Contacts of the strand formed by residues 194 - 200 (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 TYR 194 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44H PRO* 5.5 8.0 - - - +
162H ASP* 3.5 15.4 + - - -
163H TYR* 3.4 19.9 + - + -
166H GLU* 3.2 43.1 - - + +
186H ALA* 3.7 23.3 - - + -
187H VAL* 3.3 18.6 - - - -
188H LEU* 3.7 35.1 - - + +
189H GLN* 4.6 1.8 + - - -
192H GLY 5.5 0.2 - - - -
193H LEU* 1.3 88.4 - - + +
195H SER* 1.3 61.5 + - - +
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Residues in contact with SER 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159H LEU* 4.9 6.0 - - - +
160H VAL 3.3 10.1 - - - -
161H LYS* 4.3 20.2 - - - -
163H TYR* 3.8 1.3 - - - -
185H PRO 4.5 1.4 - - - +
186H ALA* 3.4 23.0 - - - +
187H VAL* 4.0 16.9 + - - +
189H GLN* 4.6 15.6 + - - +
194H TYR* 1.3 77.6 - - - +
196H LEU* 1.3 66.4 + - - +
161L GLN* 5.0 4.0 + - - -
179L THR* 5.8 4.5 - - - +
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Residues in contact with LEU 196 (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 CYS 4.3 1.8 - - - +
159H LEU* 3.3 15.1 - - - +
160H VAL* 2.8 52.5 + - + -
163H TYR* 3.4 41.3 - - + +
168H VAL* 5.6 4.7 - - + -
172H TRP* 4.4 24.2 - - + -
183H THR* 5.6 4.5 - - + -
184H PHE 3.9 18.8 - - - +
185H PRO* 5.2 0.4 - - + -
186H ALA* 4.1 8.3 - - + +
195H SER* 1.3 77.2 - - - +
197H SER* 1.3 62.2 + - - +
216H VAL* 5.9 1.3 - - + -
218H HIS* 5.0 9.4 - - + +
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Residues in contact with SER 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142H LEU* 6.1 1.0 - - - +
158H CYS 4.0 8.1 - - - -
159H LEU* 4.7 9.5 - - - +
183H THR* 4.0 3.6 - - - +
184H PHE* 3.0 55.0 + - - +
185H PRO 5.7 0.4 + - - -
196H LEU* 1.3 78.9 - - - +
198H SER* 1.3 66.4 + - - +
199H VAL* 5.6 0.7 - - - +
134L VAL* 5.5 5.5 - - - +
177L SER* 4.9 3.6 + - - -
179L THR* 5.3 7.4 - - - -
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Residues in contact with SER 198 (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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142H LEU* 5.2 4.0 - - - +
156H LEU 5.0 0.7 + - - -
157H GLY* 3.5 20.9 - - - -
158H CYS* 3.9 27.2 + - - -
172H TRP* 5.3 7.5 - - - -
182H HIS 4.1 8.5 - - - -
183H THR* 4.2 20.6 - - - -
184H PHE* 4.3 3.8 - - - -
197H SER* 1.3 80.8 + - - +
199H VAL* 1.3 71.3 + - - +
200H VAL* 5.5 3.4 - - - +
214H CYS* 4.8 1.4 - - - -
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Residues in contact with VAL 199 (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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142H LEU* 5.9 3.6 - - + -
153H THR* 6.1 0.9 - - - +
154H ALA 5.7 0.2 - - - +
155H ALA* 4.9 20.2 - - + -
156H LEU 4.5 5.2 - - - +
181H VAL* 4.5 0.5 - - - +
182H HIS* 3.0 35.2 + - + +
184H PHE* 3.7 25.5 - - + -
197H SER* 5.6 1.1 - - - +
198H SER* 1.3 80.4 - - - +
200H VAL* 1.3 67.0 + - - +
201H THR* 4.3 0.7 + - - -
119L PHE* 4.9 9.6 - - + -
136L LEU* 3.8 25.6 - - + -
138L ASN* 5.6 2.2 - - - +
175L SER* 5.4 1.8 - - - +
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Residues in contact with VAL 200 (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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153H THR* 4.2 5.1 - - - -
154H ALA 3.5 18.4 + - - +
156H LEU* 3.4 24.1 + - + +
173H ASN* 4.9 9.2 - - - +
177H LEU* 3.9 6.7 - - + -
180H GLY 4.3 4.9 - - - +
181H VAL* 3.8 29.2 - - + +
198H SER* 5.5 3.8 - - - +
199H VAL* 1.3 80.2 - - - +
201H THR* 1.3 64.2 + - - +
202H VAL* 3.2 16.7 + - + +
212H TYR* 3.6 35.4 - - + +
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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