Contacts of the strand formed by residues 181 - 188 (chain H) in PDB entry 6CMO
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 181 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172H TRP* 5.6 8.5 - - + -
173H ASN* 3.9 14.4 - - - +
177H LEU* 3.7 38.1 - - + +
178H THR 5.1 6.1 - - - +
179H SER* 4.7 7.2 - - - +
180H GLY* 1.3 85.4 + - - +
182H HIS* 1.3 74.2 + - - +
183H THR* 4.8 9.9 - - - +
199H VAL 4.5 5.2 - - - +
200H VAL* 3.8 14.4 - - + +
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Residues in contact with HIS 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 GLY 5.0 2.6 - - - -
181H VAL* 1.3 80.9 + - - +
183H THR* 1.3 62.8 + - - +
184H PHE* 4.3 7.9 - - + -
198H SER* 4.1 1.2 - - - -
199H VAL* 3.0 39.7 + - + +
201H THR* 4.4 16.6 + - - -
165L THR* 4.9 11.3 + - + -
166L GLU 5.4 4.1 + - - -
168L ASP* 3.8 39.3 + - + -
171L ASP* 4.6 6.3 + - - -
173L THR 5.8 1.3 - - - -
175L SER* 4.6 28.4 - - - +
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Residues in contact with THR 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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172H TRP* 3.7 50.6 + - + +
181H VAL* 4.2 11.1 - - - +
182H HIS* 1.3 75.4 + - - +
184H PHE* 1.3 72.7 + - - +
185H PRO* 3.8 2.6 - - - +
196H LEU* 5.6 3.8 - - + -
197H SER 4.0 10.3 - - - +
198H SER* 4.2 11.4 - - - -
165L THR* 3.6 13.2 - - - +
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Residues in contact with PHE 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 HIS* 4.3 10.8 - - + -
183H THR* 1.3 78.4 - - - +
185H PRO* 1.3 71.1 - - - +
196H LEU* 3.9 16.8 - - - +
197H SER* 3.0 50.1 + - - +
198H SER* 4.4 2.5 - - - -
199H VAL* 3.7 29.6 - - + -
134L VAL* 5.6 2.0 - - + -
136L LEU* 4.1 18.2 - - + -
163L SER* 3.9 11.0 - - - +
165L THR* 3.6 18.4 - - + -
175L SER* 3.8 21.1 - - - -
177L SER* 3.6 35.2 - - - -
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Residues in contact with PRO 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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183H THR 3.8 6.1 - - - +
184H PHE* 1.3 89.8 - - - +
186H ALA* 1.3 68.5 + - - +
187H VAL* 4.0 1.0 + - - +
195H SER 4.5 2.1 - - - +
196H LEU* 5.2 1.2 - - + -
197H SER 5.7 0.2 + - - -
163L SER* 3.2 30.8 + - - +
164L VAL 3.4 23.8 - - - +
165L THR* 4.0 9.9 - - + -
166L GLU 5.8 0.2 - - - +
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Residues in contact with ALA 186 (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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163H TYR* 3.3 26.0 - - - +
166H GLU* 6.2 0.2 - - + -
184H PHE 3.9 0.4 + - - -
185H PRO* 1.3 79.9 - - - +
187H VAL* 1.3 60.6 + - - +
194H TYR* 3.7 26.2 - - + -
195H SER 3.4 18.4 - - - +
196H LEU* 4.1 4.9 - - + +
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Residues in contact with VAL 187 (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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185H PRO 4.0 2.4 + - - +
186H ALA* 1.3 75.4 - - - +
188H LEU* 1.3 66.8 + - + +
189H GLN* 3.5 3.1 + - - +
193H LEU 3.9 0.2 - - - +
194H TYR* 3.3 22.1 - - - -
195H SER* 4.0 13.4 + - - +
161L GLN* 3.4 38.4 - - + +
162L GLU* 3.7 28.7 - - + +
163L SER* 5.6 2.0 - - - -
179L THR* 6.0 2.2 - - - -
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Residues in contact with LEU 188 (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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187H VAL* 1.3 79.4 - - + +
189H GLN* 1.3 66.6 + - - +
192H GLY* 3.4 38.6 - - - +
193H LEU 4.1 0.4 - - - +
194H TYR* 3.7 25.1 - - + +
161L GLN* 3.9 10.8 + - - +
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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