Contacts of the strand formed by residues 191 - 197 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ILE* 4.2 15.7 - - + +
168A VAL* 3.4 12.8 - - - +
169A GLY 4.2 0.4 - - - -
170A MSE 3.6 41.1 - - + +
180A VAL* 6.2 0.2 - - + -
183A ALA* 4.3 10.5 - - + -
184A LEU* 4.5 15.9 - - + -
187A PRO* 3.7 24.0 - - + -
188A HIS 3.0 18.2 + - - +
189A PRO 4.1 2.6 - - - +
190A ALA* 1.3 74.2 - - - +
192A LYS* 1.3 61.5 + - - +
193A VAL 3.5 23.6 - - - +
194A ALA* 5.0 2.5 - - + -
297A VAL* 3.7 19.8 - - + +
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Residues in contact with LYS 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A GLY 5.1 1.1 - - - -
167A LYS* 4.1 30.3 - - + +
168A VAL 2.9 4.6 + - - -
189A PRO* 2.7 27.1 + - - +
190A ALA* 3.3 18.9 - - - +
191A LEU* 1.3 73.2 - - - +
193A VAL* 1.3 63.0 + - - +
297A VAL* 4.0 4.0 - - - -
298A PRO* 3.3 23.4 - - - +
375A TYR* 3.3 35.5 - - + +
376A LEU* 3.9 7.4 - - + -
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Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A GLY* 3.3 5.2 - - - -
170A MSE 3.0 22.2 + - - -
191A LEU* 3.5 6.1 - - - +
192A LYS* 1.3 81.1 - - - +
194A ALA* 1.3 65.1 - - - +
297A VAL* 3.8 4.6 - - - +
298A PRO 3.5 9.6 - - - +
371A PHE* 3.3 40.6 - - + +
372A PHE* 3.7 21.1 - - + -
375A TYR* 4.1 15.0 - - + -
376A LEU* 3.6 37.2 - - + -
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Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A MSE 3.4 8.5 - - + -
180A VAL* 3.7 21.1 - - + -
184A LEU* 3.8 27.8 - - + -
191A LEU* 5.0 3.1 - - + -
193A VAL* 1.3 77.5 - - - +
195A VAL* 1.3 66.5 + - - +
196A PRO* 3.7 1.3 - - - -
297A VAL* 4.2 3.8 - - + -
298A PRO 3.0 6.1 + - - +
299A THR* 3.3 7.8 - - - +
300A MSE 3.0 23.6 + - - +
371A PHE* 4.4 0.5 - - - -
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A MSE 2.9 10.1 + - - +
171A ILE* 3.5 33.6 - - + +
172A GLY 3.6 1.0 + - - -
180A VAL* 4.1 2.2 - - - +
194A ALA* 1.3 80.5 - - - +
196A PRO* 1.3 62.0 - - - +
197A GLU* 3.2 27.5 + - + +
300A MSE 3.5 32.5 - - + +
302A LEU* 4.7 4.3 - - + -
363A PHE* 4.8 2.5 - - + -
368A LEU* 3.8 15.9 - - + -
371A PHE* 4.2 5.6 - - + -
372A PHE* 3.5 25.6 - - + -
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Residues in contact with PRO 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLY 4.1 3.1 - - - +
177A GLY 3.9 10.3 - - - +
180A VAL* 3.9 15.9 - - + -
181A VAL* 3.7 23.3 - - + -
184A LEU* 4.3 1.6 - - + -
194A ALA 3.7 0.9 - - - -
195A VAL* 1.3 82.3 - - - +
197A GLU* 1.3 62.1 + - - +
199A PRO* 3.7 7.7 - - + +
299A THR* 3.7 21.3 - - + -
300A MSE 3.2 14.8 - - - +
301A TRP* 3.6 27.0 - - + -
302A LEU 3.1 23.4 + - - +
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Residues in contact with GLU 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ILE* 3.7 26.1 - - - +
172A GLY* 2.9 23.7 + - - +
173A SER* 3.1 10.3 - - - +
174A SER 2.9 18.5 + - - -
177A GLY* 3.9 0.7 - - - -
195A VAL* 3.6 23.1 - - + +
196A PRO* 1.3 70.0 - - - +
198A SER* 1.3 70.7 + - - +
199A PRO* 2.9 4.3 - - - +
302A LEU* 3.5 20.4 - - + -
343A VAL* 3.8 25.0 - - + +
344A ASN* 3.4 26.7 + - - +
363A PHE* 4.1 7.6 - - - -
368A LEU* 4.9 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