Contacts of the helix formed by residues 306 - 316 (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 GLY 306 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237B ASP* 3.9 7.0 + - - +
238B ILE* 3.8 19.7 - - - +
241B ILE* 3.5 16.8 - - - +
305B LEU* 1.3 74.6 - - - +
307B LYS* 1.3 65.3 + - - -
308B LYS 3.5 1.9 + - - -
309B PHE* 4.0 3.7 + - - +
310B LYS* 3.0 28.3 + - - +
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Residues in contact with LYS 307 (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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233B PRO* 3.3 34.5 - - - +
234B ARG* 4.0 20.8 + - + -
237B ASP* 3.1 31.9 + - - +
306B GLY* 1.3 72.6 - - - +
308B LYS* 1.3 64.2 + - - +
310B LYS* 4.4 3.8 - - - -
311B ARG* 3.1 54.0 + - - +
326B SER* 4.5 21.3 - - - -
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Residues in contact with LYS 308 (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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59B LEU* 4.6 11.9 - - + -
61B THR* 3.7 34.9 + - - +
63B ALA* 5.9 1.7 - - - +
231B ASN* 6.5 0.7 - - + -
234B ARG* 4.1 36.9 + - + +
235B ASN* 3.0 32.3 + - - +
238B ILE* 4.7 17.8 - - + +
306B GLY 3.5 1.0 + - - -
307B LYS* 1.3 78.8 - - - +
309B PHE* 1.3 60.9 + - - +
311B ARG* 4.1 1.6 + - - +
312B TYR* 3.2 48.1 + - + +
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Residues in contact with PHE 309 (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* 4.5 14.4 - - + -
52B VAL* 4.6 22.9 - - + -
53B ILE* 6.0 1.6 - - + -
59B LEU* 4.5 19.4 - - + +
238B ILE* 4.2 20.5 - - + +
302B TYR* 3.5 69.5 - + + +
303B GLY* 4.0 9.4 - - - -
306B GLY 4.0 2.3 + - - +
308B LYS* 1.3 74.9 - - - +
310B LYS* 1.3 60.8 + - - +
312B TYR* 3.2 8.3 + - + -
313B PHE* 2.9 68.2 + + + +
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Residues in contact with LYS 310 (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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302B TYR 5.0 0.4 + - - -
303B GLY 3.5 20.9 - - - +
304B PHE* 3.0 32.1 + - - +
305B LEU* 4.2 7.7 - - - +
306B GLY 3.0 25.0 + - - +
307B LYS* 3.5 4.7 + - - +
309B PHE* 1.3 74.4 - - - +
311B ARG* 1.3 59.9 + - - +
313B PHE* 3.9 4.6 - - + +
314B LEU* 3.1 35.7 + - + +
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Residues in contact with ARG 311 (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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234B ARG* 5.0 7.4 - - - +
307B LYS* 3.1 52.5 + - - +
308B LYS* 4.5 2.9 - - - +
310B LYS* 1.3 77.7 - - - +
312B TYR* 1.3 64.5 + - + +
314B LEU* 3.5 7.7 + - + +
315B GLN* 3.2 19.1 + - - +
322B PRO 2.9 24.5 - - - +
323B LYS 3.4 35.8 + - - +
324B ALA* 4.3 1.8 + - - +
325B LYS* 3.4 25.9 + - - +
326B SER* 3.8 27.8 - - - +
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Residues in contact with TYR 312 (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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52B VAL* 5.4 7.0 - - + -
56B TYR* 3.4 39.3 - + + -
58B LYS* 3.2 38.0 + - + +
59B LEU* 4.2 28.0 - - + -
234B ARG* 4.9 10.6 + - - -
308B LYS* 3.2 35.5 + - + +
309B PHE* 3.2 7.6 + - + +
311B ARG* 1.3 78.7 - - + +
313B PHE* 1.3 64.2 + - - +
315B GLN* 3.4 17.9 + - - +
316B LEU* 3.2 27.5 + - + +
322B PRO 5.5 0.2 - - - -
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Residues in contact with PHE 313 (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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48B LEU* 4.8 19.3 - - + -
49B VAL* 6.2 2.2 - - + -
52B VAL* 5.7 5.1 - - + +
299B PRO 5.8 1.6 - - - -
303B GLY* 3.8 34.5 - - - -
304B PHE* 4.9 9.0 - + - -
309B PHE* 2.9 55.1 + + + +
310B LYS* 3.9 4.5 - - + +
312B TYR* 1.3 70.6 - - - +
314B LEU* 1.3 60.7 + - + +
316B LEU* 3.5 11.2 + - + +
317B LEU* 3.3 48.5 - - + +
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Residues in contact with LEU 314 (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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310B LYS* 3.1 27.2 + - + +
311B ARG* 3.6 8.5 - - + +
312B TYR 3.4 0.4 - - - -
313B PHE* 1.3 72.3 - - + +
315B GLN* 1.4 59.5 + - - +
317B LEU* 4.6 6.3 - - - -
318B LYS* 3.0 59.6 + - + +
319B TYR 3.7 0.3 + - - -
321B PRO* 3.3 36.6 - - + +
322B PRO 4.7 2.0 - - - +
323B LYS* 4.7 11.4 - - + +
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Residues in contact with GLN 315 (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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56B TYR* 3.6 16.4 + - + -
311B ARG 3.2 4.3 + - - +
312B TYR* 3.4 36.4 + - - +
314B LEU* 1.4 73.9 - - - +
316B LEU* 1.4 61.2 + - + +
317B LEU 3.3 2.9 + - - -
319B TYR* 3.2 37.3 + - - +
320B ILE 5.2 6.3 + - - +
321B PRO 3.6 12.3 - - - +
322B PRO* 3.4 37.1 - - - +
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Residues in contact with LEU 316 (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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48B LEU* 5.8 5.7 - - + +
51B ILE* 6.4 1.3 - - + -
52B VAL* 3.7 41.5 - - + -
55B PHE* 6.1 7.9 - - + -
56B TYR* 5.5 11.7 - - + -
312B TYR 3.2 15.0 + - - +
313B PHE* 3.5 7.7 + - + +
315B GLN* 1.4 75.1 - - + +
317B LEU* 1.4 66.5 + - - +
319B TYR* 3.9 36.1 + - + +
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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