Contacts of the strand formed by residues 191 - 197 (chain C) in PDB entry 1MPX
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 LEU 191 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C ILE* 4.2 12.6 - - + +
168C VAL* 3.4 15.2 - - + +
169C GLY 4.1 0.4 - - - -
170C MSE 3.7 41.3 - - + +
180C VAL* 6.1 0.2 - - + -
183C ALA* 4.5 8.3 - - + -
184C LEU* 4.3 19.7 - - + -
187C PRO* 3.7 23.6 - - + -
188C HIS* 3.0 18.0 + - - +
189C PRO 4.0 2.8 - - - +
190C ALA* 1.3 74.4 - - - +
192C LYS* 1.3 62.0 + - - +
193C VAL 3.5 22.7 - - - +
194C ALA* 4.9 2.2 - - + -
297C VAL* 3.7 19.9 - - + +
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Residues in contact with LYS 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C GLY 5.1 1.3 - - - -
167C LYS* 4.1 24.7 - - + +
168C VAL 2.9 4.6 + - - -
189C PRO* 2.8 28.3 + - - +
190C ALA* 3.4 18.3 - - - +
191C LEU* 1.3 73.9 - - - +
193C VAL* 1.3 63.1 + - - +
297C VAL* 4.0 3.4 - - - -
298C PRO* 3.2 23.2 - - - +
375C TYR* 3.4 37.1 - - + +
376C LEU* 3.9 13.0 - - + -
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Residues in contact with VAL 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C GLY* 3.3 4.4 - - - -
170C MSE 3.0 23.1 + - - -
191C LEU* 3.5 5.2 - - - +
192C LYS* 1.3 82.1 - - - +
194C ALA* 1.3 64.2 + - - +
297C VAL* 3.8 4.6 - - - +
298C PRO 3.5 9.4 - - - +
371C PHE* 3.2 38.6 - - + +
372C PHE* 3.7 21.3 - - + -
375C TYR* 4.1 16.4 - - + -
376C LEU* 3.6 37.0 - - + -
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Residues in contact with ALA 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C MSE 3.4 8.5 - - + -
180C VAL* 3.6 22.2 - - + -
184C LEU* 3.8 29.8 - - + -
191C LEU* 4.9 3.1 - - + -
193C VAL* 1.3 76.8 - - - +
195C VAL* 1.3 68.1 + - - +
196C PRO* 3.8 1.6 - - - -
297C VAL* 4.2 1.8 - - + -
298C PRO 3.0 7.2 + - - +
299C THR* 3.3 6.9 - - - +
300C MSE 3.0 24.1 + - - -
371C PHE* 4.3 1.0 - - - -
372C PHE* 4.9 0.2 - - - -
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Residues in contact with VAL 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C MSE 2.9 9.5 + - - +
171C ILE* 3.5 32.7 - - + +
172C GLY 3.6 1.4 + - - -
180C VAL* 4.2 1.8 - - - +
194C ALA* 1.3 79.2 - - - +
196C PRO* 1.3 61.0 - - - +
197C GLU* 3.3 28.8 + - + +
300C MSE 3.4 32.1 - - + +
302C LEU* 4.7 4.9 - - + -
363C PHE* 4.8 2.7 - - + -
368C LEU* 3.7 15.9 - - + -
371C PHE* 4.2 4.9 - - + -
372C PHE* 3.4 24.9 - - + -
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Residues in contact with PRO 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C GLY 4.1 2.9 - - - +
177C GLY* 3.9 12.3 - - - +
180C VAL* 3.9 16.2 - - + -
181C VAL* 3.8 15.9 - - + -
184C LEU* 4.2 2.5 - - + -
194C ALA 3.8 0.2 - - - -
195C VAL* 1.3 85.1 - - - +
197C GLU* 1.3 60.5 + - - +
199C PRO* 3.7 7.4 - - + +
299C THR* 3.7 20.4 - - + -
300C MSE 3.2 15.6 - - - +
301C TRP* 3.7 32.7 - - + -
302C LEU 3.1 23.9 + - - +
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Residues in contact with GLU 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C ILE* 3.6 27.6 - - - +
172C GLY* 2.9 18.2 + - - +
173C SER* 3.1 15.3 - - - +
174C SER 2.9 17.2 + - - -
177C GLY* 3.9 0.5 - - - -
195C VAL* 3.7 24.5 - - + +
196C PRO* 1.3 70.4 - - - +
198C SER* 1.3 70.5 + - - +
199C PRO* 2.9 5.4 - - - +
302C LEU* 3.5 20.9 - - + -
343C VAL* 3.7 15.9 - - + +
344C ASN* 3.2 29.6 + - - +
363C PHE* 4.2 13.2 - - - -
368C LEU* 4.9 1.2 - - - +
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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