Contacts of the helix formed by residues 342 - 354 (chain C) in PDB entry 4ZTZ
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 LEU 342 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107C ARG* 4.6 9.7 - - + +
110C LEU* 3.6 30.6 - - + +
111C ALA* 3.7 31.2 - - + +
114C TRP* 4.5 23.8 - - + -
211C ILE* 4.0 22.2 - - + -
235C THR* 3.3 21.8 + - - +
237C ALA* 4.0 15.5 - - + -
259C ARG* 5.8 0.2 - - - +
262C TRP* 5.1 2.2 - - + -
263C TRP* 5.2 6.1 - - + -
340C GLY 5.5 1.1 - - - +
341C ASP* 1.3 77.5 + - - +
343C ASP* 1.3 62.4 + - - +
345C GLY 3.7 1.6 - - - +
346C MET* 2.9 29.8 + - - +
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Residues in contact with ASP 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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96C HIS* 5.2 6.4 + - + -
99C PHE* 3.8 28.4 - - + -
107C ARG* 3.9 3.5 + - - -
233C GLU 4.5 3.1 - - - +
234C LYS* 4.0 10.1 - - + -
235C THR* 2.2 51.1 + - - +
341C ASP* 2.8 7.5 + - - +
342C LEU* 1.3 75.7 - - - +
344C ARG* 1.3 61.3 + - + +
345C GLY 3.1 1.3 - - - -
346C MET* 3.1 11.6 + - - +
347C LEU* 2.9 36.0 + - + +
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Residues in contact with ARG 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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91C LEU 4.8 1.1 + - - -
92C LEU* 2.8 63.5 + - - +
293C PHE* 5.4 5.7 - - - -
298C GLU* 3.4 28.8 + - - +
299C LEU* 3.6 15.7 + - - +
300C ILE* 3.7 23.3 - - + +
341C ASP* 3.3 31.6 + - + +
343C ASP* 1.3 78.8 - - + +
345C GLY* 1.3 56.6 + - - +
347C LEU* 3.8 9.9 - - - +
348C ALA* 2.9 26.9 + - - +
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Residues in contact with GLY 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU* 4.2 2.9 - - - -
263C TRP* 3.6 31.6 - - - -
300C ILE* 4.4 1.9 - - - +
341C ASP 3.2 11.7 + - - -
342C LEU 3.7 2.0 + - - -
343C ASP 3.1 0.8 - - - -
344C ARG* 1.3 75.8 - - - +
346C MET* 1.3 58.2 + - - +
348C ALA* 3.1 4.9 + - - +
349C TYR* 2.9 40.0 + - - -
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Residues in contact with MET 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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78C PHE* 5.5 0.7 - - - +
79C LEU* 5.7 0.2 - - - -
99C PHE* 3.5 45.3 - - + -
103C GLY* 3.6 24.0 - - - +
106C LEU* 3.6 27.8 - - + +
107C ARG* 3.6 34.5 - - + +
110C LEU* 4.0 8.7 - - + +
342C LEU 2.9 16.9 + - - +
343C ASP* 3.1 6.0 + - - +
345C GLY* 1.3 77.8 - - - +
347C LEU* 1.3 59.7 + - - +
349C TYR* 3.4 4.1 + - - +
350C LEU* 2.9 40.7 + - + +
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Residues in contact with LEU 347 (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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70C LEU* 6.3 1.3 - - + -
79C LEU* 5.1 1.8 - - + -
91C LEU* 3.8 49.4 - - + +
92C LEU* 4.2 18.8 - - + -
99C PHE* 4.7 13.7 - - + -
293C PHE* 4.6 12.6 - - + -
343C ASP* 2.9 23.9 + - + +
344C ARG* 3.8 11.7 - - - +
346C MET* 1.3 80.2 - - + +
348C ALA* 1.3 57.5 + - - +
350C LEU* 3.2 16.9 + - + +
351C TYR* 2.9 47.0 + - + -
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Residues in contact with ALA 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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273C PHE* 4.3 11.2 - - + -
291C TYR* 2.8 62.1 + - + -
293C PHE* 5.0 1.5 - - - -
300C ILE* 4.7 2.0 - - + -
344C ARG 2.9 19.3 + - - +
345C GLY* 3.1 11.6 + - - +
347C LEU* 1.3 76.7 - - - +
349C TYR* 1.3 58.0 + - - +
351C TYR 3.3 1.4 + - - -
352C ASP* 2.9 13.9 + - - +
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Residues in contact with TYR 349 (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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106C LEU* 5.8 1.6 - - + -
110C LEU* 3.9 20.9 - - + -
262C TRP* 4.0 3.6 + - - -
263C TRP* 3.0 57.8 + + - -
266C PHE* 3.6 43.5 - - + +
267C ALA* 3.7 7.4 - - - -
273C PHE* 3.9 11.7 - + - -
345C GLY 2.9 25.2 + - - +
346C MET* 4.0 4.3 - - - +
348C ALA* 1.3 74.1 - - + +
350C LEU* 1.3 60.6 + - - +
352C ASP* 3.6 13.2 - - - +
353C SER* 2.9 31.7 + - - -
374C LEU* 3.3 16.9 - - + +
378C LEU* 3.8 19.7 - - + -
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Residues in contact with LEU 350 (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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69C LEU* 3.7 16.8 - - + +
73C CYS* 4.2 20.4 - - - -
78C PHE* 4.1 35.7 - - + -
79C LEU* 5.2 6.5 - - + -
106C LEU* 4.3 11.7 - - + -
346C MET* 2.9 34.5 + - + +
347C LEU* 3.4 21.3 - - + +
349C TYR* 1.3 77.0 - - - +
351C TYR* 1.3 63.2 + - + +
353C SER* 3.0 16.7 + - - +
354C PHE* 3.4 8.1 + - - +
372C LEU* 4.4 16.6 - - + -
374C LEU* 4.3 7.4 - - + +
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Residues in contact with TYR 351 (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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67C GLU* 4.7 5.5 + - + -
69C LEU* 3.6 30.1 - - + -
70C LEU* 3.3 32.3 - - + +
88C ARG* 3.9 31.5 + - - +
291C TYR* 3.9 11.6 + - + +
293C PHE* 3.6 52.8 - + + +
347C LEU* 2.9 40.7 + - + +
348C ALA 3.8 4.0 - - - +
350C LEU* 1.3 77.4 - - + +
352C ASP* 1.3 61.6 + - - +
353C SER 3.3 0.4 + - - -
354C PHE* 3.9 11.8 + - + +
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Residues in contact with ASP 352 (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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266C PHE 4.3 0.7 - - - +
267C ALA* 3.5 10.6 - - - +
268C MET* 2.6 52.8 + - - +
269C SER* 3.5 18.1 + - - -
272C ASN* 4.1 6.2 + - - +
273C PHE* 5.3 0.7 - - - -
291C TYR* 3.6 13.0 - - + +
348C ALA 2.9 17.1 + - - +
349C TYR* 3.6 16.9 - - + +
350C LEU 3.2 0.2 - - - -
351C TYR* 1.3 80.4 - - - +
353C SER* 1.3 58.3 + - - +
354C PHE 3.5 0.7 - - - -
355C GLN* 4.5 9.1 + - - +
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Residues in contact with SER 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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268C MET* 6.1 0.2 - - - -
349C TYR 2.9 13.6 + - - -
350C LEU* 3.0 16.1 + - - +
352C ASP* 1.3 79.5 - - - +
354C PHE* 1.3 61.3 - - - +
355C GLN* 3.1 10.2 + - - +
371C VAL 3.3 1.9 - - - +
372C LEU* 3.3 10.6 - - - +
373C LYS* 2.8 32.4 + - - +
374C LEU* 3.4 41.4 - - - +
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Residues in contact with PHE 354 (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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67C GLU* 4.9 12.3 - - - -
68C ALA* 4.2 25.6 - - + -
69C LEU* 3.5 35.4 - - + -
72C ILE* 3.6 19.1 - - + -
350C LEU 3.4 12.7 + - - +
351C TYR* 3.9 9.9 + - + +
352C ASP 3.5 1.4 - - - -
353C SER* 1.3 76.5 + - - +
355C GLN* 1.3 80.7 + - - +
370C LYS* 4.9 20.6 - - + -
371C VAL 5.4 1.1 - - - -
372C LEU* 3.6 14.8 - - + -
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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