Contacts of the strand formed by residues 180 - 184 (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 LYS 180 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D PRO* 4.2 2.1 - - - +
179D GLU* 1.3 85.9 - - + +
181D MET* 1.3 64.9 + - - +
182D VAL* 5.4 4.7 - - - -
203D ASP* 3.5 30.3 - - + +
205D THR* 5.6 4.3 - - - -
269D ILE* 5.3 4.7 - - - +
270D THR* 2.8 37.3 + - - +
271D CYS* 3.8 6.5 - - + -
272D ASP* 2.6 43.8 + - - +
273D VAL 3.3 1.9 + - - -
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Residues in contact with MET 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D VAL* 6.1 0.9 - - - -
171D ALA* 5.9 1.6 - - - -
174D LEU* 4.8 3.6 - - - -
178D PRO* 4.2 12.1 - - + -
179D GLU 4.4 0.2 - - - -
180D LYS* 1.3 77.0 - - - +
182D VAL* 1.3 78.6 + - - +
183D VAL* 4.1 7.4 - - + -
193D LEU 4.2 1.1 - - - +
194D GLY* 4.0 22.4 - - - +
197D TRP* 3.8 39.7 - - + -
202D ALA* 4.9 0.2 - - + -
203D ASP 2.9 12.7 + - - +
204D VAL* 3.6 15.9 - - + -
205D THR* 3.2 23.0 + - - -
271D CYS* 3.9 0.2 - - - -
273D VAL* 3.4 31.9 - - + +
275D LEU* 4.6 16.6 - - + +
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Residues in contact with VAL 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D LYS* 5.4 4.9 - - - -
181D MET* 1.3 81.4 - - - +
183D VAL* 1.3 67.7 + - - +
184D ILE* 5.5 0.7 - - + -
205D THR* 3.2 16.6 - - - +
207D VAL* 4.7 10.5 - - + -
256D VAL* 4.5 6.5 - - + -
269D ILE* 3.9 35.2 - - + -
270D THR 4.8 4.0 - - - +
271D CYS* 3.4 23.1 - - + -
273D VAL 3.3 5.5 + - - -
274D LEU* 3.0 28.5 - - + +
275D LEU 3.0 22.8 + - - -
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Residues in contact with VAL 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D MET* 4.1 20.0 - - + -
182D VAL* 1.3 74.6 - - - +
184D ILE* 1.3 64.0 + - - +
185D GLY 3.4 17.7 + - - +
190D GLY* 4.0 16.8 - - - +
194D GLY* 4.2 13.7 - - - -
204D VAL* 4.2 9.6 - - + -
205D THR 2.8 8.2 + - - +
206D ALA* 3.2 12.9 - - + -
207D VAL* 3.0 27.9 + - - +
235D PHE* 5.2 0.4 - - + -
275D LEU* 3.5 36.6 - - + +
277D CYS* 4.2 5.2 - - + -
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Residues in contact with ILE 184 (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* 4.0 9.4 - - + -
158D ILE* 4.2 7.2 - - + -
182D VAL* 5.5 0.7 - - + -
183D VAL* 1.3 73.2 - - - +
185D GLY* 1.3 59.9 + - - +
207D VAL* 4.2 4.3 - - + -
243D VAL* 3.9 41.3 - - + -
274D LEU* 4.0 25.4 - - + -
275D LEU 3.0 11.4 + - - +
276D VAL* 3.6 35.7 - - + -
277D CYS* 2.9 27.2 + - - +
278D ILE* 3.5 19.5 - - + +
481D NAD 4.1 8.7 - - + +
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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
------------------------------------------------------------
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