Contacts of the helix formed by residues 353 - 371 (chain A) in PDB entry 3AFF
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 ALA 353 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A THR 4.0 11.9 - - - +
348A ALA* 3.7 21.1 - - - +
350A SER* 3.0 16.5 + - - +
351A ASN 3.3 0.4 - - - -
352A GLU* 1.3 76.2 - - - +
354A PRO* 1.4 71.2 - - + +
355A ILE* 3.0 8.5 + - + +
356A GLN* 2.8 28.3 + - - +
357A ARG* 5.1 1.3 - - - -
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Residues in contact with PRO 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ALA* 3.8 22.4 - - + +
259A HIS* 6.6 0.2 - - + -
352A GLU 3.5 8.9 - - - +
353A ALA* 1.4 83.8 - - + +
355A ILE* 1.3 63.8 + - + +
357A ARG* 3.2 29.9 + - - +
358A PHE* 3.1 29.3 + - + -
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Residues in contact with ILE 355 (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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252A ALA* 3.4 44.0 - - + +
255A ALA* 4.1 16.4 - - + +
256A HIS* 4.9 0.9 - - + -
259A HIS* 6.3 2.2 - - + -
337A ILE* 4.9 3.6 - - + +
340A LEU* 4.2 17.0 - - + +
341A PHE* 4.1 21.1 - - + +
344A SER* 4.3 23.1 - - - +
348A ALA* 4.4 15.0 - - + -
353A ALA* 3.0 10.3 + - + -
354A PRO* 1.3 79.5 - - + +
356A GLN* 1.3 67.5 + - - +
358A PHE* 3.5 3.1 + - - +
359A TRP* 3.0 20.8 + - - +
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Residues in contact with GLN 356 (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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28A GLN* 5.2 0.2 + - - -
341A PHE* 3.8 20.2 - - + -
348A ALA 3.4 16.8 + - - +
349A LEU* 4.2 6.0 - - - +
350A SER 3.1 23.5 + - - +
351A ASN* 3.5 29.2 + - - +
353A ALA 2.8 19.7 + - - +
355A ILE* 1.3 82.1 - - - +
357A ARG* 1.3 70.1 + - - +
359A TRP* 3.6 4.6 - - + +
360A ARG* 2.8 69.7 + - + +
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Residues in contact with ARG 357 (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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27A ALA* 4.0 30.7 + - - +
28A GLN* 3.2 32.6 + - - +
31A GLU* 2.7 38.8 + - - +
78A VAL 5.9 0.2 + - - -
79A CYS* 5.9 3.4 - - - +
80A GLY 5.8 2.9 - - - +
351A ASN 4.3 7.7 + - - -
352A GLU* 5.3 3.6 + - - +
353A ALA 4.8 3.0 + - - -
354A PRO* 3.2 28.9 + - - +
355A ILE 3.1 0.6 - - - -
356A GLN* 1.3 84.6 - - - +
358A PHE* 1.3 69.1 + - + +
360A ARG* 3.3 14.4 + - - +
361A ASP* 2.9 50.0 + - - +
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Residues in contact with PHE 358 (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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24A ARG* 6.2 1.3 - - + -
76A ALA 3.3 25.6 - - - -
77A SER 3.3 23.3 - - - -
78A VAL* 3.8 18.4 - - - -
79A CYS* 4.2 1.6 - - - -
80A GLY* 4.4 7.0 - - - -
248A MET* 3.5 32.8 - - + +
251A GLY* 3.6 21.5 - - - -
252A ALA* 3.8 13.2 - - + -
255A ALA* 4.6 2.0 - - + -
337A ILE* 4.4 2.1 - - - +
354A PRO* 3.1 38.1 + - + -
355A ILE* 4.0 4.5 - - - +
357A ARG* 1.3 86.2 - - + +
359A TRP* 1.3 54.1 + - - +
361A ASP* 3.9 4.2 - - - +
362A ALA* 2.8 36.6 + - - +
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Residues in contact with TRP 359 (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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337A ILE* 3.7 24.1 - - + +
338A ASP* 2.8 29.3 + - - -
341A PHE* 3.7 52.4 - + + -
355A ILE 3.0 20.5 + - - +
356A GLN* 3.6 6.7 - - + +
358A PHE* 1.3 76.0 - - - +
360A ARG* 1.3 96.5 + - + +
362A ALA* 4.0 0.5 - - - -
363A HIS* 3.1 49.7 + + + -
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Residues in contact with ARG 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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31A GLU* 2.6 36.1 + - - -
185A VAL* 2.8 51.1 + - + +
186A GLY* 3.7 9.2 - - - -
188A ARG* 3.3 27.5 - - - +
356A GLN* 2.8 45.5 + - + +
357A ARG* 3.5 15.0 - - - +
359A TRP* 1.3 93.4 - - + +
361A ASP* 1.3 63.5 + - - +
363A HIS* 3.4 4.6 + - - +
364A ALA* 2.9 30.8 + - - +
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Residues in contact with ASP 361 (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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31A GLU* 4.6 2.9 - - - +
79A CYS* 5.9 0.3 - - - -
80A GLY* 3.6 20.4 + - - -
81A SER* 3.9 6.2 + - - -
186A GLY* 3.8 2.6 - - - -
187A LEU* 2.8 47.8 + - + +
188A ARG 4.3 1.7 + - - -
248A MET* 3.6 19.6 - - - +
357A ARG* 2.9 40.7 + - - +
358A PHE* 3.9 4.5 - - - +
360A ARG* 1.3 78.4 + - - +
362A ALA* 1.3 59.4 + - - +
364A ALA 3.4 0.5 + - - -
365A GLY* 3.0 24.3 + - - -
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Residues in contact with ALA 362 (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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245A ILE* 4.5 6.5 - - + +
248A MET* 3.6 15.9 - - + -
334A ILE* 3.6 23.8 - - + +
337A ILE* 3.4 28.9 - - + -
358A PHE 2.8 19.0 + - - +
359A TRP* 4.0 3.6 - - - +
361A ASP* 1.3 79.6 - - - +
363A HIS* 1.3 61.3 + - - +
365A GLY* 3.3 2.7 + - - -
366A ARG 3.1 17.0 + - - -
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Residues in contact with HIS 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ILE* 3.5 32.1 + - + +
337A ILE* 5.5 0.9 - - + +
338A ASP* 2.7 29.4 + - - -
359A TRP* 3.1 55.3 + + + +
360A ARG* 3.9 4.7 - - - +
362A ALA* 1.3 75.2 - - + +
364A ALA* 1.3 60.0 + - - +
366A ARG* 3.3 10.9 + - - +
367A VAL* 3.0 34.1 + - + +
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Residues in contact with ALA 364 (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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141A TRP* 4.3 7.6 - - + -
185A VAL* 5.8 3.1 - - + -
186A GLY* 3.5 33.9 - - - +
187A LEU* 3.9 9.6 - - + -
360A ARG 2.9 18.1 + - - +
361A ASP 3.6 4.3 - - - +
363A HIS* 1.3 74.7 - - - +
365A GLY* 1.3 63.4 + - - +
367A VAL* 3.2 13.8 + - - +
368A HIS* 3.1 20.1 + - - +
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Residues in contact with GLY 365 (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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84A TRP* 3.7 31.8 - - - -
187A LEU* 3.6 4.6 - - - +
245A ILE* 3.8 10.3 - - - +
361A ASP 3.0 13.5 + - - -
362A ALA 3.3 4.0 + - - -
363A HIS 3.2 0.4 - - - -
364A ALA* 1.3 77.4 - - - +
366A ARG* 1.3 56.1 + - - +
368A HIS* 3.1 6.1 + - - +
369A ALA* 3.0 26.5 + - - +
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Residues in contact with ARG 366 (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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245A ILE* 4.0 4.1 - - - +
327A VAL* 3.8 30.1 - - - +
330A THR* 4.1 20.7 - - - +
331A GLY* 5.6 3.8 - - - +
334A ILE* 3.9 18.6 - - + -
362A ALA 3.1 13.5 + - - +
363A HIS* 3.4 15.5 - - - +
365A GLY* 1.3 72.0 - - - +
367A VAL* 1.3 61.2 + - + +
369A ALA* 3.4 21.0 + - - +
370A ALA* 2.8 58.9 + - - +
375A ARG* 5.3 8.1 - - - +
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Residues in contact with VAL 367 (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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141A TRP* 5.1 10.5 - - + +
363A HIS* 3.0 27.1 + - + +
364A ALA* 3.2 10.7 + - - +
366A ARG* 1.3 75.0 - - - +
368A HIS* 1.3 65.0 + - - +
370A ALA* 3.4 3.7 + - - -
371A ASN* 2.7 42.6 + - - +
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Residues in contact with HIS 368 (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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84A TRP* 3.5 24.3 - + + -
88A ILE* 5.5 4.0 - - + -
141A TRP* 3.6 61.5 + + + +
237A HIS* 6.3 2.9 - + - -
241A ILE* 4.1 17.4 - - + +
364A ALA 3.1 6.8 + - - +
365A GLY 3.1 8.5 + - - +
367A VAL* 1.3 78.1 - - - +
369A ALA* 1.3 60.6 + - - +
371A ASN* 3.0 17.6 + - + -
372A ASP* 3.4 20.4 + - + +
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Residues in contact with ALA 369 (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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241A ILE* 4.1 20.6 - - + +
242A SER* 6.0 1.1 - - - +
245A ILE* 5.0 3.4 - - + -
330A THR* 5.5 1.8 - - + -
365A GLY 3.0 12.7 + - - +
366A ARG* 3.7 27.3 + - - +
368A HIS* 1.3 76.6 + - - +
370A ALA* 1.3 62.2 - - - +
372A ASP* 3.3 20.2 + - - +
375A ARG* 3.6 10.2 - - - +
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Residues in contact with ALA 370 (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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366A ARG* 2.8 49.7 + - + +
367A VAL* 4.0 5.6 - - - +
368A HIS 3.3 0.2 - - - -
369A ALA* 1.3 74.1 - - - +
371A ASN* 1.3 62.5 + - - +
372A ASP 3.3 3.1 + - - +
375A ARG* 2.7 32.6 + - - +
379B ILE 5.6 0.2 - - - +
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Residues in contact with ASN 371 (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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367A VAL* 2.7 39.4 + - + +
368A HIS* 3.0 9.6 + - + +
370A ALA* 1.3 80.3 + - - +
372A ASP* 1.3 62.2 + - - +
373A PRO* 3.3 9.4 - - - +
381B GLY* 4.7 9.3 + - - +
382B ASN* 3.0 39.7 + - - +
384B GLU* 4.4 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
------------------------------------------------------------
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