Contacts of the helix formed by residues 346 - 363 (chain A) in PDB entry 1F7U
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 LEU 346 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ILE* 3.5 46.2 - - + +
339A GLN 4.6 1.1 - - - +
340A LYS* 4.6 12.3 - - + +
344A THR* 5.6 0.4 - - - +
345A THR* 1.3 79.5 - - - +
347A TYR* 1.3 67.2 + - + +
348A LEU* 3.2 4.9 - - + +
349A THR* 3.0 17.9 + - + +
350A ARG* 3.0 31.0 + - - +
974B C 3.5 33.2 - - + +
975B C 4.2 10.1 - - - +
976B A 3.7 15.0 - - - +
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Residues in contact with TYR 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A TYR* 4.9 2.8 + + - -
294A GLU* 3.5 23.1 - - - -
346A LEU* 1.3 72.8 - - - +
348A LEU* 1.3 61.9 + - - +
350A ARG* 3.3 12.0 + - - +
351A ASP* 3.1 22.4 + - - +
375A GLN* 2.8 23.6 + - - -
378A HIS* 3.2 30.7 - + - -
800A ARG* 2.7 48.9 + - + +
976B A 3.0 83.3 + + + +
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Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ALA* 3.5 31.9 - - + -
337A ILE 4.0 16.4 - - - +
338A VAL* 4.6 7.0 - - + -
346A LEU* 3.2 2.1 - - + +
347A TYR* 1.3 77.7 - - - +
349A THR* 1.3 65.6 + - + +
351A ASP* 3.2 11.6 + - - +
352A VAL* 3.2 15.2 + - + +
378A HIS* 3.4 30.4 - - + +
381A GLN* 4.3 6.1 - - + +
382A PHE* 3.2 43.3 - - + +
385A ILE* 4.0 16.8 - - + -
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Residues in contact with THR 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A MET* 3.8 13.8 - - - +
309A PHE* 6.0 6.4 - - - -
337A ILE 4.5 0.4 - - - +
338A VAL* 2.7 47.3 - - - +
345A THR* 3.1 25.6 - - - -
346A LEU* 3.0 27.6 + - + +
348A LEU* 1.3 74.7 - - - +
350A ARG* 1.3 64.1 + - - +
352A VAL* 3.4 9.3 + - - +
353A GLY 3.3 15.8 + - - -
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Residues in contact with ARG 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A TYR* 3.6 12.5 + - - +
192A TRP* 4.0 15.8 - - - +
193A GLY* 4.5 4.8 - - - +
252A PHE* 4.4 12.3 - - - -
294A GLU* 2.6 59.2 + - - +
297A VAL* 4.3 9.0 - - + +
302A MET* 4.6 10.8 - - + -
345A THR* 3.3 44.6 + - - +
346A LEU 3.0 19.2 + - - +
347A TYR* 3.7 10.0 - - - +
349A THR* 1.3 80.9 + - - +
351A ASP* 1.3 59.8 + - - +
353A GLY* 3.4 1.3 + - - +
354A ALA* 2.9 29.5 + - - +
976B A 2.8 36.0 + - - -
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Residues in contact with ASP 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A TYR* 3.7 12.4 + - - -
347A TYR* 3.1 15.6 + - - +
348A LEU 3.2 8.5 + - - +
350A ARG* 1.3 76.1 - - - +
352A VAL* 1.3 64.5 + - - +
354A ALA* 3.2 3.8 + - - +
355A ALA* 3.0 25.1 + - - +
358A ARG* 5.2 0.3 + - - -
369A TYR* 4.1 3.6 + - - -
378A HIS* 2.8 25.0 + - - +
382A PHE* 3.8 34.1 - - + -
800A ARG* 2.8 38.1 + - - -
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ALA* 4.3 3.6 - - + -
309A PHE* 4.2 15.0 - - + -
348A LEU* 3.2 13.8 + - + +
349A THR* 3.6 8.3 - - - +
351A ASP* 1.3 78.0 - - - +
353A GLY* 1.3 62.6 + - - +
355A ALA* 3.5 4.1 + - - +
356A MET* 3.3 31.3 + - - +
382A PHE* 4.1 22.7 - - + +
385A ILE* 4.2 22.2 - - + -
386A LEU* 3.7 21.8 - - + +
389A MET* 3.8 18.6 - - + -
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Residues in contact with GLY 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A VAL* 3.6 21.3 - - - -
301A SER* 3.6 6.8 - - - -
302A MET* 4.3 6.5 - - - -
305A ALA* 5.3 1.5 - - - +
349A THR 3.3 9.7 + - - -
350A ARG 3.4 0.4 + - - -
351A ASP 3.3 0.2 - - - -
352A VAL* 1.3 78.6 - - - +
354A ALA* 1.3 62.9 - - - +
356A MET* 3.3 15.5 + - - +
357A ASP* 3.1 26.0 + - - +
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Residues in contact with ALA 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A TYR* 3.8 28.0 - - + +
293A GLY 5.8 0.2 - - - +
297A VAL* 3.9 7.3 - - + +
350A ARG 2.9 18.2 + - - +
351A ASP* 3.2 6.3 + - - +
353A GLY* 1.3 74.3 - - - +
355A ALA* 1.3 65.8 + - - +
357A ASP* 3.1 10.6 + - - +
358A ARG* 2.9 40.9 + - - +
369A TYR* 6.0 0.2 - - - +
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Residues in contact with ALA 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ASP 3.0 16.6 + - - +
352A VAL 3.6 6.1 - - - +
354A ALA* 1.3 77.0 - - - +
356A MET* 1.3 62.2 + - - +
358A ARG* 3.5 2.7 + - - +
359A TYR* 3.2 18.5 + - - +
364A PHE* 4.3 1.9 - - - -
367A MET* 4.1 9.2 - - + -
369A TYR* 3.7 20.1 + - - +
386A LEU* 3.6 26.0 - - + -
393A TRP* 3.7 20.1 - - + -
397A LEU* 4.8 0.2 - - + -
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Residues in contact with MET 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A SER* 3.6 30.3 - - - +
304A LYS* 3.6 34.1 - - + +
305A ALA* 3.8 26.0 - - - +
308A LEU* 4.5 0.2 - - + -
352A VAL* 3.3 17.2 + - - +
353A GLY* 3.4 10.3 - - - +
354A ALA 3.1 0.6 - - - -
355A ALA* 1.3 76.2 - - - +
357A ASP* 1.3 64.9 + - - +
359A TYR* 3.5 3.3 + - - +
360A GLU* 3.2 22.6 + - - +
386A LEU* 4.5 0.7 - - + -
389A MET* 4.0 11.4 - - + -
391A PHE* 3.6 31.9 - - + -
393A TRP* 4.1 10.8 - - + -
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Residues in contact with ASP 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLN 4.0 4.5 - - - +
297A VAL* 3.3 11.3 - - - +
298A SER* 2.8 40.0 + - - -
301A SER* 2.5 24.2 + - - -
353A GLY 3.1 16.0 + - - +
354A ALA* 3.6 7.9 - - - +
356A MET* 1.3 72.6 - - - +
358A ARG* 1.3 60.6 + - + +
360A GLU* 3.2 7.7 + - - +
361A LYS* 2.9 31.6 + - - +
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Residues in contact with ARG 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 4.0 12.8 - - + +
148A GLU* 2.9 38.8 + - - +
186A MET* 3.5 33.0 - - + -
188A TYR* 3.1 38.8 - - - +
292A SER* 5.2 2.2 + - - -
351A ASP* 5.2 0.4 + - - -
354A ALA* 2.9 29.8 + - + +
355A ALA* 3.7 4.0 - - - +
357A ASP* 1.3 78.1 - - + +
359A TYR* 1.3 57.4 + - - +
361A LYS* 4.8 0.7 - - - -
362A TYR* 2.8 42.5 + - + +
364A PHE* 4.1 2.2 - - + -
367A MET* 3.5 30.3 - - - -
369A TYR* 3.5 19.6 - - - -
800A ARG* 4.6 0.6 + - - -
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Residues in contact with TYR 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ALA 3.2 12.6 + - - +
356A MET 3.9 4.3 - - - +
358A ARG* 1.3 78.5 - - - +
360A GLU* 1.3 65.1 + - - +
363A HIS* 2.7 67.3 + + - +
364A PHE* 3.6 42.8 - + + -
392A GLU* 4.2 14.5 + - + -
393A TRP* 3.5 54.6 - + + +
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Residues in contact with GLU 360 (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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301A SER* 6.1 0.2 - - - +
304A LYS* 5.2 7.4 + - - -
356A MET 3.2 11.8 + - - +
357A ASP* 3.2 12.4 + - - +
359A TYR* 1.3 84.7 - - - +
361A LYS* 1.3 57.0 + - - +
363A HIS* 3.3 33.8 + - - -
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Residues in contact with LYS 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LYS* 5.3 0.5 + - - -
290A VAL* 4.6 13.7 - - - +
357A ASP 2.9 16.8 + - - +
358A ARG* 4.1 2.5 - - - +
360A GLU* 1.3 79.4 - - - +
362A TYR* 1.3 101.9 + - + +
363A HIS* 4.8 3.2 - - - -
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Residues in contact with TYR 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LYS* 2.8 40.6 + - + +
146A ILE* 3.4 25.1 - - + -
184A ILE* 4.3 32.1 - - + -
186A MET* 4.0 20.0 - - + +
290A VAL* 3.4 24.0 - - + +
358A ARG* 2.8 33.5 + - + +
361A LYS* 1.3 124.3 + - + +
363A HIS* 1.3 72.9 + - - +
364A PHE 4.2 1.8 - - - +
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Residues in contact with HIS 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LYS* 4.8 3.1 + - - +
359A TYR* 2.7 59.2 + + + +
360A GLU* 3.3 33.2 + - - -
361A LYS 4.8 2.5 - - - -
362A TYR* 1.3 77.2 - - - +
364A PHE* 1.3 66.3 + - - +
365A ASP* 3.8 6.6 + - - +
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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