Contacts of the helix formed by residues 191 - 195 (chain D) in PDB entry 1RD3
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 CYS 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D ILE 4.3 0.2 - - - +
17D VAL* 3.3 19.1 - - - -
143D ASN 3.7 12.3 - - - +
190D ALA* 1.3 76.6 - - - +
192D GLU* 1.3 60.7 + - - +
193D GLY 3.2 4.7 - - - +
194D ASP* 2.8 36.5 + - - +
195D SER 3.9 1.7 + - - -
213D VAL* 4.5 0.5 - - - +
216D GLY* 3.9 10.9 + - - -
219D GLY 3.6 2.7 - - - +
220D CYS* 2.0 59.9 - - + +
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Residues in contact with GLU 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ARG* 3.4 24.1 - - - +
42D CYS* 5.4 2.1 - - - -
57D HIS* 3.0 17.4 + - - -
60D TRP* 3.6 24.8 - - - +
147D THR* 5.9 2.7 - - - +
191D CYS* 1.3 73.1 - - - +
193D GLY* 1.3 58.6 + - - +
194D ASP 2.8 4.2 + - - -
195D SER* 2.6 49.9 + - - -
214D SER 4.9 2.3 - - - +
215D TRP* 4.5 8.7 - - - -
216D GLY 3.6 10.7 + - - +
220D CYS* 5.2 2.4 - - + +
221D ASP* 5.2 8.6 + - - +
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Residues in contact with GLY 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LEU* 6.1 0.5 - - - +
41D LEU 4.6 9.5 - - - +
42D CYS* 4.5 16.2 - - - -
43D GLY 4.7 0.2 + - - -
141D TRP* 4.7 2.9 + - - +
142D GLY* 3.8 26.9 + - - -
143D ASN 5.1 0.6 - - - +
191D CYS* 3.2 4.2 + - - +
192D GLU* 1.3 77.8 - - - +
194D ASP* 1.3 57.1 + - - +
195D SER* 3.4 1.1 + - - -
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Residues in contact with ASP 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ILE* 2.7 42.8 + - + +
43D GLY* 4.8 2.8 + - - +
139D THR 4.7 4.7 - - - +
140D GLY* 3.2 9.8 - - - -
141D TRP 3.2 11.3 + - - -
142D GLY* 2.8 24.3 + - - -
190D ALA* 4.4 1.8 - - + -
191D CYS* 2.8 29.4 + - - +
193D GLY* 1.3 76.4 - - - +
195D SER* 1.3 69.0 + - - +
197D GLY* 3.1 15.6 + - - -
213D VAL* 3.2 20.6 - - + +
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Residues in contact with SER 195 (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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42D CYS* 3.4 7.1 - - - +
43D GLY 2.9 24.8 + - - -
57D HIS* 3.3 28.3 + - - -
58D CYS* 3.8 11.2 - - - -
191D CYS 3.9 1.5 + - - -
192D GLU* 2.6 40.3 + - - -
193D GLY 3.4 1.2 - - - -
194D ASP* 1.3 77.1 - - - +
196D GLY* 1.3 58.6 + - - +
197D GLY 3.1 0.2 + - - -
213D VAL* 3.3 12.1 - - - +
214D SER 4.1 4.5 + - - -
216D GLY 5.2 1.2 + - - -
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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