Contacts of the helix formed by residues 353 - 371 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347B THR* 3.6 23.6 - - - +
348B ALA* 4.0 10.5 - - - +
350B SER* 3.3 15.7 - - - +
351B ASN 3.2 3.6 + - - -
352B GLU* 1.3 75.7 - - - +
354B PRO* 1.3 70.5 - - + +
355B ILE* 3.2 8.5 + - + -
356B GLN* 3.0 24.2 + - - +
357B ARG* 4.6 0.4 - - - +
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Residues in contact with PRO 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ALA* 4.1 17.3 - - + -
352B GLU 3.7 8.5 - - - +
353B ALA* 1.3 82.9 - - + +
355B ILE* 1.3 62.8 + - - +
357B ARG* 2.9 41.2 + - + +
358B PHE* 3.2 22.8 + - + -
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Residues in contact with ILE 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ALA* 3.0 41.3 - - + +
255B ALA* 4.0 14.2 - - + +
256B HIS* 4.3 6.3 - - + +
337B ILE* 5.4 0.9 - - + +
340B LEU* 4.3 8.5 - - + -
341B PHE* 4.1 20.6 - - + -
344B SER* 4.1 21.3 - - - +
348B ALA* 3.9 34.8 - - + +
353B ALA* 4.4 6.5 - - + -
354B PRO* 1.3 80.0 - - + +
356B GLN* 1.3 67.1 + - - +
357B ARG 3.2 0.2 + - - -
358B PHE* 3.3 4.9 + - - +
359B TRP* 3.0 22.8 + - + +
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Residues in contact with GLN 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLN* 5.3 1.4 + - - -
31B GLU* 5.4 1.0 + - - -
341B PHE* 3.7 19.7 - - + -
348B ALA 3.4 17.7 - - - +
349B LEU* 4.5 4.5 - - - +
350B SER 3.2 21.1 - - - +
351B ASN* 3.3 30.0 + - - +
353B ALA 3.0 18.2 + - - +
355B ILE* 1.3 81.6 - - - +
357B ARG* 1.3 63.3 + - - +
359B TRP* 3.7 6.0 - - + +
360B ARG* 2.9 73.1 + - + +
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Residues in contact with ARG 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 5.0 3.0 + - - +
27B ALA* 3.4 39.7 - - - +
28B GLN* 4.5 10.1 + - - +
31B GLU* 3.3 36.5 + - + -
78B VAL 4.3 3.2 + - - -
79B CYS* 4.6 7.4 - - - +
80B GLY 5.0 2.2 - - - +
353B ALA 4.6 0.6 + - - +
354B PRO* 2.9 39.2 + - - +
356B GLN* 1.3 84.9 - - - +
358B PHE* 1.3 84.4 + - - +
360B ARG* 3.3 19.6 + - - +
361B ASP* 2.9 48.4 + - - +
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Residues in contact with PHE 358 (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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24B ARG* 6.0 2.0 - - + -
76B ALA 3.2 23.3 - - - -
77B SER 3.3 22.4 - - - -
78B VAL* 3.7 17.9 - - - -
79B CYS 4.3 0.9 - - - -
80B GLY 4.4 6.7 - - - -
248B MET* 3.3 34.0 - - + +
251B GLY* 3.6 20.6 - - - -
252B ALA* 3.8 13.9 - - + +
255B ALA* 4.7 1.3 - - + -
337B ILE* 4.3 3.6 - - - +
354B PRO* 3.2 36.4 + - + -
355B ILE 3.3 4.7 + - - +
357B ARG* 1.3 89.6 - - - +
359B TRP* 1.3 59.5 + - - +
361B ASP* 4.0 4.4 - - - +
362B ALA* 3.0 33.1 + - - +
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Residues in contact with TRP 359 (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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337B ILE* 3.7 22.1 - - + +
338B ASP* 2.7 30.9 + - - -
341B PHE* 3.7 52.1 - + + -
355B ILE 3.0 18.2 + - - +
356B GLN* 3.7 7.9 - - + +
358B PHE* 1.3 77.1 - - - +
360B ARG* 1.3 92.7 + - + +
362B ALA* 4.1 0.3 - - - -
363B HIS* 3.1 49.2 + + + -
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Residues in contact with ARG 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLU* 2.7 36.9 + - - -
185B VAL* 2.9 49.0 + - + +
186B GLY* 3.8 8.9 + - - -
188B ARG* 3.4 22.1 - - - +
356B GLN* 2.9 48.5 + - - +
357B ARG* 3.3 13.5 + - - +
359B TRP* 1.3 97.4 - - + +
361B ASP* 1.3 63.7 + - - +
363B HIS* 3.5 4.1 + - - +
364B ALA* 2.9 31.0 + - - +
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Residues in contact with ASP 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLU* 5.3 2.4 - - - +
79B CYS* 5.8 0.3 - - - -
80B GLY* 3.6 20.4 + - - -
81B SER* 3.8 5.4 + - - -
186B GLY* 3.7 3.5 - - - -
187B LEU* 2.7 48.8 + - + +
188B ARG 4.4 1.6 + - - -
248B MET* 3.6 18.5 - - - +
357B ARG* 2.9 34.4 + - - +
358B PHE* 4.0 4.5 + - - +
360B ARG* 1.3 79.3 + - - +
362B ALA* 1.3 65.7 + - - +
364B ALA* 3.4 1.7 + - - +
365B GLY* 2.9 19.9 + - - -
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Residues in contact with ALA 362 (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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245B ILE* 4.3 9.3 - - + +
248B MET* 3.5 18.5 - - + -
334B ILE* 3.6 23.6 - - + +
337B ILE* 3.5 26.5 - - + -
358B PHE 3.0 19.2 + - - +
359B TRP 4.2 2.2 - - - +
361B ASP* 1.3 74.9 - - - +
363B HIS* 1.3 59.3 + - + +
365B GLY* 3.2 1.8 + - - -
366B ARG 3.0 22.9 + - - -
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Residues in contact with HIS 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ILE* 3.5 26.1 - - + +
337B ILE* 5.5 1.1 - - + -
338B ASP* 2.8 31.3 + - - -
359B TRP* 3.1 53.8 + + + +
360B ARG* 3.8 5.2 - - - +
362B ALA* 1.3 77.8 - - + +
364B ALA* 1.3 59.4 + - - +
366B ARG* 3.2 8.5 + - - +
367B VAL* 3.0 34.4 + - + +
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Residues in contact with ALA 364 (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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141B TRP* 4.7 6.9 - - + -
185B VAL* 5.1 7.8 - - + +
186B GLY* 3.6 32.5 - - - +
187B LEU* 3.9 9.2 - - + +
360B ARG 2.9 18.7 + - - +
361B ASP 3.6 3.8 - - - +
363B HIS* 1.3 73.7 - - - +
365B GLY* 1.3 63.4 + - - +
367B VAL* 3.1 12.9 + - - +
368B HIS* 3.1 21.1 + - - +
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Residues in contact with GLY 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TRP* 3.7 30.3 - - - -
187B LEU* 3.7 2.8 - - - +
245B ILE* 3.7 12.5 - - - +
361B ASP 2.9 15.1 + - - -
362B ALA 3.6 4.3 - - - -
363B HIS 3.2 0.2 - - - -
364B ALA* 1.3 77.2 - - - +
366B ARG* 1.3 53.7 + - - +
368B HIS* 3.2 5.5 + - - +
369B ALA* 3.0 26.3 + - - +
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Residues in contact with ARG 366 (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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245B ILE* 3.9 4.4 - - + +
327B VAL* 4.5 26.1 - - - +
330B THR* 4.0 20.4 + - - +
331B GLY* 5.6 2.5 - - - +
334B ILE* 3.6 29.2 - - + -
362B ALA 3.0 8.6 + - - +
363B HIS* 3.2 8.0 + - - +
365B GLY* 1.3 72.1 - - - +
367B VAL* 1.3 62.7 + - - +
369B ALA* 4.1 14.3 + - - +
370B ALA* 2.9 62.5 + - + +
375B ARG* 5.5 7.9 - - - +
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Residues in contact with VAL 367 (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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141B TRP* 5.9 4.7 - - + +
363B HIS* 3.0 27.0 + - + +
364B ALA* 3.1 10.5 + - - +
366B ARG* 1.3 78.7 - - - +
368B HIS* 1.3 64.0 + - - +
370B ALA* 3.3 5.0 + - - +
371B ASN* 2.8 40.4 + - - +
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Residues in contact with HIS 368 (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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84B TRP* 3.5 24.5 - + + -
88B ILE* 5.6 2.9 - - + -
141B TRP* 3.5 64.0 + + + +
241B ILE* 4.0 15.8 - - + +
364B ALA 3.1 7.1 + - - +
365B GLY 3.3 8.7 - - - +
367B VAL* 1.3 78.4 - - - +
369B ALA* 1.3 61.2 + - - +
371B ASN* 3.2 15.1 + - + +
372B ASP* 3.6 10.5 + - + +
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Residues in contact with ALA 369 (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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241B ILE* 4.0 19.1 - - + -
242B SER* 6.1 0.7 - - - +
245B ILE* 4.9 3.1 - - + -
330B THR* 5.8 2.7 - - + +
365B GLY 3.0 15.9 + - - +
366B ARG* 3.3 22.8 + - - +
368B HIS* 1.3 75.2 + - - +
370B ALA* 1.3 61.9 + - - +
372B ASP* 3.3 23.2 + - - +
375B ARG* 4.1 6.6 - - - -
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Residues in contact with ALA 370 (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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366B ARG* 2.9 49.0 + - + +
367B VAL* 4.0 6.5 - - - +
368B HIS 3.3 0.2 - - - -
369B ALA* 1.3 76.2 - - - +
371B ASN* 1.3 60.8 + - - +
372B ASP 3.4 1.3 - - - -
375B ARG* 3.0 37.0 + - - +
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Residues in contact with ASN 371 (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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381A GLY* 4.6 12.5 + - - +
382A ASN* 3.0 38.3 + - - +
384A GLU* 4.4 2.3 - - - +
367B VAL* 2.8 35.6 + - - +
368B HIS* 3.2 8.9 + - + +
369B ALA 3.1 0.6 - - - -
370B ALA* 1.3 82.5 + - - +
372B ASP* 1.3 61.2 + - - +
373B PRO* 3.3 9.4 - - - +
375B ARG* 5.0 1.1 - - - +
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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