Contacts of the strand formed by residues 173 - 180 (chain H) in PDB entry 1J5O
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 173 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164H TRP* 3.9 13.7 - - + -
169H LEU* 4.3 8.5 - - + +
170H SER* 4.1 32.2 + - - +
171H SER 3.8 2.4 + - - -
172H GLY* 1.3 78.3 - - - +
174H HIS* 1.3 79.0 + - - +
175H THR* 4.0 8.5 - - - +
189H SER* 3.9 11.7 - - - +
190H SER 3.3 12.3 - - - +
191H VAL* 3.7 20.9 - - + -
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Residues in contact with HIS 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172H GLY 6.1 1.1 - - - -
173H VAL* 1.3 82.9 + - - +
175H THR* 1.3 55.5 - - - +
176H PHE* 3.6 20.3 - + + -
189H SER* 2.2 23.9 + - - -
190H SER* 2.7 28.0 + - - +
137L ASN* 3.6 16.8 - - + -
138L ASN* 2.8 33.9 + - - -
164L THR* 5.4 5.1 - - + +
167L ASP* 5.0 18.6 - - + -
172L THR* 5.5 2.0 - - - -
173L TYR 5.7 0.2 - - - -
174L SER* 3.2 26.3 + - - -
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Residues in contact with THR 175 (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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162H VAL* 5.1 15.7 + - + +
173H VAL* 4.0 9.7 - - - +
174H HIS* 1.3 73.5 + - - +
176H PHE* 1.3 68.9 + - - +
177H PRO* 4.0 3.6 - - - +
187H LEU* 4.4 14.6 - - + -
189H SER* 2.9 23.7 + - - +
164L THR* 3.9 13.4 - - - +
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Residues in contact with PHE 176 (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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174H HIS* 3.6 37.0 - - + -
175H THR* 1.3 77.2 - - - +
177H PRO* 1.3 73.0 - - + +
178H ALA* 4.2 0.2 - - - -
187H LEU* 3.1 24.7 - - - +
188H SER* 2.9 25.2 + - - +
189H SER* 3.8 1.6 - - - -
190H SER* 4.0 2.2 - - - -
135L PHE* 3.6 25.6 - + - -
137L ASN* 4.3 5.8 - - - -
162L SER* 3.9 16.6 - - - +
164L THR* 3.5 22.7 - - + -
174L SER* 3.9 25.1 - - - -
175L MET 4.3 0.7 - - - -
176L SER* 3.3 26.0 - - - +
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Residues in contact with PRO 177 (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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158H GLU* 5.8 0.7 - - - +
175H THR 4.0 5.4 - - - +
176H PHE* 1.3 85.1 - - + +
178H ALA* 1.3 66.0 + - - +
179H VAL* 4.3 1.2 - - - +
187H LEU* 4.6 3.4 - - + -
162L SER* 3.2 33.0 + - - +
163L TRP 4.7 9.0 - - - +
164L THR* 5.0 9.9 - - + -
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Residues in contact with ALA 178 (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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155H TYR* 3.5 24.7 - - - +
158H GLU* 4.6 13.0 + - - +
176H PHE 3.3 3.7 + - - -
177H PRO* 1.3 77.7 - - - +
179H VAL* 1.3 62.4 + - - +
185H TYR* 3.9 10.2 - - + -
186H THR 3.1 36.6 - - - +
187H LEU* 3.6 10.3 - - + +
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Residues in contact with VAL 179 (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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177H PRO 4.3 7.4 - - - +
178H ALA* 1.3 81.5 - - - +
180H LEU* 1.3 66.5 + - + +
181H GLN* 2.6 21.4 + - - +
184H LEU 3.2 6.5 - - - +
185H TYR* 4.3 3.4 - - - -
186H THR* 3.5 16.8 + - - +
160L LEU* 4.6 19.9 - - + +
161L ASN 4.9 10.1 - - - +
162L SER* 4.4 15.9 - - - -
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Residues in contact with LEU 180 (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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43H SER* 6.0 2.2 - - - +
178H ALA 5.9 0.2 - - - +
179H VAL* 1.3 78.6 - - + +
181H GLN* 1.3 59.7 + - - +
182H SER 3.4 3.3 + - - -
183H ASP* 3.8 12.0 + - - +
184H LEU 3.1 14.1 - - - +
185H TYR* 3.2 35.0 - - + +
160L LEU* 5.4 0.2 - - - -
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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