Contacts of the strand formed by residues 192 - 198 (chain M) in PDB entry 3QUM
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 192 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117M ILE* 5.8 1.0 - - - +
132M VAL* 5.1 12.6 - - + -
148M TRP* 6.2 4.5 - + + -
149M LYS 4.0 3.6 - - - -
150M ILE* 4.5 20.0 - - + +
179M LEU* 5.0 11.2 - - + -
181M LEU* 4.0 21.9 - - + +
186M TYR* 2.5 58.7 + + - -
189M HIS* 3.9 33.6 + - + -
190M ASN 3.9 7.6 - - - -
191M SER* 1.3 78.3 + - - +
193M THR* 1.3 54.7 + - - +
208M SER* 2.8 26.9 - - - -
209M PHE* 3.4 41.4 + + + -
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Residues in contact with THR 193 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117M ILE* 5.4 0.7 - - - -
147M LYS 4.1 0.2 - - - +
148M TRP* 3.6 12.1 - - - -
149M LYS* 2.9 65.9 + - + +
150M ILE 4.8 0.4 - - - +
151M ASP* 6.1 0.9 - - - -
191M SER* 4.2 11.4 - - - +
192M TYR* 1.3 75.6 - - - +
194M CYS* 1.3 70.6 + - - +
195M GLU* 4.9 1.2 - - - +
206M VAL* 4.1 13.1 - - + +
207M LYS 3.5 1.0 + - - -
208M SER* 3.1 25.4 - - - +
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Residues in contact with CYS 194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115M VAL* 5.2 5.2 - - - -
117M ILE* 3.0 25.9 - - + +
134M CYS* 2.1 44.0 - - - -
136M LEU* 5.2 3.6 - - - -
146M VAL* 4.3 13.9 - - - -
147M LYS 4.4 0.7 - - - -
148M TRP* 4.0 9.9 - - + -
193M THR* 1.3 76.6 + - - +
195M GLU* 1.3 64.2 + - - +
196M ALA* 5.3 1.6 - - - -
205M ILE 3.8 0.4 - - - +
206M VAL* 3.4 4.5 - - - -
207M LYS* 2.9 33.2 + - + +
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Residues in contact with GLU 195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145M ASN 3.9 1.0 - - - +
146M VAL* 3.1 6.8 - - - +
147M LYS* 2.9 66.6 + - + +
149M LYS* 2.7 40.2 + - + +
193M THR* 4.9 0.7 - - - +
194M CYS* 1.3 79.0 - - - +
196M ALA* 1.3 64.0 + - - +
197M THR* 4.2 4.1 + - - +
204M PRO* 4.1 18.2 - - + +
205M ILE 3.2 2.5 - - - +
206M VAL* 3.7 22.7 - - + +
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Residues in contact with ALA 196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113M PRO* 5.9 1.7 - - + +
115M VAL* 4.6 5.8 - - + -
136M LEU* 3.8 18.8 - - + -
144M ILE* 4.4 7.4 - - + -
145M ASN 3.8 3.1 - - - -
146M VAL* 3.7 20.4 - - + -
194M CYS* 4.3 2.2 - - - -
195M GLU* 1.3 77.0 - - - +
197M THR* 1.3 58.1 - - - +
198M HIS* 5.1 0.6 - - - +
205M ILE* 2.6 58.4 + - + +
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Residues in contact with THR 197 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144M ILE* 3.6 3.3 - - - +
145M ASN* 3.4 34.1 + - - -
147M LYS* 6.1 1.2 - - - -
195M GLU* 4.2 4.9 + - - +
196M ALA* 1.3 75.1 + - - +
198M HIS* 1.3 75.3 + - - +
201M SER 3.7 9.2 - - - +
202M THR 4.7 4.9 - - - +
203M SER 3.3 24.7 - - - +
204M PRO* 3.4 22.1 - - + +
205M ILE* 5.0 0.4 - - - -
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Residues in contact with HIS 198 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111M ALA 3.8 4.6 + - - -
113M PRO* 4.2 25.4 - - + -
139M PHE* 4.2 9.5 - + - +
141M PRO* 3.0 63.1 - - + +
143M ASP 3.0 21.1 + - - -
144M ILE* 3.9 12.3 - - + +
196M ALA 5.1 1.1 - - - +
197M THR* 1.3 83.6 - - - +
199M LYS* 1.3 69.1 + - - +
200M THR* 2.7 34.1 + - - +
201M SER* 2.7 26.4 + - - +
203M SER 4.7 0.6 + - - -
205M ILE* 5.7 2.4 - - + +
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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