Contacts of the strand formed by residues 179 - 183 (chain B) in PDB entry 1JLH
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 ARG 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B THR* 3.0 25.1 + - - +
150B ASP* 2.7 45.2 + - - +
151B VAL* 2.8 27.9 + - - +
177B GLY 3.9 0.8 + - - +
178B PRO* 1.3 72.5 - - - +
180B VAL* 1.3 60.3 + - - +
181B TRP* 3.9 15.3 - - + +
286B HIS* 4.4 5.6 - - - -
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Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B VAL* 3.3 19.3 - - + +
167B THR* 4.1 4.9 - - - -
168B GLU* 6.0 0.2 - - - +
171B LYS* 3.9 11.3 + - - +
178B PRO 3.7 1.8 + - - +
179B ARG* 1.3 77.2 - - - +
181B TRP* 1.3 69.0 + - - +
182B TYR* 3.9 27.4 - - + +
282B SER* 3.9 12.1 - - - +
286B HIS* 3.5 54.7 + - + +
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Residues in contact with TRP 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ASP* 2.7 36.7 + - + +
151B VAL 2.8 17.8 + - - +
152B ILE* 4.0 18.2 - - + -
153B ASN* 2.7 32.2 + - - +
179B ARG* 3.9 21.7 - - + +
180B VAL* 1.3 82.1 - - - +
182B TYR* 1.3 65.5 + - - +
183B VAL 4.1 0.7 - - - -
194B THR* 3.8 29.6 - - + -
197B GLN* 3.7 47.3 - - + -
198B LEU* 3.8 12.1 - - + +
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Residues in contact with TYR 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ASN* 3.5 25.4 - - + -
160B ASP* 3.5 24.7 - - - +
163B PRO* 3.3 26.8 + - + -
164B LEU* 3.4 34.1 - - + -
167B THR* 3.1 40.5 - - - +
168B GLU* 6.1 0.2 - - - -
180B VAL* 3.9 21.7 - - + +
181B TRP* 1.3 76.2 - - - +
183B VAL* 1.3 63.1 + - - +
184B SER 4.1 0.2 - - - -
190B HIS* 3.3 19.5 + - - -
194B THR* 5.1 1.3 + - - -
282B SER* 2.8 27.2 + - - -
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ILE* 3.9 14.6 - - + -
153B ASN 2.9 10.4 + - - +
154B ILE* 3.4 11.0 - - + +
155B GLY 3.3 23.0 + - - +
160B ASP* 4.6 1.1 - - - +
182B TYR* 1.3 76.0 - - - +
184B SER* 1.3 63.5 + - - +
190B HIS* 3.8 10.1 - - + +
191B ILE* 3.9 39.3 - - + +
194B THR* 3.7 37.7 - - + +
220B ASN* 4.1 18.8 - - + +
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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