Contacts of the strand formed by residues 193 - 199 (chain M) in PDB entry 5A0Q
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 193 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24M ALA* 4.1 6.3 - - + -
25M SER 3.6 24.0 - - - +
26M ASP* 4.3 0.7 - - - +
175M VAL 4.7 1.6 - - - +
176M LYS* 4.4 17.9 - - + +
179M PHE* 3.3 51.4 - - + -
190M GLY 5.4 0.2 - - - -
191M ASP 4.0 1.7 + - - +
192M ALA* 1.3 76.2 - - - +
194M ARG* 1.4 62.6 - - - +
195M ILE* 4.1 26.5 - - + +
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Residues in contact with ARG 194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M VAL 4.1 0.7 - - - +
24M ALA* 3.1 4.3 - - - +
25M SER* 3.0 37.7 + - - +
27M THR* 4.9 15.0 - - + +
39M ASP* 4.3 15.4 + - - -
40M SER 5.6 0.2 - - - -
41M PRO* 3.5 35.2 - - + +
43M CYS* 3.7 29.1 + - - -
192M ALA 4.1 0.6 + - - -
193M LEU* 1.4 74.0 - - - +
195M ILE* 1.4 60.9 + - - +
196M CYS* 4.8 0.4 - - - -
205M GLU* 3.2 36.9 + - - +
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Residues in contact with ILE 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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22M ILE* 3.3 31.0 - - + -
23M VAL 3.8 2.7 - - - -
24M ALA* 3.9 11.2 - - + -
172M MET* 4.7 6.5 - - + -
175M VAL* 4.6 7.4 - - + -
176M LYS* 3.8 40.6 - - + -
193M LEU* 4.1 16.6 + - + +
194M ARG* 1.4 78.7 - - - +
196M CYS* 1.4 64.0 + - - +
197M ILE* 3.9 19.0 - - + +
204M ARG 4.6 0.2 - - - -
205M GLU* 3.5 29.6 + - - +
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Residues in contact with CYS 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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21M ALA 2.9 15.4 - - - +
23M VAL* 3.0 24.4 + - - +
43M CYS* 3.6 31.4 - - - -
45M LYS* 5.8 4.0 - - - -
51M VAL* 3.9 24.2 - - + +
194M ARG* 4.8 0.9 - - - -
195M ILE* 1.4 77.4 - - - +
197M ILE* 1.4 60.7 + - - +
198M VAL* 4.2 2.8 - - - +
203M ILE* 4.4 9.0 - - + -
204M ARG 3.6 5.4 - - - -
205M GLU* 3.9 24.7 - - - -
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Residues in contact with ILE 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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20M PHE* 3.1 36.8 - - + -
21M ALA 3.6 3.8 - - - +
22M ILE* 4.1 10.1 - - + +
168M LEU* 5.0 0.4 - - + -
172M MET* 3.8 32.8 - - + -
195M ILE* 3.9 19.3 - - + +
196M CYS* 1.4 74.7 - - - +
198M VAL* 1.3 59.2 + - - +
199M THR* 3.9 7.4 - - + -
203M ILE* 3.6 3.8 - - - +
204M ARG* 2.8 80.2 + - + +
205M GLU 5.3 2.5 - - - -
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Residues in contact with VAL 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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19M ASP* 2.8 23.8 - - - +
20M PHE* 3.0 6.6 - - - -
21M ALA* 3.3 24.5 + - + +
23M VAL* 5.9 0.4 - - + -
48M ASP 4.9 0.9 - - - +
49M LYS* 3.5 28.3 - - - +
51M VAL* 3.8 17.9 - - + -
111M GLY* 3.6 10.5 - - - +
112M GLY 4.5 1.3 - - - -
113M LEU* 3.4 36.6 - - + +
196M CYS 4.2 0.9 - - - +
197M ILE* 1.3 81.2 - - - +
199M THR* 1.3 62.8 + - - +
202M GLY 3.9 4.3 - - - +
203M ILE* 4.3 3.4 - - + +
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Residues in contact with THR 199 (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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19M ASP* 3.0 13.5 - - + -
20M PHE* 4.2 12.6 - - + +
49M LYS* 5.8 1.2 - - - +
113M LEU* 3.1 12.7 - - - +
168M LEU* 4.7 7.0 - - + -
197M ILE* 3.9 17.9 - - + -
198M VAL* 1.3 78.3 - - - +
200M LYS* 1.4 60.6 + - - +
201M GLU* 3.1 32.6 + - - +
202M GLY* 3.0 25.5 + - - +
204M ARG* 4.2 18.8 + - - +
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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