Contacts of the helix formed by residues 283 - 294 (chain A) in PDB entry 5TE0
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 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A GLU* 2.7 33.7 + - - -
282A TYR* 1.3 73.4 - - - +
284A GLN* 1.3 63.1 + - - +
285A ASP* 3.5 11.9 + - - +
286A MET* 2.9 32.9 + - - +
287A HIS* 3.1 18.7 + - - -
314A LEU* 3.8 3.9 - - - +
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Residues in contact with GLN 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A TYR 3.9 0.6 + - - -
283A SER* 1.3 71.4 - - - +
285A ASP* 1.4 60.3 + - - +
287A HIS* 3.2 11.6 + - - +
288A CYS* 3.0 37.5 + - - -
335A GLU* 5.7 4.7 - - - +
404A GOL 3.1 37.5 + - - +
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Residues in contact with ASP 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A SER* 3.1 4.2 + - - +
284A GLN* 1.4 77.0 - - - +
286A MET* 1.3 58.9 + - - +
288A CYS* 3.3 8.1 + - - +
289A LEU* 2.9 29.1 + - - +
313A LYS* 5.1 9.9 + - - -
314A LEU* 3.6 33.3 - - + +
333A LEU* 5.0 2.1 - - - +
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Residues in contact with MET 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLU* 3.8 28.0 - - + +
151A VAL* 3.7 24.2 - - + -
152A LEU* 4.0 16.4 - - + -
252A LEU* 3.8 30.3 - - - -
256A CYS* 3.8 19.5 - - - -
282A TYR* 3.8 17.3 - - + -
283A SER* 2.9 23.4 + - - +
285A ASP* 1.3 73.8 - - - +
287A HIS* 1.3 58.6 - - + +
289A LEU* 3.2 6.5 + - - +
290A ILE* 3.0 32.4 + - + +
314A LEU* 3.6 10.9 - - + +
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Residues in contact with HIS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A TYR* 3.3 17.7 - - - -
276A ILE* 3.7 20.7 - - + +
280A SER* 2.7 32.5 + - - -
282A TYR* 3.3 28.2 + - + -
283A SER 3.1 8.3 + - - -
284A GLN* 3.5 9.8 - - - +
286A MET* 1.3 76.8 - - + +
288A CYS* 1.3 58.4 + - - +
290A ILE* 3.4 6.8 + - + +
291A ARG 3.1 20.8 + - - -
336A PRO* 3.5 29.8 - - + +
404A GOL 2.9 32.5 + - - -
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Residues in contact with CYS 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A GLN* 3.0 23.2 + - - +
285A ASP* 3.8 7.9 - - - +
287A HIS* 1.3 75.0 - - - +
289A LEU* 1.4 57.9 + - - +
291A ARG* 3.3 2.1 + - - +
292A TYR* 2.9 30.0 + - - +
333A LEU* 3.8 22.7 - - + +
334A PRO 3.5 21.7 - - - +
335A GLU* 3.2 38.6 - - - -
336A PRO* 4.3 2.5 - - - -
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A LEU* 4.9 9.2 - - + -
155A PHE* 4.3 5.4 - - + -
252A LEU* 3.7 22.4 - - + -
285A ASP 2.9 14.2 + - - +
286A MET* 3.2 10.3 + - - +
288A CYS* 1.4 71.9 - - - +
290A ILE* 1.3 65.2 + - - +
292A TYR* 3.4 19.4 + - + +
293A MET* 3.4 21.7 + - + +
307A VAL* 3.9 24.5 - - + +
310A PHE* 4.1 17.0 - - + +
311A SER* 3.9 29.2 - - - +
314A LEU* 4.9 7.2 - - + -
333A LEU* 4.0 8.4 - - + +
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A GLY* 4.1 7.1 - - - +
252A LEU* 3.8 21.5 - - + -
253A TYR* 4.0 18.2 - - + +
256A CYS* 4.2 14.4 - - - -
257A TYR* 4.0 28.5 - - + +
274A PHE* 3.9 15.0 - - + -
276A ILE* 4.0 9.0 - - + -
286A MET* 3.0 24.0 + - + +
287A HIS 3.6 6.7 - - - +
288A CYS 3.3 0.2 - - - -
289A LEU* 1.3 78.1 - - - +
291A ARG* 1.3 62.3 + - - +
293A MET* 3.3 9.6 + - - +
294A LEU* 3.1 43.3 + - + +
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A GLY 5.7 2.3 + - - -
274A PHE* 3.9 25.8 - - - -
287A HIS 3.1 13.0 + - - +
288A CYS 3.3 2.2 + - - +
290A ILE* 1.3 76.2 - - - +
292A TYR* 1.3 62.6 + - - +
294A LEU 3.2 21.7 + - - +
295A GLU* 3.0 32.3 + - - +
296A PRO* 5.5 4.3 - - - +
334A PRO* 3.6 43.1 - - + +
335A GLU 4.2 6.7 + - - -
336A PRO* 3.8 23.1 - - + +
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Residues in contact with TYR 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A CYS 2.9 18.0 + - - +
289A LEU* 3.5 16.2 - - + +
291A ARG* 1.3 77.1 - - - +
293A MET* 1.3 59.1 + - - +
295A GLU* 3.7 11.1 - - - +
300A LYS 5.5 0.7 - - - -
302A PRO* 3.0 50.1 - - + +
306A GLN* 3.3 33.1 + - - +
307A VAL* 4.9 2.5 - - + -
310A PHE* 3.7 23.3 - + - -
330A PRO* 3.4 26.4 - - + +
333A LEU* 3.6 32.3 - - + -
334A PRO* 3.8 18.8 - - + +
402A PEG 4.2 8.0 + - - -
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Residues in contact with MET 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A PHE* 3.5 26.2 - - + -
245A ILE* 3.7 13.7 - - + +
246A TRP* 4.0 5.2 - - - -
248A LEU* 3.8 7.9 - - - -
249A GLY* 3.5 32.8 - - - -
252A LEU* 3.6 19.5 - - + -
289A LEU* 3.4 25.5 + - + +
290A ILE* 3.3 2.8 + - - +
291A ARG 3.3 0.2 - - - -
292A TYR* 1.3 73.6 - - + +
294A LEU* 1.3 60.3 + - - +
295A GLU 2.9 11.6 + - - -
301A ARG* 3.4 22.9 + - - +
302A PRO* 4.2 5.8 - - + -
307A VAL* 3.6 38.1 - - + -
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A TRP* 3.4 56.1 - - + +
249A GLY* 3.9 6.7 - - - +
250A CYS* 3.7 14.6 - - - +
261A PRO* 4.1 14.8 - - + -
262A PHE* 4.0 9.9 - - + -
272A GLY* 4.8 3.6 - - - +
274A PHE* 3.7 38.8 - - + -
290A ILE* 3.1 32.7 + - + +
291A ARG* 3.2 20.0 + - - +
293A MET* 1.3 73.4 - - - +
295A GLU* 1.3 57.0 + - - +
296A PRO* 3.6 8.5 - - - +
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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