Contacts of the helix formed by residues 182 - 186 (chain J) in PDB entry 7RDB
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 PRO 182 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J TYR* 3.6 24.9 - - + +
136J TYR* 5.3 1.3 - - - +
149J GLN* 4.5 1.1 - - - +
163J TRP* 3.7 46.4 - - + +
169J HIS* 3.8 13.0 - - + -
177J LEU* 5.6 3.6 - - + -
181J VAL* 1.3 99.2 - - + +
183J TYR* 1.3 62.0 + - + +
184J THR* 4.0 9.2 - - + +
185J CYS* 2.8 27.1 + - - +
186J CYS* 4.2 1.2 + - - -
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Residues in contact with TYR 183 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E LEU* 3.5 28.6 - - + +
142E LYS* 3.1 38.8 + - - +
143E ASN* 4.3 15.8 + - - -
146E ASP* 3.9 6.8 + - - -
183E TYR* 4.9 7.8 + - - -
135J TYR* 6.1 0.7 - - - -
142J LYS* 5.6 6.9 + - - -
146J ASP* 5.7 1.5 + - - -
181J VAL 3.7 1.8 + - - -
182J PRO* 1.3 74.2 - - + +
184J THR* 1.3 77.0 + - + +
185J CYS 3.0 0.7 - - - -
186J CYS* 3.1 24.7 + - - +
188J ARG* 5.1 3.8 + - - -
196J THR* 3.7 33.4 + - + +
198J CYS* 3.8 23.3 - - - -
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Residues in contact with THR 184 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E ASN* 6.1 0.4 - - - +
135J TYR* 5.1 0.4 - - - +
146J ASP* 2.6 56.4 + - + +
149J GLN* 2.8 45.2 + - - +
150J LYS* 3.7 14.5 + - + +
182J PRO* 4.0 4.0 - - - +
183J TYR* 1.3 100.9 - - + +
185J CYS* 1.3 55.7 + - - +
186J CYS 3.5 2.8 - - - +
188J ARG* 6.3 0.9 - - - +
215J TYR* 4.7 1.6 - - - -
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Residues in contact with CYS 185 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149J GLN* 3.3 24.0 - - - -
154J CYS 4.4 1.6 - - - -
155J CYS* 2.0 50.7 - - + -
163J TRP* 3.9 1.6 - - - -
181J VAL* 3.8 18.8 - - + -
182J PRO* 2.8 15.5 + - - +
184J THR* 1.3 76.5 - - - +
186J CYS* 1.3 60.1 + - - +
214J ILE* 3.4 4.8 - - + -
215J TYR* 2.9 39.4 + - - -
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Residues in contact with CYS 186 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E LEU* 4.7 2.5 - - + -
182J PRO 4.4 0.9 - - - -
183J TYR* 3.1 16.0 + - - +
184J THR 4.7 1.4 - - - +
185J CYS* 1.3 79.5 - - - +
187J ILE* 1.3 68.6 + - - +
188J ARG* 3.5 12.6 + - - +
194J VAL* 4.3 7.0 - - + -
198J CYS* 2.0 55.0 - - + -
199J GLY* 3.5 15.9 - - - -
213J VAL 3.4 9.2 - - - +
214J ILE* 4.1 3.8 - - - +
215J TYR* 3.2 14.5 - - - -
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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