Contacts of the helix formed by residues 339 - 346 (chain C) in PDB entry 1W88
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 LYS 339 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306B VAL* 4.8 4.9 - - - -
337C LYS 4.3 7.2 - - - +
338C GLN* 1.3 77.6 - - - +
340C VAL* 1.3 60.5 + - - +
341C THR* 3.6 8.7 - - - +
342C ASP* 2.7 40.1 + - - +
343C LEU* 3.3 11.0 + - - +
366C GLU* 3.3 42.4 + - + +
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Residues in contact with VAL 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B PRO* 3.9 16.8 - - + -
296B THR* 5.7 0.2 - - + -
306B VAL* 3.4 42.6 - - + +
307B TRP* 4.0 16.6 - - + -
339C LYS* 1.3 71.0 - - - +
341C THR* 1.3 63.0 + - - +
343C LEU* 2.9 11.8 + - + +
344C ILE* 2.9 31.5 + - + +
362C TYR* 3.5 43.1 - - + -
366C GLU* 3.5 4.0 + - - +
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Residues in contact with THR 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C LYS* 3.6 9.7 - - - +
340C VAL* 1.3 74.8 - - - +
342C ASP* 1.3 62.7 + - - +
344C ILE* 3.5 3.1 + - - -
345C SER* 3.1 21.3 + - - -
359C TYR* 3.4 48.2 - - + +
362C TYR* 3.9 4.0 - - + -
363C LYS* 3.6 28.0 - - + +
366C GLU* 2.6 33.9 + - - +
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Residues in contact with ASP 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C PHE* 3.9 29.0 - - + -
337C LYS 4.1 2.4 - - - +
338C GLN* 3.6 6.1 - - - -
339C LYS* 2.7 43.9 + - - +
341C THR* 1.3 80.0 + - - +
343C LEU* 1.3 64.0 + - + +
345C SER* 3.2 19.0 + - - -
346C ILE* 3.4 18.5 + - - +
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Residues in contact with LEU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B THR* 3.7 9.9 - - + +
299B PRO* 4.1 2.9 - - + -
300B PHE* 4.2 6.7 - - + -
303B ALA* 3.8 23.3 - - + -
307B TRP* 3.9 26.0 - - + +
126C PHE* 4.4 9.9 - - + -
338C GLN* 3.9 24.0 - - + +
339C LYS 3.7 12.1 - - - +
340C VAL* 2.9 12.0 + - + +
342C ASP* 1.3 75.0 - - - +
344C ILE* 1.3 64.6 + - - +
346C ILE* 3.4 18.4 - - + +
347C MET* 3.5 13.2 - - - +
102D TYR* 3.7 36.1 - - + +
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Residues in contact with ILE 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B PRO* 5.0 1.8 - - + -
296B THR* 3.8 20.6 - - + -
340C VAL* 2.9 36.6 + - + +
341C THR* 3.8 6.5 - - - +
343C LEU* 1.3 75.3 - - - +
345C SER* 1.3 63.8 + - - +
347C MET* 3.1 22.3 + - - +
351C LEU* 3.5 30.4 - - + +
355C LEU* 3.8 25.4 - - + +
358C GLN* 3.8 17.7 - - + +
359C TYR* 3.7 32.5 - - + +
362C TYR* 4.4 1.6 - - + -
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Residues in contact with SER 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C THR 3.1 14.7 + - - -
342C ASP* 3.2 15.6 + - - -
344C ILE* 1.3 78.3 - - - +
346C ILE* 1.3 61.5 + - - +
348C PHE 3.4 17.2 - - - +
349C GLU 5.4 0.2 - - - +
351C LEU* 4.3 11.6 - - - +
359C TYR* 4.5 11.9 - - - -
101D ARG* 5.4 0.2 - - - -
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Residues in contact with ILE 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B PHE* 4.4 0.4 - - + -
126C PHE* 4.1 28.9 - - + -
130C GLN* 5.5 0.7 - - - +
342C ASP 3.4 18.2 - - - +
343C LEU* 3.4 15.7 - - + +
345C SER* 1.3 83.5 - - - +
347C MET* 1.3 56.9 + - - +
348C PHE 3.5 0.9 - - - -
101D ARG* 3.2 25.9 - - - +
102D TYR* 3.3 51.8 + - + +
105D GLY* 4.0 29.6 - - - +
106D GLY* 4.5 2.7 - - - +
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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
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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