Contacts of the helix formed by residues 296 - 304 (chain B) in PDB entry 1ZV0
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 CYS 296 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B VAL* 5.8 8.9 - - + +
293B PHE* 5.0 12.4 - - + +
295B ASN* 1.4 76.8 - - - +
297B LEU* 1.4 64.4 + - - +
299B PRO* 3.5 7.0 - - - +
300B LEU* 3.3 42.5 + - - +
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PBF 4.1 15.3 - - + +
245B ILE* 4.8 6.4 - - + +
248B PHE* 3.8 40.8 - - + +
249B PHE* 3.9 26.9 - - + +
252B SER* 4.4 8.3 - - - +
253B TRP* 5.6 1.3 - - - +
293B PHE* 4.1 15.0 - - + +
294B ASN* 3.2 39.0 - - - +
295B ASN 3.9 0.9 - - - +
296B CYS* 1.4 75.8 - - - +
298B ASN* 1.3 66.7 + - + +
300B LEU* 3.8 4.9 - - - +
301B PHE* 3.2 36.2 + - + +
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Residues in contact with ASN 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PBF 3.4 45.2 - - + -
67B LEU* 4.9 17.4 - - - +
70B LEU* 5.3 4.5 - - - +
74B ASP* 4.8 9.9 + - - -
245B ILE* 4.1 21.7 - - - +
294B ASN 5.0 3.1 - - - +
295B ASN 5.0 1.3 - - - +
297B LEU* 1.3 85.2 - - + +
299B PRO* 1.4 68.9 - - + +
301B PHE 4.0 0.2 + - - -
302B TYR* 3.5 20.4 + - - +
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Residues in contact with PRO 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B GLY* 5.4 13.2 - - - -
49B VAL* 6.1 5.2 - - + -
295B ASN 3.3 24.0 - - - +
296B CYS* 3.5 9.9 - - - +
298B ASN* 1.4 94.3 - - + +
300B LEU* 1.4 61.1 + - - +
302B TYR* 3.8 8.3 - - + +
303B GLY* 3.3 20.8 + - - -
304B PHE* 5.4 0.5 - - - -
313B PHE* 5.8 1.2 - - - -
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B CYS* 3.3 41.9 + - - +
297B LEU* 3.5 6.2 + - - +
299B PRO* 1.4 77.5 - - - +
301B PHE* 1.3 84.3 + - + +
302B TYR 3.4 0.5 + - - -
304B PHE* 3.4 55.8 + - + +
305B LEU* 5.6 2.0 - - + -
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Residues in contact with PHE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B ILE* 3.1 29.3 - - - +
244B ALA* 3.9 29.6 - - + -
245B ILE* 3.3 28.0 - - + -
248B PHE* 3.8 46.0 - + + -
297B LEU* 3.2 26.7 + - + +
300B LEU* 1.3 91.8 - - + +
302B TYR* 1.4 57.9 + - - +
305B LEU* 3.9 30.3 - - + +
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Residues in contact with TYR 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B VAL* 4.2 21.3 - - + -
53B ILE* 5.1 9.0 - - - +
59B LEU* 5.5 2.1 - - - +
64B SER* 5.4 4.3 + - - -
67B LEU* 4.3 37.0 - - + +
238B ILE* 4.5 12.9 - - + +
241B ILE* 3.5 16.2 - - + +
245B ILE* 4.4 5.1 - - + +
298B ASN* 3.5 17.7 + - - +
299B PRO* 3.8 9.0 - - + +
300B LEU 3.3 0.8 - - - -
301B PHE* 1.4 74.9 - - - +
303B GLY* 1.3 61.1 + - - +
305B LEU 2.9 21.5 - - - +
306B GLY 4.9 0.2 - - - +
309B PHE* 3.5 66.8 - + + +
310B LYS 5.0 0.2 + - - -
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Residues in contact with GLY 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B PRO 3.3 11.7 + - - -
302B TYR* 1.3 81.0 - - - +
304B PHE* 1.3 62.1 + - - +
305B LEU 3.5 0.5 + - - -
309B PHE* 4.0 8.9 - - - -
310B LYS* 3.5 25.6 - - - +
313B PHE* 3.8 35.7 - - - -
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Residues in contact with PHE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B PRO 5.4 0.2 - - - -
300B LEU* 3.4 51.5 + - + +
303B GLY* 1.3 75.1 - - - +
305B LEU* 1.3 68.4 + - + +
310B LYS* 3.0 27.5 + - - +
313B PHE* 5.9 7.9 - + - -
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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