Contacts of the helix formed by residues 358 - 369 (chain B) in PDB entry 2YWB
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 PHE 358 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B ARG* 3.4 32.8 - - + -
16B ALA* 4.3 5.2 - - + -
17B ARG* 3.1 61.5 - - + +
20B ARG* 3.7 35.2 - - + -
317B LEU* 4.6 0.7 - - - -
318B TYR* 3.9 19.3 - + - -
319B PRO* 3.8 20.6 - - + -
357B LEU* 1.3 76.2 - - - +
359B LYS* 1.3 68.6 + - - +
360B ASP* 3.2 16.6 - - - +
361B GLU* 2.7 26.8 + - - +
362B VAL* 3.3 10.4 + - - +
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Residues in contact with LYS 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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17B ARG* 5.2 4.1 - - - +
220B VAL* 4.2 24.0 - - + -
221B ASP* 4.8 13.9 - - + -
317B LEU* 3.9 30.3 - - + +
319B PRO* 5.5 0.8 - - - +
358B PHE* 1.3 72.5 - - - +
360B ASP* 1.3 60.2 + - - +
362B VAL* 2.8 24.7 + - + +
363B ARG* 3.0 34.2 + - - +
380B PRO* 4.4 22.0 - - - +
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Residues in contact with ASP 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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17B ARG* 3.6 19.9 + - - +
21B GLU* 4.7 14.0 - - - +
358B PHE* 3.2 20.3 - - - +
359B LYS* 1.3 75.8 - - - +
361B GLU* 1.3 73.3 + - - +
363B ARG* 3.2 15.6 + - - +
364B GLU* 3.0 20.4 + - - +
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Residues in contact with GLU 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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20B ARG* 2.9 33.2 + - + +
190B TRP* 2.7 32.0 + - + +
357B LEU* 3.0 24.0 - - + +
358B PHE* 2.7 33.6 + - - +
360B ASP* 1.3 93.8 + - - +
362B VAL* 1.3 57.9 + - - +
364B GLU* 3.2 10.0 + - - +
365B LEU* 3.0 31.4 + - + +
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Residues in contact with VAL 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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220B VAL* 4.4 1.3 - - + +
221B ASP* 3.7 23.1 - - - +
224B THR* 3.7 28.7 + - + +
317B LEU* 3.8 26.7 - - + -
354B PHE* 4.0 10.3 - - + -
357B LEU* 4.1 19.1 - - + -
358B PHE 3.3 12.3 + - - +
359B LYS* 2.8 11.5 + - + +
361B GLU* 1.3 74.3 - - - +
363B ARG* 1.3 65.2 + - - +
364B GLU 3.0 1.8 - - - -
365B LEU* 3.1 8.0 + - - +
366B ALA* 2.9 21.7 + - - +
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Residues in contact with ARG 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B VAL* 3.9 32.9 - - + +
359B LYS* 3.0 40.0 + - + +
360B ASP* 3.2 16.7 + - - +
362B VAL* 1.3 75.8 - - - +
364B GLU* 1.3 61.0 + - - +
366B ALA* 3.4 2.1 - - - +
367B LEU 3.2 5.5 + - - -
376B ARG* 2.8 62.4 + - + +
377B LEU* 3.7 10.8 - - + +
378B ARG 3.0 33.7 + - - +
379B HIS* 4.7 0.6 - - - +
380B PRO* 4.4 16.2 - - - +
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Residues in contact with GLU 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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192B PRO* 3.3 38.6 - - + +
360B ASP 3.0 12.7 + - - +
361B GLU* 3.3 13.9 - - - +
362B VAL 3.0 0.4 - - - -
363B ARG* 1.3 76.0 - - - +
365B LEU* 1.3 65.0 + - - +
367B LEU* 3.1 25.9 + - - +
368B LEU* 3.2 17.8 + - - +
376B ARG* 4.0 4.5 + - - +
364D GLU* 2.9 35.5 - - - +
367D LEU* 3.7 17.0 - - + +
368D LEU* 3.8 1.2 - - - +
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Residues in contact with LEU 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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192B PRO* 3.7 31.4 - - + +
195B VAL* 4.3 8.5 - - + -
196B LEU* 4.0 23.6 - - + +
199B LEU* 3.7 29.4 - - + -
224B THR* 4.2 8.7 - - + -
228B LEU* 6.0 0.9 - - + -
354B PHE* 4.1 10.8 - - + -
357B LEU* 3.8 19.1 - - + -
361B GLU* 3.0 17.8 + - + +
362B VAL* 3.1 8.5 + - - +
364B GLU* 1.3 73.0 - - - +
366B ALA* 1.3 60.0 + - - +
368B LEU* 3.1 8.0 + - + +
369B LEU* 2.8 36.3 + - + +
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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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220B VAL* 4.0 5.4 - - + -
224B THR* 3.1 30.9 - - - +
227B LEU* 5.0 0.7 - - - -
362B VAL 2.9 8.1 + - - +
363B ARG 3.4 11.9 - - - +
365B LEU* 1.3 73.4 - - - +
367B LEU* 1.3 67.6 + - - +
369B LEU* 3.1 10.1 + - - +
371B LEU* 3.0 49.1 + - + +
376B ARG* 4.1 3.6 - - + -
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Residues in contact with LEU 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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363B ARG 3.2 3.0 + - - -
364B GLU* 3.1 18.7 + - - +
366B ALA* 1.3 79.3 - - - +
368B LEU* 1.3 62.3 + - - +
370B GLY 3.1 11.4 + - - -
376B ARG* 3.2 30.7 - - - +
23D ARG* 3.2 49.4 - - - +
190D TRP 5.6 0.2 - - - +
191D THR* 3.7 9.7 - - - +
192D PRO* 4.0 17.0 - - + -
364D GLU* 3.1 44.4 - - + +
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Residues in contact with LEU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PRO* 3.4 42.2 - - + +
193B GLU* 3.6 10.3 - - + +
196B LEU* 3.8 19.9 - - + +
364B GLU* 3.3 32.1 - - - +
365B LEU* 3.1 12.9 + - + +
367B LEU* 1.3 81.0 - - + +
369B LEU* 1.3 60.3 + - - +
370B GLY 3.3 1.1 + - - -
191D THR* 3.7 7.6 - - - +
192D PRO* 3.4 19.7 - - + -
193D GLU* 2.8 44.1 - - + +
368D LEU* 4.6 1.6 - - + -
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Residues in contact with LEU 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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196B LEU* 4.0 29.8 - - + -
200B LEU* 4.9 0.2 - - + -
224B THR* 3.9 17.5 - - + +
227B LEU* 3.8 30.1 - - + +
228B LEU* 3.6 32.1 - - + +
231B LYS* 3.9 36.8 - - + -
261B LEU* 4.7 2.4 - - - +
365B LEU* 2.8 19.6 + - + +
366B ALA 3.1 4.5 + - - +
367B LEU 3.1 0.4 - - - -
368B LEU* 1.3 76.7 - - - +
370B GLY* 1.3 61.2 + - - +
371B LEU 3.5 1.5 + - - -
191D THR* 4.9 0.4 - - - -
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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