Contacts of the helix formed by residues 352 - 366 (chain B) in PDB entry 6APL
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 ASP 352 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290B SER* 2.7 39.1 + - - +
291B LYS* 4.4 2.4 + - - +
292B LEU* 3.8 8.7 - - + +
301B TYR* 3.7 10.2 + - + +
351B HIS* 1.3 72.8 - - - +
353B LEU* 1.3 59.1 + - - +
354B SER* 4.0 0.7 - - - -
355B LEU* 3.0 38.7 + - + +
356B GLU* 3.0 32.8 + - - +
165D GLN* 5.5 0.5 + - - -
168D ASN* 3.1 24.1 + - - -
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Residues in contact with LEU 353 (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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304B SER* 4.8 7.6 - - - +
326B ILE* 4.0 22.5 - - + +
351B HIS* 3.7 18.0 - - + +
352B ASP* 1.3 71.2 - - - +
354B SER* 1.3 61.3 + - - +
356B GLU* 3.1 22.4 + - - +
357B ALA* 2.7 31.5 + - - +
167D PRO* 3.8 20.0 - - + +
168D ASN* 3.1 9.5 + - - +
171D ALA* 4.2 24.0 - - + -
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Residues in contact with SER 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ASP* 4.0 0.7 - - - -
353B LEU* 1.3 75.9 - - - +
355B LEU* 1.3 57.2 + - - +
357B ALA* 3.4 3.4 + - - +
358B ALA* 2.9 29.1 + - - +
361B ARG* 4.5 2.8 + - - -
163D SER 5.3 0.2 - - - -
164D ARG* 2.9 29.0 + - - +
165D GLN* 3.4 16.6 - - - -
167D PRO* 3.6 10.3 - - - +
168D ASN* 2.9 42.4 + - - -
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Residues in contact with LEU 355 (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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287B PHE 4.8 4.5 - - - +
288B LEU* 3.8 42.6 - - + +
289B LYS 4.1 3.8 - - - +
290B SER* 3.8 21.8 - - - -
301B TYR* 4.5 1.3 - - - +
352B ASP* 3.0 28.8 + - + +
353B LEU 3.2 0.2 - - - -
354B SER* 1.3 78.3 - - - +
356B GLU* 1.3 56.8 + - - +
358B ALA* 3.1 10.5 + - + +
359B LEU* 2.9 28.8 + - + +
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Residues in contact with GLU 356 (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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288B LEU* 3.9 24.9 - - + +
301B TYR* 5.3 1.6 + - - +
303B PRO* 3.6 8.8 - - - +
304B SER* 2.8 48.8 + - - -
307B ALA* 3.5 12.5 - - + +
325B PHE* 5.9 0.5 - - - -
326B ILE* 4.7 3.4 - - + +
351B HIS* 4.4 5.9 - - - +
352B ASP 3.0 20.6 + - - +
353B LEU* 3.1 20.4 + - - +
355B LEU* 1.3 76.6 - - - +
357B ALA* 1.3 62.8 + - - +
359B LEU* 3.1 2.5 + - - +
360B TRP* 3.0 44.4 + - + +
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Residues in contact with ALA 357 (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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326B ILE* 3.8 30.4 - - + +
327B THR* 4.9 2.2 - - - -
353B LEU 2.7 19.2 + - - +
354B SER* 3.6 7.9 - - - +
356B GLU* 1.3 71.8 - - - +
358B ALA* 1.3 62.3 + - - +
360B TRP* 3.4 13.5 + - - +
361B ARG* 3.0 43.9 + - - +
167D PRO* 4.8 5.2 - - + -
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Residues in contact with ALA 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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354B SER 2.9 18.0 + - - +
355B LEU* 3.1 14.3 + - + +
357B ALA* 1.3 73.1 - - - +
359B LEU* 1.3 61.3 + - - +
361B ARG* 3.3 23.0 + - - +
362B ASP* 2.9 42.9 + - - +
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Residues in contact with LEU 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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80B PHE* 4.3 12.8 - - + -
287B PHE* 3.9 34.5 - - + +
288B LEU* 3.6 23.6 - - + -
311B LEU* 4.2 8.3 - - + -
355B LEU* 2.9 14.2 + - + +
356B GLU 3.4 8.5 - - - +
358B ALA* 1.3 76.6 - - - +
360B TRP* 1.3 79.3 + - + +
362B ASP* 3.1 5.5 + - + -
363B LEU* 2.7 58.5 + - + +
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Residues in contact with TRP 360 (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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288B LEU* 5.0 0.7 - - + -
307B ALA* 3.6 46.0 - - + -
310B LEU* 3.5 32.1 - - + -
311B LEU* 4.2 10.5 - - + -
314B LEU* 5.0 0.7 - - + -
325B PHE* 3.8 24.5 - + + -
326B ILE* 3.9 17.1 - - + +
356B GLU* 3.0 37.8 + - + +
357B ALA* 3.9 9.9 - - - +
358B ALA 3.4 0.2 - - - -
359B LEU* 1.3 102.8 - - + +
361B ARG* 1.3 62.6 + - - +
363B LEU* 3.9 16.2 - - + +
364B HIS* 3.0 24.9 + - - +
369B LEU* 4.0 12.2 - - + +
371B LEU* 3.8 21.8 - - + +
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Residues in contact with ARG 361 (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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327B THR* 5.1 1.8 - - - +
328B SER* 3.6 39.6 - - - +
354B SER 4.5 3.2 + - - -
357B ALA* 3.0 27.8 + - - +
358B ALA* 3.5 31.1 - - - +
360B TRP* 1.3 77.4 - - - +
362B ASP* 1.3 62.5 + - - +
364B HIS* 3.0 8.1 + - - +
365B LYS* 2.9 53.9 + - - +
371B LEU* 4.7 5.4 - - + -
373B GLN* 4.9 15.0 - - - +
164D ARG* 3.6 33.8 - - - +
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Residues in contact with ASP 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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79B HIS* 6.1 1.5 - - + -
80B PHE* 3.9 20.6 - - + -
358B ALA* 2.9 29.4 + - - +
359B LEU* 3.1 6.1 + - + +
361B ARG* 1.3 79.1 + - - +
363B LEU* 1.3 63.2 + - - +
364B HIS 3.2 0.5 + - - -
365B LYS* 3.4 17.7 + - - +
366B ALA* 3.3 23.2 + - - +
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Residues in contact with LEU 363 (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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80B PHE* 3.4 41.5 - - + -
84B PHE* 4.7 6.7 - - + -
287B PHE* 5.2 1.3 - - + -
311B LEU* 4.7 4.9 - - + -
314B LEU* 4.0 27.6 - - + -
359B LEU* 2.7 37.0 + - + +
360B TRP* 3.9 18.8 - - + +
362B ASP* 1.3 73.3 - - - +
364B HIS* 1.3 58.6 + - - +
366B ALA 3.7 0.7 + - - -
367B GLY 3.6 1.2 + - - -
368B ILE* 2.9 51.0 + - + +
369B LEU* 3.1 18.9 + - + -
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Residues in contact with HIS 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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360B TRP 3.0 17.7 + - - +
361B ARG* 3.0 9.0 + - - +
363B LEU* 1.3 74.9 - - - +
365B LYS* 1.3 71.8 + - + +
366B ALA 3.1 1.8 - - - -
367B GLY* 2.9 15.1 + - - -
369B LEU 2.9 24.1 + - - +
370B GLN* 3.4 25.4 - - - -
371B LEU* 3.3 32.1 + - + -
373B GLN* 3.7 25.1 + - - -
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Residues in contact with LYS 365 (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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77B HIS* 4.4 4.0 + - - -
361B ARG* 2.9 43.5 + - - +
362B ASP* 3.4 18.5 + - - +
364B HIS* 1.3 83.7 - - + +
366B ALA* 1.3 57.9 + - - +
367B GLY 3.3 1.1 + - - -
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Residues in contact with ALA 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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73B ALA* 3.8 8.0 - - - +
77B HIS* 3.0 52.0 + - + +
80B PHE* 4.2 11.2 - - + -
362B ASP 3.3 15.9 + - - +
364B HIS 3.1 1.2 - - - -
365B LYS* 1.3 76.0 - - - +
367B GLY* 1.3 56.4 + - - +
368B ILE* 3.1 23.9 + - + +
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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