Contacts of the strand formed by residues 183 - 187 (chain X) in PDB entry 1JJ2
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 GLU 183 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173X ALA 4.8 1.7 - - - +
175X ARG 4.7 6.6 - - - +
176X GLY* 4.3 11.6 - - - +
177X LYS* 3.1 42.3 - - - +
181X GLY 4.9 0.4 - - - +
182X PHE* 1.3 73.6 - - - +
184X GLU* 1.3 65.4 + - - +
200X THR* 3.2 20.3 + - + +
201X GLU* 3.3 19.4 - - + +
202X ALA 3.1 20.9 + - - -
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Residues in contact with GLU 184 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13250 G 4.5 4.5 + - - +
13260 U 5.7 0.5 - - - +
176X GLY 5.1 7.1 + - - +
178X HIS* 3.2 32.0 - - + +
182X PHE 3.8 0.2 + - - -
183X GLU* 1.3 77.6 + - - +
185X VAL* 1.3 66.1 + - - +
186X ARG 5.4 0.4 - - - +
202X ALA 3.5 5.4 - - - +
204X ARG* 2.4 52.0 + - + +
229X LEU* 3.5 15.5 - - + -
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Residues in contact with VAL 185 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183X GLU* 4.1 0.9 - - + +
184X GLU* 1.3 80.7 - - - +
186X ARG* 1.3 67.7 + - - +
192X ASP* 5.0 6.1 - - + +
196X VAL* 4.2 20.6 - - + -
201X GLU* 3.9 40.6 - - + +
202X ALA 3.1 10.5 + - - +
203X VAL* 3.1 18.1 - - + +
204X ARG* 3.0 23.4 + - - -
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Residues in contact with ARG 186 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13330 U 3.1 48.4 + - - -
13340 C 2.8 25.3 + - - -
13450 A 6.0 4.8 - - - -
184X GLU* 4.2 1.4 - - - +
185X VAL* 1.3 78.2 - - - +
187X VAL* 1.3 61.0 + - - +
188X HIS* 3.5 35.2 + - + +
192X ASP* 4.6 5.9 - - - +
204X ARG* 3.5 16.2 - - - +
206X ALA* 3.6 14.8 - - + +
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Residues in contact with VAL 187 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185X VAL* 5.6 0.4 - - + -
186X ARG* 1.3 74.7 - - - +
188X HIS* 1.3 62.7 + - - +
189X ASN 3.3 15.5 - - - +
192X ASP* 3.0 37.0 - - + +
193X LEU* 4.0 11.9 - - + -
203X VAL* 3.4 23.3 - - + -
204X ARG 2.9 11.9 + - - +
205X ILE* 3.4 36.5 - - + +
206X ALA* 2.9 21.7 + - - +
217X ILE* 4.4 6.7 - - + -
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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