Contacts of the strand formed by residues 254 - 258 (chain D) in PDB entry 1ZMC
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D THR* 4.0 12.1 - - - +
165D ILE* 3.4 21.8 - - + -
246D ALA* 3.9 18.2 - - + -
247D THR 3.6 6.1 - - - +
248D LYS* 3.5 31.4 - - + +
252D GLY 3.7 0.4 - - - +
253D LYS* 1.3 76.4 - - - +
255D ASP* 1.3 76.9 + - - +
256D VAL* 3.9 10.9 + - + -
269D ILE 3.7 0.3 - - - +
270D THR* 3.3 7.3 - - - +
271D CYS* 3.0 39.4 + - - +
272D ASP 3.6 24.0 - - - +
273D VAL* 4.5 1.8 - - - -
274D LEU* 4.1 9.2 - - + +
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Residues in contact with ASP 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D ALA* 3.2 5.5 - - - -
247D THR* 3.1 39.6 + - - +
249D LYS* 3.2 42.6 + - - +
254D ILE* 1.3 72.3 - - - +
256D VAL* 1.3 62.6 + - - +
257D SER* 3.9 2.0 + - - -
268D VAL* 3.8 17.8 - - + +
269D ILE 3.5 2.5 - - - -
270D THR* 2.5 28.8 + - - -
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Residues in contact with VAL 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D VAL* 4.5 4.3 - - + -
243D VAL* 3.5 38.8 - - + -
245D GLY 3.6 3.6 - - - +
246D ALA* 4.3 1.8 - - + -
254D ILE* 3.9 13.0 - - + -
255D ASP* 1.3 74.8 - - - +
257D SER* 1.3 64.8 + - - +
258D ILE* 3.7 6.1 + - + -
268D VAL* 3.3 6.6 - - - -
269D ILE* 2.9 53.7 + - + +
271D CYS* 4.1 11.0 - - - -
274D LEU* 3.8 30.1 - - + -
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Residues in contact with SER 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D VAL* 3.4 6.9 - - - +
244D THR* 2.8 45.0 + - - -
245D GLY* 2.7 22.6 + - - +
246D ALA* 4.7 0.9 - - - -
247D THR* 5.6 1.7 + - - -
255D ASP 4.6 3.1 + - - -
256D VAL* 1.3 72.3 - - - +
258D ILE* 1.3 60.5 + - - +
267D GLU 3.9 4.0 - - - -
268D VAL* 4.4 10.9 - - - +
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Residues in contact with ILE 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D VAL* 4.6 3.8 - - + -
238D LYS* 4.3 14.6 - - + -
241D THR* 3.7 24.5 - - + -
242D LYS 3.3 7.6 - - - +
243D VAL* 4.1 22.0 - - + -
244D THR* 4.5 3.6 + - - +
256D VAL* 4.2 4.3 - - + +
257D SER* 1.3 79.9 - - - +
259D GLU* 1.3 71.2 + - - +
266D ALA* 3.4 5.0 - - - +
267D GLU* 2.9 63.2 + - + +
268D VAL* 4.7 0.7 - - - +
269D ILE* 4.2 32.5 - - + -
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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