Contacts of the strand formed by residues 191 - 197 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B ILE* 4.1 16.4 - - + +
168B VAL* 3.4 18.6 - - - +
170B MSE 3.7 41.7 - - + +
180B VAL 5.6 0.2 - - - +
183B ALA* 4.3 10.5 - - + -
184B LEU* 4.6 14.8 - - + -
187B PRO* 3.9 22.4 - - + -
188B HIS 3.0 17.6 + - - +
189B PRO 4.1 2.6 - - - +
190B ALA* 1.3 74.4 - - - +
192B LYS* 1.3 60.1 + - - +
193B VAL 3.5 19.7 - - - +
194B ALA* 5.0 2.2 - - + -
297B VAL* 3.8 20.2 - - + +
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Residues in contact with LYS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B GLY 5.1 1.3 - - - -
167B LYS* 4.0 30.7 - - + +
168B VAL 2.9 5.1 + - - -
189B PRO* 2.8 27.0 + - - +
190B ALA* 3.4 17.3 - - - +
191B LEU* 1.3 73.6 - - - +
193B VAL* 1.3 63.0 + - - +
297B VAL* 3.9 4.0 - - - -
298B PRO* 3.3 22.5 - - - +
375B TYR* 3.4 37.9 - - + +
376B LEU* 3.9 7.4 - - + -
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B VAL 4.0 0.4 + - - -
169B GLY* 3.3 5.0 - - - -
170B MSE 3.0 22.2 + - - -
191B LEU* 3.5 7.3 - - - +
192B LYS* 1.3 79.6 - - - +
194B ALA* 1.3 64.7 + - - +
297B VAL* 3.7 4.4 - - - +
298B PRO 3.5 9.2 - - - +
371B PHE* 3.2 41.3 - - + +
372B PHE* 3.7 20.0 - - + -
375B TYR* 4.1 16.4 - - + -
376B LEU* 3.6 37.2 - - + -
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Residues in contact with ALA 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B MSE 3.4 8.7 - - + +
180B VAL* 3.7 22.0 - - + -
184B LEU* 3.8 27.4 - - + -
191B LEU* 5.0 2.7 - - + -
193B VAL* 1.3 76.4 - - - +
195B VAL* 1.3 67.4 + - - +
196B PRO* 3.7 1.1 - - - -
297B VAL* 4.2 3.8 - - + -
298B PRO 3.0 6.9 + - - +
299B THR* 3.3 8.4 - - - +
300B MSE 2.9 23.7 + - - +
371B PHE* 4.3 1.0 - - - -
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B MSE 3.0 9.2 + - - +
171B ILE* 3.5 33.2 - - + +
172B GLY 3.6 1.2 + - - -
180B VAL* 4.2 1.5 - - - +
194B ALA* 1.3 80.7 - - - +
196B PRO* 1.3 62.0 - - - +
197B GLU* 3.3 28.6 + - + +
300B MSE 3.5 32.3 - - + +
302B LEU* 4.7 4.5 - - + -
363B PHE* 4.8 3.4 - - + -
368B LEU* 3.8 15.7 - - + -
371B PHE* 4.2 4.9 - - + -
372B PHE* 3.4 26.0 - - + -
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Residues in contact with PRO 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B GLY 4.1 2.7 - - - +
177B GLY 3.9 10.8 - - - +
180B VAL* 3.9 15.0 - - + -
181B VAL* 3.7 23.8 - - + -
184B LEU* 4.2 1.8 - - + -
194B ALA 3.7 0.4 - - - -
195B VAL* 1.3 86.0 - - - +
197B GLU* 1.3 59.3 + - - +
199B PRO* 3.8 7.4 - - + +
299B THR* 3.7 21.5 - - + -
300B MSE 3.2 15.3 - - - +
301B TRP* 3.7 25.1 - - + -
302B LEU 3.1 24.9 + - - +
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Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ILE* 3.7 27.2 - - - +
172B GLY* 2.9 23.5 + - - +
173B SER* 3.1 12.2 - - - +
174B SER 2.9 18.4 + - - -
177B GLY* 3.9 0.5 - - - -
195B VAL* 3.7 23.3 - - + +
196B PRO* 1.3 70.0 - - - +
198B SER* 1.3 70.8 + - - +
199B PRO* 2.9 4.8 - - - +
302B LEU* 3.5 20.6 - - + -
343B VAL* 3.9 17.0 - - + +
344B ASN* 3.4 28.2 + - - +
363B PHE* 4.1 13.9 - - - -
368B LEU* 4.8 0.9 - - - +
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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