Contacts of the helix formed by residues 284 - 290 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279K PRO 3.5 0.8 + - - -
280K TYR* 3.3 10.5 + - - +
282K ILE 3.1 0.2 - - - -
283K ALA* 1.3 80.9 - - - +
285K LYS* 1.3 59.7 + - - +
286K TYR 3.4 0.7 - - - -
287K ALA 3.4 1.7 + - - -
288K GLN* 2.9 30.3 + - - +
318K SER* 4.1 1.3 - - - -
321K TYR* 3.3 36.6 - - - -
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Residues in contact with LYS 285 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J GLU* 2.9 24.2 + - - +
76J LYS* 4.2 11.3 + - - +
78J PHE* 3.5 27.6 - - + +
101J TRP* 5.4 2.9 + - - -
103J HIS* 3.6 17.0 + - - -
270K TYR* 3.7 19.3 - - + -
280K TYR* 3.1 10.1 + - + +
281K LEU* 3.5 38.0 + - + +
284K GLY* 1.3 71.8 - - - +
286K TYR* 1.3 58.2 + - - +
288K GLN* 3.4 1.0 + - - +
289K ASP* 2.9 55.5 + - - +
321K TYR* 3.5 23.6 + - + +
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Residues in contact with TYR 286 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263K GLU* 2.6 38.2 + - - -
264K VAL* 4.4 9.4 - - + -
267K CYS* 4.1 12.6 + - - +
268K SER* 3.3 34.8 - - - -
269K GLN 5.2 0.7 - - - -
270K TYR* 3.7 14.1 - + + -
281K LEU 2.7 21.2 + - - +
282K ILE* 3.5 13.2 + - + +
284K GLY 3.4 0.2 - - - -
285K LYS* 1.3 72.6 - - - +
287K ALA* 1.3 56.7 + - - +
290K PHE* 2.9 65.5 + + + +
291K GLY 3.0 14.3 + - - -
292K LEU* 3.7 16.8 - - + -
315K ARG* 4.0 3.8 + - - -
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Residues in contact with ALA 287 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243K LEU* 4.2 1.1 - - + -
282K ILE 2.9 11.8 + - - +
283K ALA 3.1 15.5 - - - +
286K TYR* 1.3 76.5 - - - +
288K GLN* 1.3 58.9 + - - +
291K GLY* 3.3 10.8 - - - +
292K LEU* 4.0 22.0 - - + -
317K TYR* 3.1 29.9 - - - -
318K SER* 3.1 30.1 - - - +
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Residues in contact with GLN 288 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G LEU* 3.9 16.7 - - + +
108G ARG* 3.0 31.0 + - - +
76J LYS* 2.7 35.9 + - - +
103J HIS* 5.1 1.7 - - - -
105J VAL 4.6 6.0 - - - +
284K GLY 2.9 16.5 + - - +
285K LYS 3.8 3.1 - - - +
286K TYR 3.3 0.2 - - - -
287K ALA* 1.3 76.9 - - - +
289K ASP* 1.3 71.0 + - - +
317K TYR* 3.3 5.3 - - - -
318K SER 3.2 27.5 + - - +
319K SER* 3.4 21.2 + - - +
320K GLU* 4.4 1.0 - - - +
321K TYR* 3.7 19.3 + - + -
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Residues in contact with ASP 289 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G ARG* 3.9 8.9 + - - +
26J ARG* 2.6 37.1 + - - -
103J HIS* 3.2 35.4 + - - -
110J TRP* 3.8 13.2 - - + -
270K TYR* 3.0 19.3 + - - +
285K LYS* 2.9 33.2 + - - +
288K GLN* 1.3 91.7 - - - +
290K PHE* 1.3 71.3 + - + +
321K TYR* 5.6 0.2 + - - -
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Residues in contact with PHE 290 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J ARG* 3.4 44.9 + - + +
27J ASP* 5.5 0.4 - - - -
28J VAL 6.1 0.2 - - - -
101J TRP* 5.7 3.8 - - - -
110J TRP* 3.7 23.8 - + - -
270K TYR* 3.7 28.9 - + - -
286K TYR* 2.9 47.3 + + + +
289K ASP* 1.3 79.0 - - + +
291K GLY* 1.3 61.3 + - - +
315K ARG* 2.8 30.2 + - - +
317K TYR* 3.5 11.4 + - - -
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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