Contacts of the strand formed by residues 180 - 184 (chain E) 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 LYS 180 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E PRO* 4.0 4.5 - - - +
179E GLU* 1.3 82.5 - - + +
181E MET* 1.3 66.6 + - - +
182E VAL* 5.1 1.6 - - - -
203E ASP* 3.3 31.2 - - + +
205E THR* 4.9 9.2 - - - -
236E LYS* 4.9 4.5 - - - +
269E ILE* 3.8 23.5 - - - +
270E THR* 3.3 27.8 + - - +
271E CYS* 3.9 9.0 - - + -
272E ASP* 2.9 37.2 + - - +
273E VAL 3.3 5.5 + - - -
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Residues in contact with MET 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171E ALA* 5.4 3.4 - - + -
174E LEU* 3.4 25.4 - - + -
178E PRO* 3.5 16.6 - - + -
180E LYS* 1.3 76.7 - - - +
182E VAL* 1.3 75.9 + - - +
183E VAL* 4.3 16.4 - - + -
193E LEU 5.3 2.0 - - - +
194E GLY* 5.3 0.2 - - - -
197E TRP* 4.0 25.1 - - + -
202E ALA* 4.9 0.4 - - + -
203E ASP 2.9 11.3 + - - +
204E VAL* 3.4 15.6 - - + +
205E THR* 3.1 24.3 + - - -
273E VAL* 3.3 37.0 - - + +
275E LEU* 4.5 12.1 - - + -
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Residues in contact with VAL 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E LYS* 5.1 1.8 - - - -
181E MET* 1.3 77.5 - - - +
183E VAL* 1.3 73.2 + - - +
184E ILE* 4.4 4.3 - - + -
205E THR* 3.2 13.2 - - - +
207E VAL* 4.3 16.8 - - + -
256E VAL* 4.2 11.0 - - + -
269E ILE* 3.6 34.5 - - + -
271E CYS* 3.7 18.6 - - + +
273E VAL 3.1 6.1 + - - +
274E LEU* 3.5 26.1 - - + +
275E LEU 2.8 25.3 + - - -
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Residues in contact with VAL 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181E MET* 4.3 9.2 - - - -
182E VAL* 1.3 78.7 - - - +
184E ILE* 1.3 60.0 + - - +
185E GLY 3.6 11.2 - - - +
190E GLY* 3.7 12.6 - - - +
194E GLY* 4.5 8.7 - - - -
204E VAL* 4.1 22.2 - - + -
205E THR 2.8 9.1 + - - +
206E ALA* 3.0 15.3 - - + +
207E VAL* 2.7 32.2 + - - +
275E LEU* 3.4 24.5 - - + -
277E CYS* 3.4 29.2 - - - -
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Residues in contact with ILE 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E PHE* 4.2 12.8 - - + -
158E ILE* 4.4 12.1 - - + -
182E VAL* 4.4 5.4 - - + -
183E VAL* 1.3 76.1 - - - +
185E GLY* 1.3 60.5 + - - +
207E VAL* 3.6 5.2 - - + +
243E VAL* 3.2 45.5 - - + -
256E VAL* 4.3 3.1 - - + -
274E LEU* 3.9 27.4 - - + -
275E LEU 2.8 14.1 + - - +
276E VAL* 4.8 7.2 - - + -
277E CYS* 3.1 30.5 + - - +
278E ILE* 3.6 18.2 - - + +
481E NAI 4.0 15.3 - - + -
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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