Contacts of the strand formed by residues 285 - 290 (chain A) in PDB entry 5IZL
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 ARG 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ASN* 4.0 21.4 + - - +
9A ASN* 4.5 4.7 - - - +
53A PHE* 3.5 42.6 - - - +
55A CYS* 6.4 0.2 - - - -
89A THR* 4.2 17.9 + - - +
229A ASP* 3.1 36.8 + - - -
230A HIS* 4.4 2.8 + - - -
242A THR* 4.0 11.8 + - - -
243A GLY 3.5 12.2 - - - +
244A THR* 4.0 15.0 - - + +
272A MET* 3.8 17.0 - - - +
273A PHE* 5.6 1.4 - - - -
283A GLY 3.9 0.4 + - - -
284A ASP* 1.3 76.1 - - - +
286A LEU* 1.3 65.7 + - - +
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Residues in contact with LEU 286 (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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226A MET* 4.4 8.3 - - + -
242A THR* 3.2 6.8 - - - -
243A GLY 2.9 30.0 + - - +
245A ILE* 4.2 13.7 - - + -
250A ILE* 5.0 0.9 - - + -
270A MET* 4.7 7.6 - - + -
271A GLN 3.4 15.5 - - - +
272A MET* 4.1 12.6 - - + +
277A ILE* 4.1 12.8 - - + -
280A ALA* 3.3 34.3 - - + -
284A ASP* 5.0 1.3 - - + -
285A ARG* 1.3 76.7 - - - +
287A GLY* 1.3 75.4 + - - +
288A ILE* 3.3 35.2 - - + +
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Residues in contact with GLY 287 (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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240A VAL* 4.7 5.8 - - - -
241A MET 3.3 8.3 - - - -
242A THR* 3.9 14.1 - - - -
269A SER 4.1 0.2 - - - +
270A MET* 3.5 4.3 - - - -
271A GLN* 3.2 31.9 + - - +
286A LEU* 1.3 81.9 - - - +
288A ILE* 1.3 61.8 + - - -
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Residues in contact with ILE 288 (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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224A PHE* 4.8 0.7 - - + -
226A MET* 4.0 18.8 - - + -
239A THR 3.8 0.9 - - - +
240A VAL* 3.2 5.9 - - - +
241A MET* 2.8 48.4 + - + +
250A ILE* 3.6 35.0 - - + -
256A VAL* 5.2 3.8 - - + -
267A VAL* 4.2 13.5 - - + -
269A SER 3.6 2.7 - - - -
270A MET* 4.0 10.5 - - + -
286A LEU* 3.3 24.7 - - + -
287A GLY* 1.3 73.2 - - - +
289A CYS* 1.3 64.4 + - - +
290A VAL* 3.8 24.5 - - + -
303A VAL* 6.1 1.6 - - + -
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Residues in contact with CYS 289 (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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237A GLN* 2.8 44.6 - - - +
239A THR 3.7 4.3 - - - -
240A VAL* 3.8 22.7 - - + -
267A VAL* 3.9 1.2 - - - -
268A LYS* 3.0 31.2 + - + +
269A SER* 2.8 33.9 + - - +
288A ILE* 1.3 74.1 - - - +
290A VAL* 1.3 67.0 + - - +
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Residues in contact with VAL 290 (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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238A GLY* 3.2 6.1 - - - -
239A THR 2.9 31.6 + - - +
241A MET* 3.7 20.9 - - + -
256A VAL* 4.7 5.2 - - + -
258A ILE* 4.9 0.9 - - + -
265A LYS* 3.9 23.3 - - + -
266A LYS 3.3 26.7 - - - +
267A VAL* 4.2 3.4 - - + -
268A LYS* 4.4 6.3 - - - -
288A ILE* 3.8 18.4 - - + -
289A CYS* 1.3 78.2 - - - +
291A THR* 1.3 77.8 + - - +
293A PHE* 4.0 9.6 - - + -
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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