 4.3 17.9 - - + -
354G ASN* 4.9 3.1 - - + +
355G TYR* 3.3 32.8 - - + +
356G GLY 3.2 0.4 - - - -
357G GLY* 1.3 74.6 - - - +
359G ALA* 1.3 61.8 + - - +
361G MET* 3.3 9.5 + - - -
362G TRP* 3.0 58.3 + - + -
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Residues in contact with ALA 359 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339G PHE* 4.5 6.9 - - + -
355G TYR 3.2 8.7 + - - +
356G GLY* 3.5 11.0 - - - +
357G GLY 3.1 0.4 - - - -
358G ILE* 1.3 80.3 - - - +
360G LEU* 1.3 62.3 + - - +
362G TRP* 3.0 19.8 + - - +
363G ARG* 3.3 8.0 + - - +
373G LEU* 3.3 19.9 - - + +
376G ILE* 3.6 31.4 - - + -
377G LYS* 4.5 4.7 - - - -
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Residues in contact with LEU 360 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G VAL* 4.5 18.4 - - + +
166G THR* 4.7 4.7 - - + +
168G GLU* 3.6 27.1 - - + +
169G PRO 3.2 27.8 - - - +
170G CYS* 4.2 7.5 - - + +
356G GLY 3.3 2.0 + - - -
357G GLY* 3.1 9.5 + - - +
359G ALA* 1.3 78.8 - - - +
361G MET* 1.3 57.9 + - + +
363G ARG* 3.4 5.5 + - + -
364G GLY* 2.9 28.1 + - - +
373G LEU* 3.4 26.8 - - + +
377G LYS* 3.2 33.9 - - - +
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Residues in contact with MET 361 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G SER* 2.1 39.9 + - - +
141G LEU 3.4 16.8 - - - +
142G MET* 3.5 24.3 - - + +
169G PRO 5.3 0.4 - - - +
170G CYS 4.0 14.1 - - - +
172G ASP* 3.3 48.0 - - + +
173G TRP 5.0 2.0 - - - +
174G VAL* 3.6 18.6 - - + -
183G VAL* 5.5 2.7 - - + -
357G GLY* 2.8 30.0 + - - +
358G ILE* 3.7 9.6 - - - +
359G ALA 3.2 0.2 - - - -
360G LEU* 1.3 76.9 - - + +
362G TRP* 1.3 62.2 + - + +
363G ARG 3.3 0.4 - - - -
366G CYS* 3.4 3.5 - - - -
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Residues in contact with TRP 362 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G MET* 3.7 19.0 - - + +
183G VAL* 3.5 35.2 - - + +
186G VAL* 3.9 22.7 - - + -
187G HIS* 3.5 19.6 - + + +
190G ILE* 4.0 19.7 - - + -
335G TYR* 4.3 13.9 - + - -
338G GLY 5.7 1.6 - - - -
339G PHE* 4.2 22.4 - + - -
342G LEU* 4.2 10.5 - - + -
358G ILE* 3.0 33.2 + - + +
359G ALA* 3.0 12.6 + - - +
361G MET* 1.3 78.1 - - + +
363G ARG* 1.3 58.3 + - - +
366G CYS* 3.2 23.2 - - - +
368G ILE* 3.5 36.9 - - + +
369G ARG* 3.7 4.7 + - - -
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Residues in contact with ARG 363 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163G LYS 5.3 0.5 - - - +
164G VAL 5.1 11.0 + - - +
166G THR* 5.1 12.7 - - - +
359G ALA 3.3 3.7 + - - +
360G LEU* 4.1 4.7 - - + +
362G TRP* 1.3 79.9 - - - +
364G GLY* 1.3 54.0 + - - +
365G GLY 2.6 19.9 + - - -
369G ARG* 3.1 30.5 + - + +
370G SER* 2.9 43.2 + - - +
371G VAL* 3.0 23.0 - - - +
373G LEU* 3.5 43.0 - - + +
374G GLY 6.0 0.2 - - - +
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Residues in contact with GLY 364 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G GLY 3.7 5.0 - - - +
139G PRO 4.4 0.2 - - - -
140G SER* 3.8 13.9 + - - -
161G ALA 5.5 0.3 - - - -
162G ALA 3.6 18.7 - - - +
163G LYS* 4.4 13.9 - - - -
164G VAL* 5.1 2.7 - - - -
170G CYS* 3.6 28.0 - - - +
360G LEU* 2.9 12.3 + - - -
361G MET 4.3 1.6 - - - -
362G TRP 3.9 0.6 - - - -
363G ARG* 1.3 75.8 - - - +
365G GLY* 1.3 54.5 + - - -
366G CYS 3.9 0.7 - - - -
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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