Contacts of the strand formed by residues 181 - 185 (chain H) in PDB entry 1G9N
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 PHE 181 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179H HIS 3.4 12.8 - - - -
180H THR* 1.3 74.3 - - - +
182H PRO* 1.3 75.5 - - + +
193H LEU* 3.1 23.8 - - - +
194H SER* 2.8 40.8 + - - +
196H VAL* 3.8 22.0 - - + -
135L VAL* 5.8 1.6 - - + -
137L LEU* 3.9 21.1 - - + -
164L SER* 3.2 21.8 - - - +
166L THR* 3.4 11.4 - - + -
176L SER* 2.8 42.0 - - - -
177L LEU 3.0 18.6 - - - -
178L SER* 3.3 18.2 - - - +
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Residues in contact with PRO 182 (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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180H THR 4.2 2.2 - - - +
181H PHE* 1.3 85.8 - - + +
183H ALA* 1.3 70.1 + - - +
184H VAL* 3.7 2.9 + - - +
193H LEU* 4.1 3.6 - - + +
164L SER* 2.9 26.1 + - - +
165L VAL 3.2 27.4 - - - +
166L THR* 3.7 12.1 - - + -
167L GLU* 5.3 6.7 - - + +
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Residues in contact with ALA 183 (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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160H TYR* 3.0 32.1 - - + +
163H GLN* 3.1 22.5 + - - +
165H VAL* 5.2 0.2 - - + -
181H PHE 3.5 1.6 + - - -
182H PRO* 1.3 81.1 - - - +
184H VAL* 1.3 62.4 + - - +
191H TYR* 4.1 7.9 - - + -
193H LEU* 3.5 21.3 - - + +
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Residues in contact with VAL 184 (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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182H PRO 3.8 1.3 - - - +
183H ALA* 1.3 81.4 - - - +
185H LEU* 1.3 65.2 + - - +
186H GLN* 3.5 5.5 + - + +
191H TYR* 3.1 6.4 - - - -
192H SER* 2.9 35.9 + - - +
162L GLN* 3.2 44.2 - - + +
163L GLU 3.4 22.0 - - - +
164L SER* 3.6 16.4 - - - +
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Residues in contact with LEU 185 (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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127H THR* 5.9 4.7 - - + +
184H VAL* 1.3 74.8 - - - +
186H GLN* 1.3 64.8 + - - +
189H GLY* 3.3 32.5 - - - +
190H LEU 3.6 9.4 - - - +
191H TYR* 3.5 38.3 - - + +
162L GLN* 3.0 17.7 + - - +
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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