Contacts of the strand formed by residues 185 - 189 (chain J) in PDB entry 6AHR
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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152J PHE* 3.4 30.5 - - + +
154J LEU* 4.7 9.9 - - + -
176J LEU* 3.9 19.7 - - + -
177J MET* 3.9 32.8 - - + -
180J CYS* 4.4 11.4 - - - -
182J GLY* 5.1 4.7 - - - -
183J LYS 4.1 1.4 - - - +
184J ASN* 1.3 81.2 - - - +
186J ILE* 1.3 70.4 + - - +
187J ILE* 4.3 7.6 + - + +
212J LEU* 4.2 21.3 - - + +
220J ALA* 5.2 4.9 - - - +
221J VAL* 5.2 3.1 + - - +
224J ASN* 4.4 2.0 - - - +
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Residues in contact with ILE 186 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J ASP* 4.1 14.1 - - - +
76J ARG* 5.9 0.2 - - - +
124J LEU* 4.1 16.2 - - + -
151J ALA* 4.5 5.4 - - + -
152J PHE 2.9 15.6 + - - +
153J GLU* 3.7 25.1 - - + -
154J LEU* 2.9 24.1 + - - +
185J VAL* 1.3 75.7 - - - +
187J ILE* 1.3 68.5 + - - +
188J SER* 5.3 3.1 - - - -
220J ALA 4.2 0.2 - - - +
221J VAL* 3.7 25.4 - - + -
224J ASN* 3.7 30.1 - - + +
225J CYS* 3.8 26.2 - - - +
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Residues in contact with ILE 187 (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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7J LEU* 3.3 20.8 - - - +
154J LEU* 3.2 22.7 - - + +
156J TYR* 3.7 9.6 - - + -
185J VAL* 4.9 7.4 - - + +
186J ILE* 1.3 80.9 - - - +
188J SER* 1.3 62.7 + - - +
203J VAL* 3.4 38.1 - - + +
206J LEU* 3.7 17.3 - - + -
207J GLY* 3.6 20.0 - - - +
210J PHE* 3.7 23.8 - - + -
221J VAL* 4.6 11.2 - - + +
225J CYS* 5.7 0.2 - - - -
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Residues in contact with SER 188 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J LEU* 4.3 7.6 - - - -
8J ASP* 3.3 43.4 + - - +
153J GLU* 5.5 1.0 + - - +
154J LEU 2.9 7.0 + - - -
155J VAL* 3.3 26.2 - - - +
156J TYR* 2.7 40.9 + - - -
186J ILE* 5.3 5.1 - - - +
187J ILE* 1.3 76.4 - - - +
189J SER* 1.3 56.8 + - - +
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Residues in contact with SER 189 (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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7J LEU* 4.4 8.4 - - - +
8J ASP 2.9 19.2 + - - +
9J LEU* 3.4 18.9 - - - +
10J ARG 4.2 0.2 + - - -
155J VAL* 4.7 2.5 - - - -
156J TYR* 3.4 26.4 - - - -
157J SER* 6.1 0.2 - - - -
188J SER* 1.3 74.8 - - - +
190J ALA* 1.3 62.9 + - - +
196J GLU 4.2 7.2 + - - -
197J ILE* 3.3 29.2 - - - +
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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