Contacts of the helix formed by residues 338 - 348 (chain C) in PDB entry 2WZJ
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 THR 338 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336C GLY 4.3 5.8 - - - +
337C TYR* 1.3 74.5 - - - +
339C ARG* 1.3 65.2 + - - +
340C GLU* 2.6 37.2 + - - +
341C GLU* 3.1 32.0 + - - +
342C ILE* 3.2 14.2 - - - +
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Residues in contact with ARG 339 (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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329C THR* 3.9 16.7 - - + +
330C GLU* 2.9 30.1 + - - -
333C VAL* 3.7 29.8 - - + +
337C TYR 4.0 1.8 + - - -
338C THR* 1.3 72.8 - - - +
340C GLU* 1.3 60.5 + - - +
342C ILE* 4.2 13.1 + - - +
343C GLN* 3.9 23.4 + - - +
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Residues in contact with GLU 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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338C THR* 2.6 32.1 + - - +
339C ARG* 1.3 79.4 - - - +
341C GLU* 1.3 68.8 + - + +
343C GLN* 3.2 7.4 + - - +
344C ASP* 3.0 37.9 + - - +
320D LEU* 6.2 1.1 - - + -
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Residues in contact with GLU 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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336C GLY 4.2 1.9 - - - +
337C TYR* 3.4 14.0 - - - -
338C THR* 3.1 49.1 + - - +
340C GLU* 1.3 83.9 - - + +
342C ILE* 1.3 64.1 + - + +
344C ASP* 3.9 9.0 - - - +
345C SER* 2.7 36.8 + - - +
354C VAL* 4.2 21.2 - - + +
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Residues in contact with ILE 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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323C TYR 4.9 3.6 - - - +
329C THR* 4.2 27.1 - - + +
332C MET* 3.7 44.2 - - + -
333C VAL* 4.8 1.6 - - + +
337C TYR* 4.0 11.0 - - + +
338C THR 3.2 19.7 - - - +
339C ARG* 4.2 6.3 - - - +
340C GLU 3.3 0.2 - - - -
341C GLU* 1.3 77.0 - - - +
343C GLN* 1.3 57.3 + - - +
345C SER* 3.9 0.9 - - - -
346C LEU* 3.1 40.7 + - + +
354C VAL* 3.6 10.5 - - + +
358C TYR* 3.7 31.0 - - + -
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Residues in contact with GLN 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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323C TYR* 4.8 13.0 - - + +
324C LYS* 3.5 33.2 - - + +
339C ARG 3.9 13.6 + - - +
340C GLU* 3.2 11.1 + - - +
341C GLU 3.2 0.2 - - - -
342C ILE* 1.3 77.5 - - - +
344C ASP* 1.3 58.0 + - - +
346C LEU* 3.1 5.3 + - - -
347C VAL* 2.8 43.7 + - + +
323D TYR* 3.1 22.2 + - + +
324D LYS* 3.0 39.0 - - - +
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Residues in contact with ASP 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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340C GLU* 3.0 32.6 + - - +
341C GLU* 3.9 6.6 - - - +
343C GLN* 1.3 75.5 - - - +
345C SER* 1.3 58.6 + - - +
347C VAL* 4.9 0.7 - - - -
348C GLY* 2.9 27.4 + - - -
350C ARG* 4.8 2.6 + - - -
320D LEU* 3.9 31.1 - - + +
321D PRO* 3.5 28.3 - - + +
323D TYR* 4.0 17.7 + - - -
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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 GLU* 2.7 27.0 + - - +
342C ILE 3.9 3.1 - - - -
344C ASP* 1.3 77.5 - - - +
346C LEU* 1.3 61.8 + - - +
349C GLN* 3.2 2.6 + - - -
350C ARG* 2.9 38.1 + - - +
352C ASN* 3.3 34.3 + - - -
354C VAL* 3.7 16.7 - - - +
355C MET* 4.0 8.3 - - - +
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Residues in contact with LEU 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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323C TYR* 3.5 43.9 - - + +
342C ILE* 3.1 22.2 + - + +
343C GLN 3.1 4.3 + - - +
345C SER* 1.3 74.7 - - - +
347C VAL* 1.3 63.3 + - - +
349C GLN* 3.1 28.7 + - - +
355C MET* 3.6 35.2 - - + +
358C TYR* 3.4 55.2 - - + -
359C LEU* 4.5 8.1 - - + -
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Residues in contact with VAL 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C TYR* 4.0 22.2 - - + -
343C GLN* 2.8 28.8 + - + +
344C ASP 4.3 1.6 - - - +
346C LEU* 1.3 67.9 - - - +
348C GLY* 1.3 59.5 + - - +
349C GLN* 3.0 14.5 + - - +
321D PRO* 4.4 8.1 - - + -
323D TYR* 4.0 52.9 - - + +
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Residues in contact with GLY 348 (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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344C ASP 2.9 18.7 + - - -
345C SER 4.1 0.4 - - - -
347C VAL* 1.3 75.2 - - - +
349C GLN* 1.3 71.5 + - - +
350C ARG* 3.0 19.9 + - - -
321D PRO* 3.7 14.0 - - - +
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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