Contacts of the helix formed by residues 308 - 318 (chain A) in PDB entry 1ZSV
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 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A ILE* 3.7 17.8 - - + +
304A GLU 2.6 25.3 + - - -
305A GLY* 3.1 11.8 + - - +
307A GLU* 1.3 93.5 + - - +
309A MET* 1.3 57.5 + - - +
310A PRO* 3.6 1.6 - - - -
311A ALA* 3.5 13.9 + - + +
312A ALA* 2.9 27.3 + - - +
327A VAL* 4.9 0.2 - - - -
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Residues in contact with MET 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A TRP* 3.9 4.7 - - + +
44A LEU* 3.7 39.7 - - + -
45A THR 3.7 19.7 - - - +
46A VAL* 3.8 16.1 - - + +
91A TRP* 3.8 38.3 - - + +
305A GLY 4.2 0.2 + - - -
306A PHE* 3.2 25.3 + - + +
308A ASN* 1.3 73.9 - - - +
310A PRO* 1.3 76.8 - - + +
312A ALA* 3.2 7.0 + - - +
313A PHE* 2.9 24.1 + - - +
327A VAL* 3.6 23.1 - - + -
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Residues in contact with PRO 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A TRP* 3.4 50.0 - - + -
19A ASN* 4.8 3.6 - - - +
22A PHE* 3.7 29.2 - - + -
91A TRP* 3.9 12.8 - - + -
307A GLU 4.0 2.2 - - - +
308A ASN 3.9 1.1 - - - -
309A MET* 1.3 95.0 - - + +
311A ALA* 1.3 55.2 + - - +
313A PHE* 3.3 3.6 + - + +
314A MET* 2.9 43.2 + - + +
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ASN* 5.1 2.6 + - - +
303A ILE* 6.3 0.2 - - + -
308A ASN* 3.5 18.0 + - + +
309A MET 3.2 0.6 - - - -
310A PRO* 1.3 76.6 - - - +
312A ALA* 1.3 56.2 + - - +
314A MET* 3.7 11.2 - - + +
315A GLY* 2.7 33.8 + - - -
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A VAL* 3.9 6.5 - - + +
303A ILE* 3.4 32.9 - - + +
308A ASN 2.9 14.0 + - - +
309A MET 3.4 8.1 - - - +
311A ALA* 1.3 75.2 - - - +
313A PHE* 1.3 57.8 + - - +
315A GLY* 3.8 0.5 - - - -
316A MET* 3.0 30.7 + - - +
321A ASN* 4.0 1.4 - - - +
325A THR* 3.9 9.8 - - + +
327A VAL* 3.6 20.2 - - + -
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Residues in contact with PHE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE* 4.1 14.1 - + - -
17A PRO* 4.0 13.9 - - + -
22A PHE* 3.8 19.5 - + - -
46A VAL* 4.0 17.4 - - + +
47A ASP 3.7 20.0 - - - -
50A MET* 3.7 13.5 - - + -
51A ARG* 3.6 25.1 - - - -
63A MET* 4.5 5.6 - - + -
91A TRP* 3.7 18.2 - + + -
309A MET 2.9 12.2 + - - +
310A PRO 3.5 6.7 - - - +
312A ALA* 1.3 77.2 - - - +
314A MET* 1.3 57.5 + - + +
316A MET* 3.4 21.7 + - + +
317A LEU* 2.9 58.3 + - + +
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Residues in contact with MET 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TYR* 5.4 0.7 - - - -
17A PRO* 3.5 47.8 - - + +
18A THR* 3.8 8.1 - - - -
19A ASN* 3.1 33.0 - - - +
22A PHE* 4.0 6.3 - - + -
310A PRO* 2.9 43.8 + - + +
311A ALA* 3.8 7.9 - - - +
313A PHE* 1.3 75.1 - - + +
315A GLY* 1.3 59.2 + - - +
317A LEU* 3.4 7.6 + - - +
318A LYS* 3.0 34.7 + - + +
18D THR* 4.0 8.3 - - + +
19D ASN* 4.3 3.6 - - + +
20D SER* 5.6 8.5 - - - +
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Residues in contact with GLY 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A ALA 2.7 21.2 + - - -
312A ALA 3.8 1.1 - - - -
314A MET* 1.3 71.7 - - - +
316A MET* 1.3 63.1 + - - +
318A LYS 3.3 1.7 + - - -
319A GLY 3.2 3.8 + - - -
320A ASP* 2.9 45.7 + - - +
321A ASN* 3.8 10.8 - - - -
20D SER* 5.9 2.0 - - - -
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Residues in contact with MET 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A VAL* 3.9 7.4 - - + -
47A ASP* 3.4 26.9 - - - +
48A PRO* 3.7 29.6 - - - -
312A ALA 3.0 16.5 + - - +
313A PHE* 3.4 37.7 - - + +
315A GLY* 1.3 74.3 - - - +
317A LEU* 1.3 64.4 + - + +
319A GLY* 2.9 19.3 + - - -
320A ASP 4.8 0.9 - - - +
321A ASN* 3.6 9.2 + - - +
325A THR* 3.7 13.9 - - - +
408A CL 3.7 23.3 - - + -
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TYR* 3.8 22.5 + - + -
17A PRO* 3.5 37.5 - - + -
48A PRO* 4.5 12.1 - - + +
51A ARG* 4.1 20.9 - - + -
245A TYR* 5.7 2.7 - - + -
246A ASN* 4.1 15.4 + - - +
313A PHE* 2.9 49.0 + - + +
314A MET* 3.7 6.5 - - - +
315A GLY 3.2 0.2 - - - -
316A MET* 1.3 85.8 - - + +
318A LYS* 1.3 60.8 + - - +
319A GLY 3.1 1.1 + - - -
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Residues in contact with LYS 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TYR* 3.2 45.1 + - + +
194A LYS* 4.8 10.6 + - - -
314A MET* 3.0 19.5 + - + +
315A GLY 3.8 1.8 - - - +
316A MET 3.3 0.2 - - - -
317A LEU* 1.3 76.8 - - - +
319A GLY* 1.3 60.1 + - - +
320A ASP* 3.5 22.4 + - - +
12D HIS 5.1 1.0 + - - -
14D VAL* 3.7 30.3 + - - +
16D TYR 5.3 0.6 + - - -
18D THR* 3.7 18.1 - - + +
20D SER* 4.1 13.7 - - - +
21D ASP* 3.7 23.5 + - - +
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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