Contacts of the strand formed by residues 241 - 248 (chain D) 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 THR 241 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207D VAL* 3.4 28.9 - - + +
208D GLU 2.9 5.1 + - - -
209D PHE* 3.1 23.7 + - - +
238D LYS* 3.4 17.2 + - + +
239D LEU 2.9 14.4 + - - -
240D ASN* 1.3 77.4 + - - +
242D LYS* 1.3 63.0 + - - +
258D ILE* 3.8 28.3 - - + -
259D GLU 3.3 18.2 - - - +
260D ALA* 5.1 1.2 - - - -
261D ALA* 3.9 1.6 - - - +
481D NAI 3.9 0.9 - - - -
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Residues in contact with LYS 242 (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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209D PHE* 3.7 24.9 - - + -
241D THR* 1.3 76.4 - - - +
243D VAL* 1.3 65.0 + - - +
244D THR* 3.6 12.9 + - + +
258D ILE* 3.1 4.9 - - - +
259D GLU* 2.9 61.7 + - + +
260D ALA 3.0 20.9 + - - +
261D ALA* 3.5 17.7 + - - +
262D SER 4.6 0.2 - - - -
263D GLY* 4.0 6.1 - - - +
481D NAI 4.2 10.1 - - - +
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Residues in contact with VAL 243 (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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155D PHE* 3.0 37.5 - - + -
158D ILE* 4.1 9.0 - - + -
182D VAL* 5.7 0.9 - - + -
184D ILE* 4.0 26.0 - - + -
207D VAL* 4.2 15.9 - - + -
242D LYS* 1.3 79.5 - - - +
244D THR* 1.3 59.8 + - - +
245D GLY 3.5 15.3 - - - +
256D VAL* 3.5 28.3 - - + -
257D SER 3.3 5.6 - - - +
258D ILE* 3.9 16.2 - - + -
481D NAI 4.1 6.6 + - - +
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Residues in contact with THR 244 (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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155D PHE* 4.6 6.1 - - - -
242D LYS* 4.3 14.6 - - - +
243D VAL* 1.3 74.8 - - - +
245D GLY* 1.3 56.9 + - - +
257D SER* 2.7 37.9 + - - +
258D ILE 4.1 1.3 + - - -
259D GLU* 3.0 41.1 - - + +
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Residues in contact with GLY 245 (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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155D PHE* 4.8 1.6 - - - -
157D GLY* 5.9 2.5 - - - -
158D ILE* 4.0 12.6 - - - -
243D VAL* 3.3 10.1 - - - +
244D THR* 1.3 84.7 + - - +
246D ALA* 1.3 64.7 + - - +
256D VAL* 3.5 1.7 - - - -
257D SER* 2.8 29.6 + - - -
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Residues in contact with ALA 246 (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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157D GLY 4.7 9.4 + - - +
158D ILE* 3.7 19.4 - - + +
165D ILE* 5.6 4.3 - - + -
245D GLY* 1.3 75.7 - - - +
247D THR* 1.3 72.9 + - - +
254D ILE* 3.9 7.2 - - + -
255D ASP 3.1 11.9 - - - +
256D VAL* 4.3 2.7 - - + -
257D SER* 4.7 0.9 - - - +
274D LEU* 3.7 30.5 - - + -
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Residues in contact with THR 247 (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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165D ILE* 6.0 0.9 - - - -
246D ALA* 1.3 83.9 - - - +
248D LYS* 1.3 66.1 + - - +
249D LYS* 3.4 1.4 + - - +
254D ILE* 3.5 4.6 - - - -
255D ASP* 2.9 44.8 + - - +
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Residues in contact with LYS 248 (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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161D ASP* 5.0 4.0 - - - +
164D THR* 2.7 37.3 + - - +
165D ILE* 3.9 19.3 - - + -
247D THR* 1.3 71.5 - - - +
249D LYS* 1.3 67.1 + - - +
250D SER 3.9 0.2 + - - -
252D GLY* 2.8 35.5 + - - -
253D LYS 3.8 1.3 - - - -
254D ILE* 3.4 18.8 - - + +
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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