Contacts of the helix formed by residues 285 - 295 (chain C) in PDB entry 6G2T
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 ASP 285 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ARG* 2.8 24.5 + - - -
62A GLY* 2.7 40.3 - - - +
201A THR* 5.0 15.1 + - - +
203A ALA* 5.2 3.8 - - + +
204A GLU* 5.3 4.5 - - - +
170C LEU* 4.5 5.2 - - - +
172C HIS* 5.6 2.8 + - - -
283C LYS 4.8 2.9 - - - +
284C CYS* 1.3 76.2 - - - +
286C VAL* 1.3 65.8 + - + +
287C ASP 4.4 2.0 - - - +
288C ILE* 3.3 14.1 - - + +
289C ARG* 3.0 23.4 + - - +
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Residues in contact with VAL 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PHE* 5.3 7.9 - - + -
203A ALA* 6.0 0.9 - - + -
204A GLU* 3.7 40.1 + - + +
207A ILE* 5.0 4.7 - - + -
241A LEU* 5.0 12.1 - - + -
242A PRO* 4.0 9.0 - - + -
243A ASP* 3.6 35.6 + - + +
245A GLN* 5.8 1.8 - - - +
284C CYS 3.9 0.2 + - - -
285C ASP* 1.3 73.8 - - + +
287C ASP* 1.3 69.8 + - + +
288C ILE 3.4 0.2 + - - -
289C ARG* 3.1 39.9 + - - +
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Residues in contact with ASP 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLN 3.7 3.3 - - - +
59A SER 3.8 14.8 - - - +
61A ARG* 3.3 49.7 + - + +
62A GLY* 3.5 23.6 + - - +
203A ALA* 5.2 3.8 - - + +
207A ILE* 6.2 0.7 - - + -
242A PRO* 4.2 12.4 - - + +
165C TYR* 4.3 1.7 + - - -
285C ASP* 3.3 2.1 - - + +
286C VAL* 1.3 87.8 - - + +
288C ILE* 1.3 63.4 + - - +
289C ARG 3.7 0.3 + - - -
290C LYS* 3.0 37.7 + - - +
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Residues in contact with ILE 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLY* 3.7 25.1 - - - -
63A ILE* 4.3 5.8 - - + +
165C TYR* 3.5 52.7 - - + -
170C LEU* 3.9 28.7 - - + -
284C CYS* 4.0 8.5 - - + -
285C ASP* 3.3 21.1 - - + +
287C ASP* 1.3 78.1 - - - +
289C ARG* 1.3 62.6 + - - +
290C LYS 3.4 0.2 - - - -
291C ASP* 2.7 29.4 - - - +
292C LEU* 3.3 20.6 - - + +
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Residues in contact with ARG 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ASP* 2.6 47.4 + - - +
245A GLN* 5.4 1.0 + - - -
281C ILE* 3.1 27.9 + - + +
282C MET* 2.7 38.8 + - - +
284C CYS* 2.8 20.2 + - + -
285C ASP* 3.0 17.4 + - - +
286C VAL* 3.1 29.9 - - - +
287C ASP 3.4 1.2 - - - -
288C ILE* 1.3 77.6 - - - +
290C LYS* 1.3 62.4 + - - +
292C LEU* 3.2 16.2 + - - +
293C TYR* 2.9 34.5 + - + -
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Residues in contact with LYS 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A SER 5.4 3.6 + - - -
242A PRO* 3.0 39.4 + - + +
165C TYR* 5.6 2.4 + - - -
286C VAL 4.4 0.4 + - - -
287C ASP* 3.0 34.4 + - - +
289C ARG* 1.3 78.8 - - - +
291C ASP* 1.3 73.8 + - + +
293C TYR* 3.8 8.5 + - - +
294C ALA* 3.9 11.4 + - - +
324C MET* 3.5 27.8 - - + +
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Residues in contact with ASP 291 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C THR* 3.1 25.9 - - + +
165C TYR* 3.1 23.1 - - - -
287C ASP 4.1 0.7 - - - +
288C ILE* 2.7 33.4 - - - +
290C LYS* 1.3 89.5 + - + +
292C LEU* 1.3 72.2 + - - +
294C ALA* 3.3 4.5 + - - +
295C ASN* 2.9 40.7 + - - +
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Residues in contact with LEU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C GLY* 3.1 32.1 - - - +
150C ILE* 3.3 26.9 - - + +
163C PRO* 4.0 15.0 - - + -
164C ILE 3.8 12.6 - - - +
165C TYR* 5.0 1.6 - - + +
281C ILE* 4.8 15.7 - - + -
284C CYS* 4.0 28.9 - - + -
288C ILE* 3.3 32.3 - - + +
289C ARG* 3.2 10.9 + - - +
291C ASP* 1.3 82.1 - - - +
293C TYR* 1.3 63.4 + - - +
295C ASN* 3.3 12.5 + - - -
296C THR 3.7 0.3 + - - -
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Residues in contact with TYR 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ASP* 4.6 13.2 + - - -
150C ILE* 5.5 0.2 - - - -
278C PHE* 4.0 13.2 - + - -
281C ILE* 3.3 43.3 - - + +
282C MET* 3.3 29.1 - - - +
289C ARG* 2.9 35.8 + - + +
290C LYS 4.1 4.9 - - - +
291C ASP 3.3 0.2 - - - -
292C LEU* 1.3 79.2 - - - +
294C ALA* 1.3 56.1 + - + +
295C ASN 3.3 0.2 - - - -
296C THR* 3.1 19.3 + - - -
316C ILE* 4.2 11.1 - - + +
320C ALA* 3.5 31.6 - - + +
321C PRO* 4.8 6.8 - - + +
324C MET* 4.1 12.1 - - - -
326C ILE* 3.2 39.5 - - + +
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Residues in contact with ALA 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C ARG* 4.6 0.3 + - - -
290C LYS 3.9 7.1 + - - +
291C ASP* 3.3 7.3 + - - +
293C TYR* 1.3 75.8 - - + +
295C ASN* 1.3 67.4 + - - +
325C LYS 4.0 12.8 - - - +
327C LYS* 3.0 62.9 - - + +
329C ILE* 5.6 0.5 + - - +
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Residues in contact with ASN 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C ARG* 2.8 31.2 + - - +
148C THR* 3.4 20.5 - - - +
149C GLY* 3.2 19.3 - - - -
150C ILE 3.4 8.9 + - - -
291C ASP* 2.9 35.5 + - - +
292C LEU 3.3 5.0 + - - +
294C ALA* 1.3 88.4 + - - +
296C THR* 1.3 65.8 + - - +
297C VAL* 3.3 15.7 + - - +
327C LYS* 5.2 3.2 - - - +
329C ILE* 4.9 3.4 - - - -
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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