Contacts of the helix formed by residues 334 - 348 (chain C) in PDB entry 1CZY
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 ALA 334 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335C MET* 1.3 66.7 + - - +
336C ALA* 3.2 4.3 - - - +
337C ASP* 3.3 22.9 + - + +
338C LEU* 3.5 9.7 + - - +
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Residues in contact with MET 335 (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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335A MET* 6.2 3.1 - - - -
338B LEU* 4.5 11.7 - - + +
334C ALA* 1.3 75.7 - - - +
336C ALA* 1.3 60.1 + - - +
338C LEU* 3.3 9.4 + - - +
339C GLU* 2.9 29.3 + - - +
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Residues in contact with ALA 336 (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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334C ALA* 3.2 2.1 - - - +
335C MET* 1.3 79.1 - - - +
337C ASP* 1.3 56.6 + - - +
339C GLU* 3.7 6.6 - - - +
340C GLN* 3.0 28.4 + - - +
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Residues in contact with ASP 337 (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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334C ALA* 3.3 20.7 + - + +
335C MET 3.2 0.4 - - - -
336C ALA* 1.3 78.3 - - - +
338C LEU* 1.3 64.1 + - - +
340C GLN* 3.4 7.3 + - - +
341C LYS* 3.1 21.0 + - - +
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Residues in contact with LEU 338 (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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335A MET* 4.7 13.2 - - + +
338A LEU* 3.5 39.0 - - + -
339A GLU* 4.0 18.6 - - + +
342A VAL* 3.7 31.9 - - + -
343A LEU* 5.9 1.8 - - + -
338B LEU* 3.6 13.2 - - + -
334C ALA 3.5 8.0 + - - +
335C MET* 3.3 10.4 + - - +
337C ASP* 1.3 77.7 - - - +
339C GLU* 1.3 60.1 + - - +
341C LYS* 3.1 8.5 + - + +
342C VAL* 2.8 36.5 + - + +
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Residues in contact with GLU 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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338B LEU* 4.1 20.8 - - + +
335C MET 2.9 17.1 + - - +
336C ALA* 3.7 8.1 - - - +
338C LEU* 1.3 76.2 - - - +
340C GLN* 1.3 59.9 + - - +
342C VAL* 3.1 1.3 + - - -
343C LEU* 2.6 42.0 + - + +
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Residues in contact with GLN 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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336C ALA 3.0 19.5 + - - +
337C ASP* 3.6 7.4 - - - +
338C LEU 3.2 0.2 - - - -
339C GLU* 1.3 76.2 - - - +
341C LYS* 1.3 62.5 + - - +
343C LEU* 3.4 5.9 + - - +
344C GLU* 3.0 25.0 + - - +
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Residues in contact with LYS 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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342A VAL* 4.7 13.7 - - + -
346A GLU* 6.1 1.6 - - - +
337C ASP 3.1 9.7 + - - +
338C LEU* 3.1 13.3 + - + +
340C GLN* 1.3 80.1 - - - +
342C VAL* 1.3 63.2 + - - +
344C GLU* 3.3 6.3 + - - +
345C MET* 3.0 33.1 + - + +
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Residues in contact with VAL 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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342A VAL* 4.3 11.4 - - + -
338B LEU* 3.9 25.8 - - + -
341B LYS* 4.6 9.9 - - + -
342B VAL* 4.1 20.2 - - + -
345B MET* 3.5 26.0 - - + +
338C LEU* 2.8 28.4 + - + +
339C GLU 3.5 7.0 - - - +
341C LYS* 1.3 77.4 - - - +
343C LEU* 1.3 64.3 + - + +
345C MET* 3.3 6.7 + - - -
346C GLU* 2.8 28.9 + - + +
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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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338B LEU* 5.6 1.8 - - + -
339C GLU* 2.6 45.2 + - + +
340C GLN* 3.9 5.6 - - - +
342C VAL* 1.3 83.5 - - + +
344C GLU* 1.3 62.2 + - - +
346C GLU* 3.2 26.2 + - - +
347C ALA* 3.1 24.9 + - - +
379C PRO* 5.2 1.1 - - - +
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Residues in contact with GLU 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 GLN 3.0 18.1 + - - +
341C LYS* 3.7 6.5 - - - +
343C LEU* 1.3 73.5 - - - +
345C MET* 1.3 67.3 + - + +
347C ALA* 3.2 5.5 + - - +
348C SER* 2.9 24.4 + - - -
379C PRO* 5.0 9.3 - - + +
380C ALA* 4.7 9.1 + - + +
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Residues in contact with MET 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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342A VAL* 3.4 34.8 - - + +
345A MET* 3.7 27.4 - - + +
346A GLU* 3.5 46.7 - - + +
345B MET* 3.8 11.8 - - + +
385B ARG* 4.9 0.3 + - - -
341C LYS* 3.0 22.7 + - + +
342C VAL* 3.7 5.6 - - - +
344C GLU* 1.3 77.4 - - + +
346C GLU* 1.3 64.1 + - - +
348C SER* 2.7 25.8 + - - +
350C TYR* 5.8 0.7 - - - -
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Residues in contact with GLU 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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341B LYS* 5.7 4.0 - - - +
345B MET* 3.4 29.9 - - + +
350B TYR* 5.0 5.3 + - - +
385B ARG* 2.8 26.7 + - - -
342C VAL* 2.8 19.3 + - - +
343C LEU* 3.2 32.6 - - - +
345C MET* 1.3 78.1 - - - +
347C ALA* 1.3 51.2 + - + +
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Residues in contact with ALA 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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385B ARG* 3.5 6.9 + - - +
386B TYR* 4.4 1.7 + - - -
343C LEU 3.1 17.3 + - - +
344C GLU 3.9 1.3 - - - +
345C MET 3.2 0.4 - - - -
346C GLU* 1.3 77.0 - - + +
348C SER* 1.3 65.2 + - - +
349C THR* 3.7 2.9 - - - +
354C PHE* 3.4 23.4 - - + -
379C PRO* 3.6 33.2 - - + -
380C ALA 4.4 0.9 - - - -
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Residues in contact with SER 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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385B ARG* 3.0 21.3 + - - -
344C GLU 2.9 13.4 + - - -
345C MET* 2.7 23.3 + - - +
347C ALA* 1.3 77.2 - - - +
349C THR* 1.3 57.5 + - - +
350C TYR* 3.4 33.8 + - - -
380C ALA 3.5 15.9 + - - -
382C TYR* 4.2 9.2 - - - -
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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