Contacts of the helix formed by residues 255 - 264 (chain E) in PDB entry 5ZR1
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 ILE 255 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40E GLY* 3.4 31.3 + - - +
192E TYR* 4.6 8.5 - - + -
197E VAL* 3.8 32.8 - - + +
200E ILE* 4.4 17.0 - - + -
201E LEU* 4.3 8.9 - - + +
253E ASN 4.0 1.5 + - - +
254E ASP* 1.3 82.8 - - - +
256E PHE* 1.3 65.4 + - + +
257E ALA 3.4 0.9 - - - -
258E LEU* 3.5 5.9 + - - +
259E ASN* 2.9 49.2 + - - +
2001E AGS 3.5 30.1 - - + +
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Residues in contact with PHE 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C ARG* 5.5 0.7 - - - -
39E SER* 4.3 10.1 - - - -
40E GLY* 4.3 8.5 - - - -
254E ASP* 4.2 1.2 - - + +
255E ILE* 1.3 79.6 - - + +
257E ALA* 1.3 62.3 + - - +
259E ASN* 3.7 13.4 + - + +
260E ASP* 3.1 31.3 + - - +
2001E AGS 3.3 78.5 - - - -
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Residues in contact with ALA 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C ARG* 3.5 34.5 + - - +
458D ASN* 4.9 0.9 - - - +
251E THR* 3.8 20.9 - - + -
254E ASP* 3.6 27.6 - - + +
255E ILE 3.4 0.2 - - - -
256E PHE* 1.3 78.7 - - - +
258E LEU* 1.3 63.6 + - - +
260E ASP* 3.4 2.1 + - - +
261E LEU* 3.2 28.1 + - - +
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Residues in contact with LEU 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E VAL* 4.4 6.7 - - + -
201E LEU* 3.7 22.0 - - + -
243E ILE* 4.2 10.8 - - + +
244E VAL* 3.8 35.2 - - + +
247E PHE* 4.9 5.8 - - + +
248E HIS* 5.5 2.5 - - - +
251E THR* 3.2 33.9 - - + +
252E GLY 4.2 5.8 - - - +
254E ASP 3.3 26.0 - - - +
255E ILE* 3.5 8.4 + - - +
256E PHE 3.4 0.2 - - - -
257E ALA* 1.3 78.8 - - - +
259E ASN* 1.3 57.7 + - - +
261E LEU* 3.3 6.4 + - + +
262E ILE* 3.0 35.6 + - - +
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Residues in contact with ASN 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C ARG* 5.4 1.6 + - - +
201E LEU* 3.3 16.9 - - - +
204E SER* 5.6 3.0 + - - -
205E ARG* 3.1 44.0 + - - +
255E ILE* 2.9 42.3 + - - +
256E PHE* 4.0 17.4 - - + +
257E ALA 3.3 0.4 - - - -
258E LEU* 1.3 75.2 - - - +
260E ASP* 1.3 62.8 + - - +
262E ILE* 4.1 1.3 - - - -
263E ASP* 3.7 14.9 + - - +
2001E AGS 5.3 4.2 + - - -
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Residues in contact with ASP 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C SER 5.1 2.4 - - - +
257C ARG* 3.7 40.0 + - - +
258C LEU* 5.0 0.5 + - - -
261C ARG* 2.4 41.2 + - - +
256E PHE* 3.1 19.7 + - - +
257E ALA 3.4 4.5 + - - +
258E LEU 3.2 0.6 - - - -
259E ASN* 1.3 79.3 - - - +
261E LEU* 1.3 59.1 + - - +
262E ILE 3.2 0.2 - - - -
263E ASP* 3.5 2.2 + - - +
264E PHE* 3.0 43.8 + - + -
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Residues in contact with LEU 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C ARG* 5.1 2.5 - - - -
243E ILE* 3.9 13.0 - - + +
247E PHE* 3.8 34.5 - - + -
250E TYR* 4.1 10.5 - - + -
251E THR* 3.8 22.2 - - + -
257E ALA 3.2 12.8 + - - +
258E LEU* 3.3 8.0 + - + +
260E ASP* 1.3 74.7 - - - +
262E ILE* 1.3 64.3 + - - +
264E PHE* 4.1 4.7 - - + -
265E LYS* 3.3 45.6 - - + +
295E THR* 4.3 6.5 - - - +
297E ASP* 3.4 34.1 - - - +
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Residues in contact with ILE 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E LEU* 3.7 35.0 - - + -
205E ARG* 4.4 16.4 - - + +
209E LEU* 4.0 28.0 - - + -
239E PHE* 3.9 19.4 - - + -
240E ILE* 4.2 14.4 - - + -
243E ILE* 3.7 20.9 - - + -
258E LEU 3.0 22.1 + - - +
259E ASN* 4.2 6.3 - - - +
260E ASP 3.2 0.2 - - - -
261E LEU* 1.3 76.0 - - - +
263E ASP* 1.3 56.8 + - - +
265E LYS 2.9 3.8 + - - -
266E TRP* 2.6 38.4 + - + +
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Residues in contact with ASP 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C LYS* 3.6 31.3 + - - +
205E ARG* 4.3 19.7 + - - +
209E LEU* 6.4 0.4 - - - -
212E ASP* 4.8 7.6 - - - +
259E ASN 3.7 12.7 + - - +
260E ASP* 3.5 4.4 + - - +
262E ILE* 1.3 80.5 - - - +
264E PHE* 1.3 64.4 + - + +
265E LYS 3.3 0.2 - - - -
266E TRP* 4.5 5.4 - - - +
267E PRO* 3.3 25.8 - - - +
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Residues in contact with PHE 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C LYS* 5.8 3.4 - - - -
257C ARG* 3.3 39.9 - - + -
260C LYS* 3.6 58.6 - - + +
261C ARG* 4.1 19.1 - - + -
260E ASP* 3.0 28.5 + - + +
261E LEU* 4.5 5.6 - - + +
263E ASP* 1.3 84.8 - - + +
265E LYS* 1.3 63.0 + - + +
266E TRP 3.8 0.2 - - - -
267E PRO* 4.4 3.5 - - - +
268E LYS* 3.4 21.7 + - - +
295E THR 6.1 0.7 - - - +
297E ASP* 4.0 15.0 - - - +
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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