Contacts of the helix formed by residues 200 - 210 (chain E) in PDB entry 1Z6Z
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 200 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15E GLY* 3.7 22.7 - - - -
16E PHE 4.0 2.0 - - - +
198E LEU* 2.9 16.3 + - + -
199E ASP* 1.3 80.4 - - - +
201E ASP* 1.3 66.5 + - - +
202E MET 3.4 5.4 + - - -
203E GLN* 3.3 2.1 + - - +
204E GLN* 3.1 22.3 + - - +
231E CYS* 3.7 19.5 - - - -
805E NAP 2.4 49.2 + - - +
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Residues in contact with ASP 201 (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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41B ASP* 5.2 7.6 - - - +
14E ARG* 2.9 47.1 + - - +
200E THR* 1.3 74.7 - - - +
202E MET* 1.3 56.8 + - - +
204E GLN* 3.5 19.0 + - - +
205E LEU* 2.9 28.2 + - - +
805E NAP 3.8 3.8 + - - +
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Residues in contact with MET 202 (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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99E GLY 3.5 28.0 - - - +
100E SER* 3.7 18.2 - - - -
101E LEU* 3.8 22.2 - - + +
167E TYR* 4.0 16.6 - - - -
200E THR* 3.2 1.8 + - - -
201E ASP* 1.3 75.9 - - - +
203E GLN* 1.3 66.9 + - - +
205E LEU* 3.2 9.6 + - + +
206E ALA* 3.0 22.4 + - - +
805E NAP 3.6 75.5 + - - +
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Residues in contact with GLN 203 (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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164E TRP* 5.9 3.2 - - - -
197E PRO* 4.1 9.7 - - - +
198E LEU 2.9 26.0 + - - +
200E THR* 3.3 9.4 + - - +
202E MET* 1.3 77.3 - - - +
204E GLN* 1.3 52.0 + - - +
206E ALA* 3.2 9.4 + - - +
207E ARG* 2.8 50.5 + - - +
219E LEU* 3.3 35.8 - - - +
222E LEU* 4.4 1.2 - - - +
228E LEU* 3.8 26.1 - - + +
805E NAP 2.8 29.3 + - - +
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Residues in contact with GLN 204 (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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41B ASP* 5.0 5.1 - - - +
45B ARG* 4.9 15.3 + - - -
200E THR 3.1 13.2 + - - +
201E ASP* 3.6 23.7 - - - +
203E GLN* 1.3 73.6 - - - +
205E LEU* 1.3 60.6 + - - +
207E ARG* 3.1 32.4 + - - +
208E GLU* 2.9 57.9 + - - +
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Residues in contact with LEU 205 (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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101E LEU* 4.1 26.5 - - + +
102E GLY 4.6 8.1 - - - +
104E VAL* 5.3 0.7 - - + -
201E ASP 2.9 15.1 + - - +
202E MET* 3.2 12.3 + - + +
204E GLN* 1.3 74.1 - - - +
206E ALA* 1.3 56.2 + - - +
208E GLU* 4.9 4.0 - - - +
209E THR* 2.6 59.9 + - + +
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Residues in contact with ALA 206 (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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101E LEU* 3.7 17.6 - - + +
104E VAL* 4.5 0.7 - - - -
164E TRP* 3.7 29.2 - - + -
202E MET 3.0 12.7 + - - +
203E GLN* 3.4 13.5 - - - +
205E LEU* 1.3 76.8 - - - +
207E ARG* 1.3 61.6 - - - +
208E GLU 3.3 0.5 + - - -
210E SER* 2.7 33.7 + - - -
216E ARG* 4.5 0.3 - - - +
219E LEU* 3.6 10.5 - - + +
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Residues in contact with ARG 207 (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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199E ASP* 4.7 6.3 + - - -
203E GLN* 2.8 44.3 + - - +
204E GLN* 3.1 39.0 + - - +
206E ALA* 1.3 73.3 - - - +
208E GLU* 1.3 65.6 + - + +
216E ARG* 3.7 14.5 - - - +
219E LEU* 3.6 32.0 + - + +
220E GLN* 3.4 49.5 + - + +
223E LYS* 3.9 32.0 - - - +
228E LEU* 4.2 13.3 - - - +
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Residues in contact with GLU 208 (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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204E GLN* 2.9 44.7 + - + +
205E LEU* 4.1 3.2 + - - +
207E ARG* 1.3 88.9 + - + +
209E THR* 1.3 68.0 + - + +
210E SER 3.8 0.7 - - - -
216E ARG* 3.7 12.8 - - - +
220E GLN* 5.1 4.5 - - - +
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Residues in contact with THR 209 (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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103E ASP* 5.8 0.2 - - - -
104E VAL* 3.3 16.6 + - - +
105E SER* 3.2 33.9 + - - -
205E LEU* 2.6 44.4 + - + +
208E GLU* 1.3 88.5 - - + +
210E SER* 1.3 65.5 + - - +
211E VAL* 4.4 0.2 - - - -
216E ARG* 4.6 0.2 - - - -
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Residues in contact with SER 210 (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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104E VAL* 3.5 10.1 - - - +
162E LYS 5.7 1.3 - - - -
164E TRP* 3.1 30.4 + - - -
206E ALA* 2.7 27.3 + - - -
208E GLU 3.8 1.0 - - - -
209E THR* 1.3 79.5 + - - +
211E VAL* 1.3 53.9 + - - +
212E ASP* 4.3 8.1 - - - -
215E MET* 4.5 9.6 - - - -
216E ARG* 2.7 45.6 + - - +
219E LEU* 4.6 0.2 - - - +
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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