Contacts of the helix formed by residues 268 - 278 (chain B) in PDB entry 3TQI
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 ASN 268 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B ARG* 3.2 1.2 - - - +
267B LEU* 1.3 101.2 + - - +
269B GLU* 1.3 65.2 + - - +
270B VAL* 3.4 2.7 - - - -
271B ASP* 3.2 21.0 + - + +
272B GLU* 3.0 42.3 + - + +
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Residues in contact with GLU 269 (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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236B GLY 6.4 0.2 - - - +
237B GLY 5.4 0.9 + - - -
265B LEU* 4.3 18.1 - - + +
266B ARG* 3.0 41.0 + - - +
267B LEU 3.5 0.2 - - - -
268B ASN* 1.3 76.5 - - - +
270B VAL* 1.3 64.2 + - - +
272B GLU* 3.3 9.1 + - - +
273B VAL* 3.1 36.8 + - + +
399B ARG* 2.8 48.2 + - - +
402B PHE* 4.3 22.9 - - - +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LEU* 4.1 19.7 - - + -
261B ASP* 4.0 36.1 - - + +
265B LEU* 4.7 12.1 - - + +
266B ARG 4.7 1.8 + - - +
267B LEU 5.3 2.9 + - - +
268B ASN 3.4 0.2 - - - -
269B GLU* 1.3 75.8 - - + +
271B ASP* 1.3 67.5 + - - +
273B VAL* 3.0 23.7 - - - +
274B LEU* 3.0 22.0 + - + +
287B CYS* 5.6 3.8 - - + -
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Residues in contact with ASP 271 (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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267B LEU 5.5 0.5 - - - +
268B ASN* 3.2 25.0 + - + +
270B VAL* 1.3 83.2 - - - +
272B GLU* 1.3 57.9 + - + +
274B LEU* 3.3 8.0 + - - +
275B ASN* 2.9 44.5 + - - +
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Residues in contact with GLU 272 (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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268B ASN* 3.0 33.2 + - + +
269B GLU* 3.9 9.4 - - - +
270B VAL 3.3 0.2 - - - -
271B ASP* 1.3 78.2 - - + +
273B VAL* 1.3 62.9 + - + +
275B ASN* 3.6 11.8 + - - +
276B VAL* 3.3 23.6 + - - +
395B ASP* 6.2 0.2 - - - -
396B LEU* 5.6 1.2 - - - +
399B ARG* 3.9 21.5 + - - +
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Residues in contact with VAL 273 (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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234B LEU* 4.5 20.0 - - + +
235B SER* 6.2 0.2 - - - -
237B GLY* 6.1 2.5 - - - +
259B LEU* 3.2 33.4 - - + -
269B GLU* 3.1 25.3 + - + +
270B VAL* 3.0 19.3 - - - +
272B GLU* 1.3 76.5 - - + +
274B LEU* 1.3 60.4 + - - +
276B VAL* 2.9 12.9 - - + +
277B PHE* 2.8 40.7 + - + +
396B LEU* 5.6 6.7 - - + -
399B ARG* 5.3 7.9 - - - +
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Residues in contact with LEU 274 (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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234B LEU* 5.5 0.4 - - + -
259B LEU* 3.8 11.7 - - + -
270B VAL* 3.0 28.4 + - + +
271B ASP* 3.7 8.7 - - - +
273B VAL* 1.3 78.6 - - - +
275B ASN* 1.3 60.1 + - - +
277B PHE* 5.1 0.4 - - - -
278B GLN* 2.7 62.5 + - + +
279B LYS* 3.1 6.5 + - - +
285B VAL* 3.6 31.0 - - + -
287B CYS* 3.8 23.8 - - - -
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Residues in contact with ASN 275 (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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271B ASP* 2.9 33.4 + - - +
272B GLU* 3.8 12.0 - - - +
273B VAL 3.2 0.2 - - - -
274B LEU* 1.3 76.1 - - - +
276B VAL* 1.3 57.8 + - - +
279B LYS* 3.5 37.5 + - + +
280B HIS* 3.0 30.7 + - - +
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Residues in contact with VAL 276 (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 GLU 3.3 13.4 + - - +
273B VAL* 2.9 25.6 - - - +
275B ASN* 1.3 81.1 - - - +
277B PHE* 1.3 68.6 + - + +
280B HIS* 2.4 34.9 - - - +
281B LEU* 3.2 12.0 - - + +
392B LEU* 4.0 26.5 - - + -
393B PRO* 4.1 20.2 - - + -
396B LEU* 4.2 13.5 - - + -
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Residues in contact with PHE 277 (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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234B LEU* 3.6 36.8 - - + -
241B ALA* 3.5 39.5 - - + -
244B ALA* 3.6 22.4 - - + -
245B THR* 3.7 17.7 - - - -
248B HIS* 6.3 0.4 - - + -
255B LEU* 6.0 1.3 - - + -
257B CYS* 4.5 7.6 - - - -
273B VAL* 2.8 23.8 + - + +
274B LEU* 5.1 0.4 - - - -
276B VAL* 1.3 107.7 - - + +
278B GLN* 1.3 58.8 + - - +
280B HIS 3.7 0.9 - - - -
281B LEU* 2.9 23.6 - - + +
282B GLY 2.8 17.2 - - - +
283B ALA* 2.9 15.4 - - + +
285B VAL* 4.2 6.7 - - + -
392B LEU* 4.3 5.4 - - + -
396B LEU* 5.1 1.8 - - + -
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Residues in contact with GLN 278 (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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274B LEU* 2.7 56.2 + - + +
277B PHE* 1.3 74.8 - - - +
279B LYS* 1.3 72.0 + - + +
282B GLY* 2.8 21.5 - - - +
283B ALA 4.2 7.6 - - - +
285B VAL* 3.5 29.1 + - + +
287B CYS* 5.0 2.8 - - - -
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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