Contacts of the strand formed by residues 254 - 260 (chain H) in PDB entry 1ZMD
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 254 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164H THR* 3.4 43.5 - - - +
165H ILE* 3.7 15.5 - - + -
246H ALA* 4.5 4.9 - - + -
247H THR 3.6 10.8 - - - +
248H LYS* 4.4 9.0 - - + -
252H GLY 4.2 6.7 - - - +
253H LYS* 1.3 78.3 - - - +
255H ASP* 1.3 72.6 + - - +
256H VAL* 3.9 12.5 + - + -
269H ILE 3.6 1.6 - - - +
270H THR* 3.2 4.7 - - - -
271H CYS* 2.9 47.8 + - - +
272H ASP 4.1 4.9 - - - +
273H VAL* 4.4 0.7 - - - -
274H LEU* 3.9 22.0 - - + +
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Residues in contact with ASP 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246H ALA* 3.1 5.5 - - - +
247H THR* 3.0 45.9 + - + +
249H LYS* 2.8 36.5 + - - +
253H LYS 4.3 0.2 - - - -
254H ILE* 1.3 71.4 - - - +
256H VAL* 1.3 61.7 + - - +
257H SER* 4.0 2.7 + - - +
268H VAL* 3.7 20.3 - - + +
269H ILE 3.7 1.6 - - - -
270H THR* 2.7 27.3 + - - +
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Residues in contact with VAL 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182H VAL* 4.2 19.3 - - + -
184H ILE* 4.9 0.9 - - + -
207H VAL* 5.5 0.4 - - + -
243H VAL* 3.9 27.6 - - + -
245H GLY 3.6 3.1 - - - +
246H ALA* 4.3 2.0 - - + +
254H ILE* 4.2 12.8 - - + -
255H ASP* 1.3 76.3 - - - +
257H SER* 1.3 62.8 + - - +
258H ILE* 3.8 15.2 + - + +
268H VAL* 3.3 4.1 - - - +
269H ILE* 2.8 45.7 + - + +
271H CYS* 4.3 6.7 - - - -
274H LEU* 3.7 31.4 - - + -
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Residues in contact with SER 257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243H VAL* 3.4 3.3 - - - +
244H THR* 2.8 45.8 + - - -
245H GLY 2.7 21.5 + - - +
255H ASP* 4.0 3.0 + - - +
256H VAL* 1.3 72.7 - - - +
258H ILE* 1.3 59.0 + - - +
267H GLU 3.5 7.6 - - - -
268H VAL* 3.8 16.9 - - - +
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Residues in contact with ILE 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207H VAL* 4.2 8.1 - - + -
238H LYS* 4.3 11.7 - - + -
241H THR* 3.6 18.8 - - + -
242H LYS 3.2 13.2 - - - +
243H VAL* 3.9 17.9 - - + -
244H THR* 4.2 2.4 + - - +
256H VAL* 4.1 13.5 - - + +
257H SER* 1.3 81.2 - - - +
259H GLU* 1.3 66.3 + - - +
266H ALA* 3.3 5.4 - - - +
267H GLU* 2.8 74.4 + - + +
269H ILE* 3.7 25.4 - - + -
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Residues in contact with GLU 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241H THR* 3.1 8.8 - - - +
242H LYS* 2.8 36.7 + - + +
244H THR* 3.5 25.9 - - + +
258H ILE* 1.3 82.2 - - - +
260H ALA* 1.3 66.2 + - - +
263H GLY* 4.1 5.7 - - - -
264H GLY* 3.3 30.2 + - - +
265H LYS 3.7 4.9 - - - -
266H ALA* 4.0 14.8 - - + +
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Residues in contact with ALA 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240H ASN 3.7 8.7 - - - +
241H THR* 4.5 2.5 - - - +
242H LYS* 4.4 2.9 - - - +
259H GLU* 1.3 78.5 - - - +
261H ALA* 1.3 61.2 + - - +
262H SER* 4.2 7.6 - - - +
263H GLY* 2.8 39.3 + - - +
264H GLY 2.8 12.8 + - - +
265H LYS* 4.1 16.9 + - + +
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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