Contacts of the strand formed by residues 185 - 189 (chain H) in PDB entry 2JG7
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 VAL 185 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H THR* 3.4 36.3 - - + +
67H ARG* 5.2 0.2 - - - -
70H TRP* 3.7 34.3 - - + +
73H TRP* 3.9 7.9 - - + -
157H GLY 3.0 11.7 + - - +
158H LEU* 3.3 10.6 - - + +
159H VAL* 2.7 32.6 + - - +
184H ASN* 1.3 76.2 - - - +
186H CYS* 1.3 57.0 + - - +
218H ILE* 3.5 38.6 - - + +
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Residues in contact with CYS 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H THR* 4.2 1.9 + - - -
158H LEU* 4.1 2.7 - - - -
159H VAL* 3.3 4.7 - - - -
161H ILE* 3.9 23.6 - - + -
172H TYR* 4.4 8.3 - - + +
176H ASN* 3.7 26.0 - - - +
179H ALA* 3.9 22.9 - - - -
180H LEU* 3.7 17.9 - - - -
185H VAL* 1.3 75.5 - - - +
187H LEU* 1.3 60.5 + - - +
217H ALA 3.9 2.9 - - - +
218H ILE 2.8 14.8 + - - +
219H CYS* 4.4 2.0 - - - -
220H SER* 2.9 27.8 + - - +
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Residues in contact with LEU 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H TYR* 4.0 10.8 - - + -
62H THR* 3.8 28.3 - - + -
63H VAL* 3.7 31.6 - - + +
66H THR* 4.7 3.8 - - - +
158H LEU* 3.7 18.3 - - + +
159H VAL 2.9 7.3 + - - +
160H GLY* 3.5 3.5 - - - -
161H ILE* 2.7 33.4 + - - +
186H CYS* 1.3 75.6 - - - +
188H TRP* 1.3 60.9 + - - +
220H SER* 3.4 5.6 - - - +
222H THR* 3.6 23.6 - - + +
232H MET* 3.8 24.0 - - + +
238H VAL* 6.0 2.5 - - + -
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Residues in contact with TRP 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161H ILE* 3.3 12.8 - - - -
163H THR* 3.1 30.1 + - + +
168H PRO 3.3 25.8 - - - -
169H VAL* 5.3 0.2 - - - -
172H TYR* 3.3 62.6 - + + -
187H LEU* 1.3 75.8 - - - +
189H LYS* 1.3 74.0 + - - +
190H GLY* 3.6 7.2 + - - +
198H SER* 3.4 46.7 - - - -
201H VAL* 3.7 18.8 - - + -
202H THR* 3.7 14.6 - - - -
220H SER 2.8 16.2 + - - +
221H MET* 3.3 9.3 - - + +
222H THR 2.9 27.5 + - - +
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Residues in contact with LYS 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H ILE 2.9 10.1 + - - +
162H ILE* 3.4 18.4 - - + -
163H THR 3.4 18.9 + - - -
187H LEU 4.1 0.8 + - - -
188H TRP* 1.3 72.6 - - - +
190H GLY* 1.3 78.8 + - - +
192H PRO* 4.3 0.2 - - - +
222H THR* 3.2 21.5 - - - +
224H GLY 2.9 34.4 + - - +
225H GLY 3.6 8.5 - - - +
228H ILE* 4.0 8.3 - - + -
229H GLY* 3.6 30.5 - - - +
232H MET* 3.9 18.3 - - - +
1510H NAD 2.8 39.1 + - - -
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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
------------------------------------------------------------
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