Contacts of the helix formed by residues 352 - 361 (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 ASN 352 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C GLU* 3.8 6.5 - - - -
118C VAL 5.2 1.8 - - - -
345C SER* 3.3 27.2 + - - -
350C ARG* 3.7 23.8 - - + +
351C TYR* 1.3 76.4 - - - +
353C GLU* 1.3 69.0 + - + +
354C VAL* 3.1 11.2 + - - +
355C MET* 3.2 24.8 + - - +
356C ALA* 3.3 13.3 + - - +
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Residues in contact with GLU 353 (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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52C ASN* 3.3 31.0 + - - +
72C HIS* 5.0 1.2 + - - -
74C LEU* 5.5 0.2 - - - +
117C GLU* 3.3 24.9 + - - +
337C TYR* 3.6 17.9 + - - -
352C ASN* 1.3 79.8 - - + +
354C VAL* 1.3 70.6 + - + +
356C ALA* 3.6 1.9 + - - +
357C THR* 3.2 26.2 + - - -
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Residues in contact with VAL 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C MET* 3.7 16.1 - - + +
337C TYR* 3.5 28.9 - - + -
341C GLU* 4.0 18.4 - - + +
342C ILE* 3.6 37.5 - - + +
345C SER* 3.7 16.2 - - - +
352C ASN* 3.2 7.5 + - - +
353C GLU* 1.3 81.3 - - + +
355C MET* 1.3 67.1 + - - +
356C ALA 3.1 0.9 + - - -
357C THR* 3.2 4.7 + - - -
358C TYR* 3.1 18.4 + - - +
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Residues in contact with MET 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C LYS* 4.7 2.0 - - - +
116C PHE 4.7 0.7 - - - +
345C SER* 4.0 10.0 - - - +
346C LEU* 3.6 26.2 - - + -
349C GLN* 3.5 45.5 - - - +
350C ARG 3.8 1.6 - - - -
351C TYR* 3.3 52.0 - - + +
352C ASN* 3.2 20.6 + - - +
354C VAL* 1.3 79.5 - - - +
356C ALA* 1.3 57.2 + - - +
358C TYR* 3.6 3.5 + - - +
359C LEU* 3.0 52.6 + - + +
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Residues in contact with ALA 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C TYR* 3.7 8.3 - - - +
72C HIS* 5.0 0.9 - - - +
116C PHE* 3.3 28.3 - - + +
117C GLU* 3.5 30.3 - - + +
352C ASN 3.3 6.3 + - - +
353C GLU 4.0 1.8 - - - +
354C VAL 3.1 0.4 - - - -
355C MET* 1.3 74.8 - - - +
357C THR* 1.3 67.8 + - - +
358C TYR 3.2 1.1 - - - -
359C LEU* 4.4 3.1 - - - +
360C LEU* 2.9 34.1 + - + +
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Residues in contact with THR 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C HIS* 3.3 26.5 + - + -
74C LEU* 4.5 0.3 - - - +
75C THR* 3.9 7.9 - - + +
332C MET* 3.7 26.7 - - + -
335C MET* 4.0 12.8 - - - -
337C TYR* 3.0 32.0 + - + -
353C GLU 3.2 8.4 + - - -
354C VAL 3.2 9.3 + - - -
356C ALA* 1.3 78.5 - - - +
358C TYR* 1.3 62.6 + - - +
360C LEU* 3.9 1.6 - - - +
361C LEU* 3.1 32.8 + - + +
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Residues in contact with TYR 358 (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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322C ASP 2.6 26.9 + - - -
323C TYR* 3.4 10.1 - + - -
325C ASP* 3.3 22.2 + - - +
328C ARG* 2.8 72.5 + - + -
329C THR* 4.3 9.6 - - - -
332C MET* 3.6 27.6 - - + -
342C ILE* 3.7 15.0 - - + -
346C LEU* 3.4 37.2 - - + -
354C VAL 3.1 14.4 + - - +
355C MET* 3.8 4.5 - - - +
356C ALA 3.2 0.2 - - - -
357C THR* 1.3 79.3 - - - +
359C LEU* 1.3 66.9 + - + +
361C LEU* 3.4 4.2 + - - -
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Residues in contact with LEU 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C LYS* 4.0 13.5 - - - +
115C LEU 3.9 22.0 - - - +
116C PHE* 3.8 24.7 - - + +
323C TYR* 6.3 2.7 - - + -
328C ARG* 4.2 5.5 + - - +
346C LEU* 4.5 9.9 - - + -
355C MET* 3.0 49.0 + - + +
356C ALA* 4.1 2.0 - - - +
357C THR 3.4 0.2 - - - -
358C TYR* 1.3 88.1 - - + +
360C LEU* 1.3 63.3 + - - +
362C GLY* 3.1 12.8 + - - -
363C TYR* 3.2 18.7 - - + -
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Residues in contact with LEU 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C TYR* 4.5 6.5 - - - +
72C HIS* 3.6 42.2 - - + +
75C THR* 4.1 13.2 - - + +
77C LYS* 3.8 25.2 + - + +
78C GLU 5.1 1.3 - - - +
79C VAL* 3.8 17.3 - - + -
116C PHE* 3.5 40.8 - - + -
356C ALA* 2.9 26.7 + - + +
357C THR 3.9 3.1 - - - +
359C LEU* 1.3 76.9 - - - +
361C LEU* 1.3 61.4 + - - +
362C GLY 3.3 0.7 + - - -
363C TYR* 3.4 21.1 + - + +
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Residues in contact with LEU 361 (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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75C THR* 3.9 23.6 - - + +
77C LYS* 5.6 1.1 + - - +
327C ARG* 3.1 21.5 + - - +
328C ARG* 3.6 30.3 - - + +
331C LEU* 4.1 23.3 - - + -
332C MET* 3.5 34.1 - - + -
335C MET* 4.5 10.1 - - + -
357C THR* 3.1 26.4 + - + +
358C TYR* 4.5 0.4 - - - -
359C LEU 3.2 1.0 - - - -
360C LEU* 1.3 72.0 - - - +
362C GLY* 1.3 56.2 + - - +
363C TYR* 3.1 13.5 + - - -
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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