Contacts of the helix formed by residues 283 - 299 (chain A) in PDB entry 1TF5
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 HIS 283 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ILE* 3.3 48.3 - - + +
276A ASP 5.0 1.1 - - - -
277A ASN 3.1 23.5 + - - -
278A LEU* 3.7 14.1 - - + +
280A ASP* 2.7 16.8 + - + +
282A LYS* 1.3 110.4 - - + +
284A VAL* 1.3 62.4 + - - -
285A ALA* 3.2 3.4 - - - -
286A LEU* 3.1 20.1 + - + +
287A ASN* 2.8 21.1 + - - +
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Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ASP 3.6 1.0 + - - -
281A VAL* 3.3 26.7 + - - +
282A LYS 3.5 0.8 - - - -
283A HIS* 1.3 75.6 - - - +
285A ALA* 1.3 58.5 + - - +
287A ASN* 3.7 2.1 - - - +
288A HIS* 2.8 28.0 + - + +
730A ALA* 3.6 24.5 - - + +
733A GLN* 3.7 19.3 - - + +
734A LEU* 3.8 15.7 - - + +
741A ARG* 3.5 30.5 + - - +
759A MET* 3.4 20.2 - - + -
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 4.5 9.4 - - + -
282A LYS 5.2 1.7 + - - +
283A HIS 3.2 0.8 - - - -
284A VAL* 1.3 77.7 - - - +
286A LEU* 1.3 58.7 + - - +
288A HIS* 3.0 2.6 + - - +
289A HIS* 2.8 44.0 + - + +
729A ASP* 5.4 2.7 - - - +
730A ALA* 5.4 4.6 - - + +
733A GLN* 3.4 25.3 + - - +
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 3.7 29.5 - - + +
237A ALA* 5.6 0.9 - - + -
273A PHE* 3.5 59.0 - - + -
275A ILE* 3.9 22.7 - - + -
278A LEU* 4.6 4.9 - - + -
283A HIS* 3.1 20.9 + - + +
285A ALA* 1.3 78.4 - - - +
287A ASN* 1.3 63.8 + - - +
289A HIS* 3.4 3.0 + - + +
290A ILE* 3.1 30.8 + - + +
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Residues in contact with ASN 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 5.6 1.8 - - - +
266A MET* 5.7 0.6 - - - -
278A LEU* 3.3 49.4 + - + +
279A PHE* 4.8 16.2 - - - -
283A HIS 2.8 13.6 + - - +
284A VAL 3.7 3.9 - - - +
286A LEU* 1.3 73.9 - - - +
288A HIS* 1.3 66.7 + - - +
290A ILE* 3.4 5.4 + - - +
291A ASN* 3.0 50.4 + - - +
740A LEU* 5.6 2.3 - - - +
741A ARG* 3.8 20.7 + - - +
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Residues in contact with HIS 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A VAL* 2.8 18.3 + - + +
285A ALA 3.4 4.3 - - - +
287A ASN* 1.3 78.8 + - - +
289A HIS* 1.3 61.9 + + - +
291A ASN* 3.1 13.0 + - + +
292A GLN* 3.0 48.1 + - + +
331A GLU* 2.9 32.3 + - + +
332A GLY* 5.6 1.3 - - - -
733A GLN* 3.2 45.4 + - + +
736A GLN* 4.2 18.5 + - + -
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Residues in contact with HIS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LYS* 4.2 20.4 + - - -
230A SER 5.6 0.6 + - - -
233A LEU* 3.8 26.8 - - + +
234A TYR* 3.4 60.0 - + - -
237A ALA* 3.7 16.4 - - + +
285A ALA* 2.8 36.8 + - + +
286A LEU 3.7 5.4 - - - +
288A HIS* 1.3 78.2 - + - +
290A ILE* 1.3 56.8 + - - +
292A GLN* 3.8 6.6 - - + +
293A ALA* 2.9 30.1 + - - +
336A ALA* 5.5 0.5 - - - +
733A GLN* 4.3 12.5 + - - -
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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
----------------------------------------------------------
237A ALA* 4.4 9.6 - - + -
240A PHE* 4.0 26.2 - - + -
241A VAL* 4.1 4.7 - - + +
244A LEU* 5.5 0.4 - - + -
261A LEU* 4.3 21.8 - - + -
269A ALA* 4.0 18.4 - - + -
273A PHE* 3.8 28.0 - - + -
278A LEU* 4.5 11.9 - - + -
286A LEU* 3.1 30.7 + - + +
287A ASN* 3.8 6.3 - - - +
288A HIS 3.2 0.2 - - - -
289A HIS* 1.3 73.2 - - - +
291A ASN* 1.3 65.1 + - - +
293A ALA* 4.0 2.9 - - - +
294A LEU* 2.9 28.6 + - + +
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Residues in contact with ASN 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A VAL 4.5 15.3 - - - +
260A GLN* 5.2 0.7 - - - -
261A LEU* 5.0 13.7 + - - +
287A ASN* 3.0 43.5 + - - +
288A HIS* 3.1 12.3 + - + +
290A ILE* 1.3 80.9 - - - +
292A GLN* 1.3 59.0 - - + +
294A LEU* 3.4 9.6 + - - +
295A LYS* 2.9 28.2 + - - +
740A LEU* 4.2 22.6 - - + +
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Residues in contact with GLN 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TYR* 6.3 1.1 - - + -
288A HIS* 3.0 42.5 + - + +
289A HIS* 3.8 7.2 - - + +
291A ASN* 1.3 78.5 - - - +
293A ALA* 1.3 59.5 + - - +
295A LYS* 3.4 22.5 + - - +
296A ALA* 2.8 28.8 + - - +
330A SER 3.9 2.8 + - - -
331A GLU* 2.8 31.1 + - - +
332A GLY* 4.4 4.5 - - - +
333A LEU* 3.5 24.7 - - - +
336A ALA* 3.6 17.5 - - + +
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TYR 5.4 0.7 - - - +
237A ALA* 3.9 16.6 - - + +
238A ASN* 4.1 11.7 - - + +
241A VAL* 3.4 24.2 - - + -
289A HIS 2.9 17.9 + - - +
290A ILE 4.0 0.2 - - - +
292A GLN* 1.3 74.9 - - - +
294A LEU* 1.3 64.4 + - - +
296A ALA* 3.4 2.9 + - - +
297A HIS* 3.0 32.2 + - - +
336A ALA* 4.1 12.7 - - + +
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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
----------------------------------------------------------
241A VAL* 3.6 25.5 - - + +
244A LEU* 3.9 9.0 - - + -
250A TYR* 3.6 44.0 - - + -
259A VAL* 3.5 30.7 - - + +
260A GLN 4.3 9.9 - - - -
261A LEU* 3.9 16.8 - - + +
290A ILE* 2.9 20.5 + - + +
291A ASN* 3.5 10.3 - - - +
293A ALA* 1.3 78.6 - - - +
295A LYS* 1.3 62.8 + - - +
297A HIS* 3.2 2.3 + - - +
298A VAL* 3.0 30.7 + - + +
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Residues in contact with LYS 295 (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 LYS* 3.7 33.1 + - - +
259A VAL* 4.3 17.0 - - + +
291A ASN 2.9 18.6 + - - +
292A GLN* 3.6 22.7 - - - +
294A LEU* 1.3 77.4 - - - +
296A ALA* 1.3 56.5 + - - +
299A ALA* 2.8 33.0 + - + +
300A MET* 3.4 15.7 + - + +
333A LEU* 3.8 28.9 - - + -
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Residues in contact with ALA 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLN 2.8 18.8 + - - +
293A ALA* 3.6 7.0 - - - +
294A LEU 3.2 0.2 - - - -
295A LYS* 1.3 77.8 - - - +
297A HIS* 1.3 58.3 + - - +
300A MET* 3.5 20.7 - - - +
333A LEU* 4.2 2.0 - - + +
336A ALA* 4.0 17.0 - - + +
337A ILE* 3.9 26.1 - - + +
340A LYS* 2.8 29.2 + - + +
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Residues in contact with HIS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ASN* 2.6 38.8 + - - -
241A VAL* 4.2 16.2 - - + +
242A ARG* 3.8 33.2 + - + +
293A ALA 3.0 28.5 + - - +
294A LEU 3.2 2.7 + - - +
296A ALA* 1.3 80.0 - - + +
298A VAL* 1.3 66.8 + - + +
300A MET 4.7 2.5 - - - +
336A ALA 5.5 0.2 - - - -
340A LYS* 3.6 35.5 + - + +
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A TYR* 3.6 39.9 - - + +
252A TYR* 3.2 42.1 + - + -
259A VAL* 4.4 8.1 - - + -
294A LEU* 3.0 18.8 + - + +
297A HIS* 1.3 88.8 - - + +
299A ALA* 1.3 60.8 + - - +
300A MET 3.6 2.0 - - - -
301A GLN* 5.6 3.5 - - - +
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A TYR* 3.7 22.4 - - + -
257A LYS* 3.7 44.6 + - + +
259A VAL* 4.0 4.7 - - + -
295A LYS* 2.8 25.3 + - + +
298A VAL* 1.3 73.5 - - - +
300A MET* 1.3 68.9 + - - +
301A GLN* 4.2 4.4 + - - +
305A ASP* 3.7 7.8 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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