Contacts of the helix formed by residues 342 - 347 (chain H) in PDB entry 1YKN
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 SER 342 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116G ASN* 4.0 20.0 - - - -
117G ALA* 4.4 8.1 - - - +
122G MET* 3.6 26.8 - - - +
142G ARG* 3.9 1.6 + - - -
157G VAL* 5.9 2.0 - - - -
304H ASP* 4.1 5.2 - - - -
340H PRO 3.5 3.3 + - - -
341H GLN* 1.3 73.5 - - - +
343H ILE* 1.3 64.1 + - - +
344H SER* 3.0 13.0 + - - -
345H GLU* 2.7 24.1 + - - -
346H THR* 3.1 24.9 + - - +
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Residues in contact with ILE 343 (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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79G TYR* 3.9 26.8 - - + +
114G VAL* 4.1 20.2 - - + -
115G ASN 4.1 14.0 + - - +
116G ASN 5.7 0.2 - - - -
117G ALA 5.5 0.6 - - - +
302H ALA 3.5 24.5 - - - +
303H GLN* 4.2 0.9 - - - -
304H ASP* 3.8 30.1 - - + +
342H SER* 1.3 77.6 - - - +
344H SER* 1.4 62.6 + - - +
345H GLU 3.4 0.3 + - - -
346H THR* 3.7 8.1 - - - -
347H THR* 2.8 44.2 + - + +
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Residues in contact with SER 344 (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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71G TRP* 3.4 23.9 + - - -
79G TYR* 2.4 31.8 + - - -
114G VAL* 4.0 4.3 - - - +
122G MET* 4.1 0.2 - - - +
125G HIS* 2.7 23.2 + - - -
127G ASN* 3.4 12.1 + - - -
142G ARG* 3.7 1.6 + - - -
342H SER* 3.0 8.4 + - - -
343H ILE* 1.4 80.0 - - - +
345H GLU* 1.4 73.0 + - - +
347H THR* 4.2 0.6 + - - +
470H ILE* 3.5 7.8 - - - +
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Residues in contact with GLU 345 (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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127G ASN* 3.8 3.6 - - - +
142G ARG* 2.8 31.8 + - - -
157G VAL* 6.0 0.2 - - - +
200G PHE* 3.4 49.2 - - + -
339H ILE* 3.8 13.7 - - - +
340H PRO 3.9 3.1 - - - +
341H GLN* 3.9 6.2 - - + -
342H SER* 2.7 44.9 + - - +
344H SER* 1.4 80.7 - - - +
346H THR* 1.4 62.8 + - + +
347H THR 3.5 1.8 + - - -
469H SER* 3.7 0.2 - - - -
470H ILE* 3.7 9.4 - - + +
471H ALA* 3.2 29.4 + - - +
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Residues in contact with THR 346 (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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303H GLN 5.0 2.3 - - - +
304H ASP* 2.8 24.9 + - - -
305H ASN 5.9 0.2 + - - -
306H SER* 3.5 28.9 - - - +
307H ARG* 3.6 3.8 - - - +
308H PHE* 3.9 19.2 - - + -
341H GLN* 3.5 35.9 - - + +
342H SER 3.1 15.1 + - - +
343H ILE* 3.7 5.4 + - - -
344H SER 3.6 0.2 - - - -
345H GLU* 1.4 76.4 - - - +
347H THR* 1.3 60.6 + - - +
468H PRO 4.6 1.6 - - - +
469H SER* 3.5 12.9 - - - -
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Residues in contact with THR 347 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G TRP* 3.0 26.7 + - - -
79G TYR* 4.1 3.5 - - + -
302H ALA* 3.4 33.9 - - + -
303H GLN 3.9 15.0 - - - +
343H ILE* 2.8 39.4 + - + +
346H THR* 1.3 84.9 - - - +
348H GLY* 1.3 60.5 + - - +
468H PRO 4.5 1.6 - - - -
469H SER* 3.7 5.6 - - - -
470H ILE* 3.1 20.4 + - - +
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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