Contacts of the helix formed by residues 299 - 309 (chain B) in PDB entry 1TE6
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 299 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251B TYR* 4.7 9.2 - - + -
254B GLY 5.6 0.5 - - - +
256B TYR* 2.7 37.0 + - - +
272B GLY* 5.2 1.2 - - - -
295B PHE* 4.3 1.3 - - + -
296B ASP* 2.9 18.5 + - + +
297B GLN 3.6 0.2 - - - -
298B ASP* 1.3 74.0 - - - +
300B TRP* 1.3 62.6 + - - +
301B ALA* 3.2 6.5 + - - +
302B ALA* 3.1 32.4 + - - +
303B TRP* 3.2 15.6 + - - -
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Residues in contact with TRP 300 (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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297B GLN 4.1 4.4 + - - -
298B ASP* 3.0 29.0 + - - +
299B ASP* 1.3 75.4 - - - +
301B ALA* 1.3 61.9 + - - +
303B TRP* 3.2 6.7 + - - +
304B SER* 3.0 27.5 + - - -
319B LEU* 3.9 26.5 - - + -
326B ARG* 3.3 42.4 - - - +
329B ARG* 3.3 49.5 - - + +
330B ALA* 3.5 40.2 - - + -
333B GLU* 3.5 24.9 - - - +
335B ALA* 3.7 22.2 - - + -
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Residues in contact with ALA 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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299B ASP* 3.1 7.0 + - - +
300B TRP* 1.3 77.8 - - - +
302B ALA* 1.3 61.9 + - - +
304B SER* 4.0 3.6 - - - -
305B LYS* 3.1 27.0 + - - +
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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
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272B GLY* 5.0 7.4 - - - -
295B PHE* 3.5 32.2 - - + -
299B ASP* 3.1 30.6 + - - +
301B ALA* 1.3 76.1 - - - +
303B TRP* 1.3 65.9 + - - +
305B LYS* 3.5 6.0 + - - +
306B PHE* 3.0 27.0 + - - +
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Residues in contact with TRP 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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293B ASP* 3.2 40.8 - - - -
294B PRO* 3.6 13.7 - - + -
295B PHE* 3.3 33.6 + - + -
296B ASP 3.0 22.8 + - - -
299B ASP 3.2 26.4 + - - -
300B TRP 3.2 7.0 + - - +
302B ALA* 1.3 77.6 - - - +
304B SER* 1.3 64.0 + - - +
306B PHE* 3.2 3.3 + - - +
307B THR* 2.9 27.7 + - - -
314B ILE* 3.8 15.3 - - + -
315B VAL 3.6 15.5 - - - -
316B GLY* 3.8 1.8 - - - -
319B LEU* 3.5 43.2 - - + +
335B ALA* 3.3 38.8 - - + +
336B CYS* 3.9 5.8 - - + -
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Residues in contact with SER 304 (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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300B TRP 3.0 14.0 + - - -
301B ALA* 4.1 3.6 - - - -
303B TRP* 1.3 77.7 - - - +
305B LYS* 1.3 62.2 + - - +
307B THR* 3.7 1.2 + - - -
308B ALA* 3.1 25.6 + - - +
333B GLU* 2.7 37.9 + - - +
334B LYS* 3.6 12.8 - - - +
335B ALA* 3.7 5.6 - - - +
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Residues in contact with LYS 305 (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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273B ASP* 3.8 35.4 + - - +
301B ALA 3.1 19.3 + - - +
302B ALA* 3.9 5.2 - - - +
304B SER* 1.3 77.1 - - - +
306B PHE* 1.3 63.7 + - - +
308B ALA* 3.4 5.0 + - - +
309B ASN* 3.0 46.5 + - - +
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Residues in contact with PHE 306 (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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276B GLY* 3.5 34.1 - - - -
279B TYR* 3.4 31.4 - + + -
280B GLN* 3.8 17.3 - - - -
283B VAL* 5.6 1.3 - - + -
291B ILE* 5.2 4.0 - - + -
294B PRO* 4.5 14.1 - - + -
295B PHE* 3.5 20.0 - + + -
302B ALA 3.0 18.6 + - - +
303B TRP* 3.7 2.7 - - - +
305B LYS* 1.3 75.8 - - - +
307B THR* 1.3 66.9 + - - +
309B ASN* 3.0 14.9 + - + +
310B VAL* 3.3 41.3 + - + +
312B ILE* 4.6 15.7 - - + -
314B ILE* 4.6 10.3 - - + -
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Residues in contact with THR 307 (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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303B TRP 2.9 9.6 + - - -
304B SER 4.1 0.2 - - - -
306B PHE* 1.3 76.3 - - - +
308B ALA* 1.3 63.4 + - - +
309B ASN 3.3 0.9 + - - -
310B VAL* 3.3 25.4 - - - +
314B ILE* 3.7 30.9 - - + +
334B LYS* 3.8 21.5 - - + +
335B ALA 2.8 21.8 + - - -
336B CYS* 4.3 12.6 - - - +
337B ASN* 4.3 7.4 - - + +
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Residues in contact with ALA 308 (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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304B SER 3.1 19.0 + - - +
305B LYS* 3.8 5.4 - - - +
306B PHE 3.2 0.2 - - - -
307B THR* 1.3 75.8 - - - +
309B ASN* 1.3 65.9 + - - +
310B VAL 3.6 1.4 + - - +
334B LYS* 6.5 0.9 - - + -
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Residues in contact with ASN 309 (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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280B GLN* 4.2 17.6 + - - +
305B LYS* 3.0 44.1 + - - +
306B PHE* 3.0 7.9 + - + +
308B ALA* 1.3 86.4 - - - +
310B VAL* 1.3 63.5 + - + +
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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