Contacts of the helix formed by residues 284 - 290 (chain H) in PDB entry 4CDC
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 GLY 284 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279H PRO 3.4 1.2 + - - -
280H TYR* 3.2 14.1 + - - +
282H ILE 3.1 0.8 - - - -
283H ALA* 1.3 80.0 - - - +
285H LYS* 1.3 61.0 + - - +
286H TYR 3.4 1.1 - - - -
287H ALA* 3.3 2.6 + - - +
288H GLN* 2.9 28.6 + - - +
318H SER* 4.1 1.1 - - - -
321H TYR* 3.3 33.2 - - - -
431I VAL* 5.5 0.8 - - - +
433I ALA* 4.2 0.6 - - - +
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Residues in contact with LYS 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G GLU* 2.8 26.6 + - - +
76G LYS* 3.8 13.7 + - - +
78G PHE* 3.6 35.3 - - + +
101G TRP* 5.2 3.8 - - - -
103G HIS* 3.3 24.6 + - - -
270H TYR* 3.8 17.5 - - + -
280H TYR* 3.0 10.3 + - + +
281H LEU* 3.6 22.6 + - + +
284H GLY* 1.3 72.1 - - - +
286H TYR* 1.3 57.1 + - - +
288H GLN* 3.4 0.7 + - - +
289H ASP* 2.9 51.6 + - - +
321H TYR* 3.5 24.5 + - + +
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Residues in contact with TYR 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263H GLU* 2.4 45.5 + - - -
264H VAL* 4.3 11.0 - - + -
267H CYS* 3.9 11.1 + - - +
268H SER* 3.0 37.0 - - - -
269H GLN 4.9 1.6 - - - -
270H TYR* 3.7 13.2 - + + -
281H LEU 2.7 21.9 + - - +
282H ILE* 3.6 13.5 - - + +
284H GLY 3.4 0.2 - - - -
285H LYS* 1.3 72.7 - - - +
287H ALA* 1.3 58.3 + - - +
290H PHE* 2.8 62.3 + + + +
291H GLY 3.1 15.8 + - - -
292H LEU* 3.6 16.8 - - + -
315H ARG* 3.7 3.3 + - - -
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Residues in contact with ALA 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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243H LEU* 4.2 0.4 - - + -
282H ILE 3.1 12.0 + - - +
283H ALA 3.3 13.9 - - - +
284H GLY 3.3 0.6 + - - +
286H TYR* 1.3 77.2 - - - +
288H GLN* 1.3 59.8 + - - +
291H GLY* 3.3 11.0 + - - +
292H LEU* 3.8 24.0 - - + -
316H TYR 4.8 0.2 - - - +
317H TYR* 3.2 30.5 - - - -
318H SER* 3.2 29.2 - - - +
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Residues in contact with GLN 288 (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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76G LYS* 2.8 34.7 + - - +
103G HIS* 5.0 1.8 - - + -
105G VAL 4.6 7.5 - - - +
284H GLY 2.9 17.1 + - - +
285H LYS 3.8 3.8 - - - +
287H ALA* 1.3 76.6 - - - +
289H ASP* 1.3 70.3 + - - +
317H TYR* 3.4 6.9 - - - -
318H SER 3.5 20.2 + - - +
319H SER* 3.3 26.5 + - - +
320H GLU* 4.1 1.2 - - - +
321H TYR* 3.6 22.2 + - + -
106J LEU* 4.2 16.8 - - + +
108J ARG* 2.9 30.1 + - - +
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Residues in contact with ASP 289 (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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26G ARG* 3.1 28.6 + - - -
103G HIS* 3.1 36.0 + - - -
107G GLY* 5.7 0.2 - - - -
110G TRP* 3.7 10.9 - - + -
270H TYR* 2.7 22.3 + - - -
285H LYS* 2.9 32.7 + - - +
288H GLN* 1.3 89.5 - - - +
290H PHE* 1.3 79.0 + - + +
108J ARG* 3.9 10.3 + - - +
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Residues in contact with PHE 290 (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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26G ARG* 3.3 51.2 + - + +
27G ASP* 5.5 0.9 - - - -
101G TRP* 5.7 3.8 - + - -
110G TRP* 3.7 18.2 - + - -
269H GLN* 6.2 4.9 - - + -
270H TYR* 3.5 29.8 - + - -
286H TYR* 2.8 52.1 + + + +
289H ASP* 1.3 82.2 - - + +
291H GLY* 1.3 58.7 + - - +
315H ARG* 2.8 27.9 + - - +
317H TYR* 3.5 11.7 + - - -
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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