Contacts of the helix formed by residues 289 - 299 (chain C) in PDB entry 1TYG
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 289 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A GLU* 2.7 33.6 + - - -
333A SER* 4.0 5.4 - - - -
338A ARG* 2.7 28.6 + - - -
287C ILE* 3.8 2.1 - - - +
288C GLY* 1.3 75.8 - - - +
290C PRO* 1.3 65.3 - - - +
291C LYS* 3.1 6.0 - - - +
292C ASP* 2.7 27.2 + - - +
293C ALA 3.1 8.3 + - - -
319C MET* 5.0 1.6 - - - -
323C MET* 3.6 12.1 - - - +
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Residues in contact with PRO 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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294A ALA* 4.9 4.3 - - + -
298A GLU* 4.2 0.9 - - - +
329A ALA* 3.3 36.3 - - + +
330A GLY* 4.5 1.6 - - - +
333A SER* 3.0 27.8 - - - +
289C SER* 1.3 83.8 - - - +
291C LYS* 1.3 65.3 + - - +
292C ASP 2.7 0.9 + - - -
293C ALA* 2.8 1.1 + - + -
294C ALA* 2.7 29.2 + - - +
319C MET* 4.3 0.2 - - - -
322C ALA* 3.9 13.9 - - + +
323C MET* 3.7 12.3 - - + -
326C ALA* 3.3 25.4 - - + -
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Residues in contact with LYS 291 (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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291A LYS* 4.0 25.3 - - + +
294A ALA* 4.1 13.9 - - + +
295A TYR* 3.4 62.6 + - + +
298A GLU* 3.7 27.3 + - - +
338A ARG* 4.9 5.5 - - - +
289C SER* 4.5 2.0 - - - +
290C PRO* 1.3 80.1 - - - +
292C ASP* 1.3 75.1 + - - +
294C ALA* 4.3 1.0 - - - -
295C TYR* 3.4 23.0 + - - +
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Residues in contact with ASP 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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338A ARG* 5.3 0.7 + - - -
261C GLY 4.3 1.9 - - - +
262C GLN 3.9 2.3 - - - -
263C GLY* 2.9 39.0 + - - -
264C ILE* 4.4 7.0 + - - +
287C ILE* 3.8 22.3 - - + +
288C GLY* 3.4 14.7 + - - +
289C SER* 2.7 19.5 + - - +
291C LYS* 1.3 99.7 + - - +
293C ALA* 1.3 66.4 + - - +
294C ALA 3.3 1.1 - - - -
295C TYR* 3.3 15.1 + - - +
296C ALA* 3.3 8.8 + - - +
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Residues in contact with ALA 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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287C ILE* 3.7 17.5 - - + +
289C SER 3.1 2.6 + - - +
290C PRO* 2.8 8.4 + - + +
292C ASP* 1.3 80.1 - - - +
294C ALA* 1.3 61.2 + - - +
296C ALA* 3.3 17.2 + - - +
297C MET* 3.7 7.8 + - - +
304C VAL* 3.7 9.0 - - + +
306C LEU* 4.4 4.7 - - + -
323C MET* 3.9 27.1 - - - -
326C ALA* 4.0 9.2 - - + -
327C VAL* 4.3 15.3 - - + -
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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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290A PRO* 4.9 3.6 - - + -
291A LYS* 4.6 15.7 - - - +
326A ALA* 6.1 1.1 - - + -
290C PRO 2.7 19.3 + - - +
291C LYS* 4.3 3.1 - - - +
293C ALA* 1.3 70.4 - - - +
295C TYR* 1.3 63.7 + - - +
297C MET* 3.5 2.8 + - - -
298C GLU* 3.3 22.7 + - - +
326C ALA* 3.3 28.0 + - + +
329C ALA* 5.1 0.9 - - + -
330C GLY* 3.5 20.4 - - - +
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Residues in contact with TYR 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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291A LYS* 3.7 42.4 - - + +
264C ILE* 3.5 28.7 - - + -
267C PRO* 3.3 37.3 - - + +
291C LYS 3.4 16.0 + - - +
292C ASP* 3.3 11.2 + - - +
294C ALA* 1.3 74.3 - - - +
296C ALA* 1.3 69.0 + - - +
298C GLU* 3.4 19.1 + - + +
299C LEU* 3.4 34.0 + - + +
338C ARG* 6.1 2.2 - - - -
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Residues in contact with ALA 296 (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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264C ILE* 3.6 16.0 - - + +
270C LEU* 5.5 1.8 - - - +
283C VAL* 3.8 26.0 - - + -
287C ILE* 4.9 1.1 - - + -
292C ASP 3.3 7.3 + - - +
293C ALA 3.3 12.5 + - - +
294C ALA 3.2 0.4 - - - -
295C TYR* 1.3 80.3 - - - +
297C MET* 1.3 64.8 + - - +
299C LEU* 3.0 15.2 + - - +
300C GLY 3.7 0.5 + - - -
301C ALA* 3.5 14.1 + - + +
304C VAL* 3.7 18.8 - - + -
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Residues in contact with MET 297 (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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114C ARG* 3.9 13.9 - - - -
293C ALA 3.7 12.8 - - - +
294C ALA 3.5 2.6 + - - +
295C TYR 3.4 0.4 - - - -
296C ALA* 1.3 75.1 - - - +
298C GLU* 1.3 53.4 - - - +
300C GLY* 2.7 28.9 + - - -
301C ALA* 3.1 31.1 + - - +
302C ASP 3.5 18.6 - - - +
303C GLY* 3.5 23.6 - - - +
304C VAL* 3.9 5.8 - - - -
327C VAL* 3.7 40.4 - - + +
330C GLY* 3.7 4.9 - - - -
331C ARG* 3.6 31.0 + - + +
334C TYR* 3.9 7.6 - - - +
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Residues in contact with GLU 298 (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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289A SER* 2.6 42.1 + - - +
290A PRO* 3.2 17.4 - - - +
291A LYS* 3.4 17.8 + - - +
294C ALA 3.3 15.3 + - - +
295C TYR* 3.6 19.7 - - + +
296C ALA 3.2 1.0 + - - -
297C MET* 1.3 78.1 - - - +
299C LEU* 1.3 61.8 + - + +
300C GLY 3.2 0.4 - - - -
330C GLY* 3.8 2.9 + - - +
333C SER* 3.3 26.4 + - - +
334C TYR* 3.5 23.0 - - - +
338C ARG* 4.3 5.4 + - - -
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Residues in contact with LEU 299 (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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264C ILE* 3.9 20.2 - - + -
267C PRO* 4.7 13.5 - - + -
270C LEU* 4.6 14.8 - - + -
271C SER* 4.6 22.9 - - - +
274C ILE* 3.3 24.5 - - + +
275C GLU* 4.9 4.5 - - - +
295C TYR* 3.4 49.4 - - + +
296C ALA* 3.0 8.7 + - - +
298C GLU* 1.3 78.1 - - + +
300C GLY* 1.3 56.3 + - - +
301C ALA 3.8 0.9 - - - -
334C TYR* 4.3 4.8 - - - -
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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