Contacts of the helix formed by residues 284 - 296 (chain H) in PDB entry 5YWB
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 284 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283H GLY* 1.3 72.8 - - - -
285H ARG* 1.3 66.0 + - + +
287H ILE* 3.3 18.9 - - - +
288H TRP* 3.6 7.8 + - - +
607H VAL* 4.2 6.7 - - + +
608H GLN* 4.9 18.4 - - + +
611H SER* 3.3 27.6 + - - +
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Residues in contact with ARG 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283H GLY* 3.4 0.4 - - - -
284H ALA* 1.3 77.9 - - + +
286H ALA* 1.3 66.9 + - - +
288H TRP* 3.2 8.6 + - - +
289H ARG* 3.0 23.3 + - - +
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Residues in contact with ALA 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270H PHE* 5.6 5.6 - - + -
273H GLN* 3.7 29.2 - - + +
274H ALA* 6.0 0.9 - - - +
283H GLY* 3.4 19.6 + - - +
284H ALA 3.3 0.8 - - - -
285H ARG* 1.3 80.2 - - - +
287H ILE* 1.3 61.0 + - + +
289H ARG* 3.2 6.6 + - - +
290H ALA* 2.9 27.6 + - - +
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Residues in contact with ILE 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270H PHE* 3.6 32.1 - - + -
283H GLY 3.6 12.8 - - - +
284H ALA 3.3 12.6 - - - +
286H ALA* 1.3 75.5 - - + +
288H TRP* 1.3 60.8 + - - +
290H ALA* 3.5 8.5 - - - +
291H LEU* 2.9 49.2 + - + +
394H LYS* 5.3 3.8 - - - +
607H VAL* 3.5 26.9 - - + +
610H LEU* 5.2 13.7 - - + -
611H SER* 3.4 16.4 - - - +
614H LEU* 5.2 11.2 - - + -
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Residues in contact with TRP 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284H ALA 3.6 6.3 + - - +
285H ARG* 3.2 11.8 + - - +
286H ALA 3.2 0.4 - - - -
287H ILE* 1.3 83.2 - - - +
289H ARG* 1.3 65.2 + - - +
291H LEU* 3.2 11.4 + - + +
292H CYS* 3.0 35.4 + - - +
428H LEU* 5.8 1.3 - - + -
431H PHE* 4.3 29.8 - + - -
432H PHE* 6.1 2.2 - - - -
600H THR 5.3 0.9 - - - -
603H ALA* 4.0 8.3 - - + -
604H LEU* 3.8 42.8 - - + -
607H VAL* 3.3 43.1 - - + -
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Residues in contact with ARG 289 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273H GLN* 3.6 21.8 - - - +
285H ARG 3.0 13.3 + - - +
286H ALA* 3.5 9.0 - - - +
288H TRP* 1.3 76.3 - - - +
290H ALA* 1.3 58.3 + - - +
292H CYS* 3.4 5.9 + - - +
293H HIS* 2.9 29.6 + - - +
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Residues in contact with ALA 290 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266H LEU* 4.9 8.7 - - + -
269H ALA* 4.4 11.8 - - + +
270H PHE* 4.4 29.8 - - + +
273H GLN* 4.4 6.7 + - + -
286H ALA 2.9 14.3 + - - +
287H ILE* 3.5 12.1 - - - +
288H TRP 3.2 0.2 - - - -
289H ARG* 1.3 77.3 - - - +
291H LEU* 1.3 57.7 + - - +
293H HIS* 3.5 6.7 - - - +
294H ALA* 2.8 31.4 + - - +
394H LYS* 6.0 0.2 - - - +
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Residues in contact with LEU 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266H LEU* 3.8 24.0 - - + -
287H ILE* 2.9 38.1 + - + +
288H TRP* 3.6 14.6 - - + +
290H ALA* 1.3 75.3 - - - +
292H CYS* 1.3 64.0 + - - +
294H ALA* 3.1 13.3 + - - +
295H PHE* 2.9 35.8 + - + -
387H LEU* 3.9 26.7 - - + -
391H ILE* 4.1 14.8 - - + -
428H LEU* 5.2 7.6 - - + -
432H PHE* 5.3 6.1 - - + -
607H VAL* 4.8 12.6 - - + -
610H LEU* 6.4 0.9 - - + -
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Residues in contact with CYS 292 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288H TRP* 3.0 30.6 + - + +
289H ARG* 3.8 6.3 - - - +
291H LEU* 1.3 75.3 - - - +
293H HIS* 1.3 63.6 + - - +
295H PHE* 4.5 5.1 - - - +
296H GLY* 3.3 18.4 + - - -
299H LEU* 5.2 16.3 - - - +
432H PHE* 5.3 6.9 - - - -
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Residues in contact with HIS 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265H ARG* 6.4 1.8 - - + -
269H ALA* 4.1 18.1 - - + +
273H GLN* 6.0 0.9 - - - +
289H ARG 2.9 17.9 + - - +
290H ALA* 3.5 7.9 - - - +
291H LEU 3.2 0.2 - - - -
292H CYS* 1.3 79.6 - - - +
294H ALA* 1.3 69.1 + - - +
296H GLY* 3.4 11.8 + - - -
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Residues in contact with ALA 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265H ARG* 3.8 36.5 + - + +
266H LEU* 4.7 16.8 - - + -
269H ALA* 4.9 6.3 - - + -
290H ALA 2.8 17.4 + - - +
291H LEU* 3.1 6.0 + - - +
293H HIS* 1.3 81.2 + - - +
295H PHE* 1.3 74.5 + - + +
296H GLY* 4.3 0.3 - - - -
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Residues in contact with PHE 295 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266H LEU* 6.4 0.4 - - + -
291H LEU* 2.9 35.9 + - + +
292H CYS* 4.6 2.0 - - - +
294H ALA* 1.3 82.5 - - + +
296H GLY* 1.3 65.9 + - - +
297H ARG 3.3 2.4 + - - -
298H ARG* 3.5 17.9 + - - +
299H LEU* 4.4 8.5 - - + -
383H THR* 3.3 31.6 - - + +
386H ASN* 4.4 5.6 - - + -
387H LEU* 2.9 62.8 - - + -
390H ALA* 6.0 1.3 - - + -
432H PHE* 3.2 35.4 - + + -
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Residues in contact with GLY 296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292H CYS 3.3 12.5 + - - -
293H HIS* 3.6 13.2 - - - -
294H ALA 3.3 1.6 - - - -
295H PHE* 1.3 77.1 - - - +
297H ARG* 1.3 59.7 + - - -
299H LEU* 3.0 8.9 + - - +
300H ILE* 2.9 37.0 + - - +
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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