Contacts of the strand formed by residues 189 - 195 (chain M) in PDB entry 6K4Y
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 ASN 189 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150M ARG* 2.9 42.2 + - - +
163M PHE* 3.5 18.7 - - + -
164M GLY 3.1 5.2 - - - +
165M TYR* 3.3 6.6 - - - -
183M LYS 3.1 5.2 - - - +
184M ILE* 3.2 0.5 - - - -
185M ALA* 2.7 38.2 + - + +
187M ASN* 2.8 34.8 + - - +
188M GLY* 1.3 76.5 - - - +
190M VAL* 1.3 57.9 + - - +
191M TYR* 4.7 2.3 - - + -
18N T 5.7 1.8 - - + +
19N T 3.8 16.4 + - - +
42T T 5.9 0.6 + - - -
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Residues in contact with VAL 190 (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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162M ILE 3.5 1.9 - - - +
163M PHE* 3.1 11.1 - - - -
164M GLY 2.9 46.8 + - - +
167M MET* 3.8 39.3 - - + +
172M ILE* 4.5 15.3 - - + -
182M CYS* 5.9 2.0 - - + -
183M LYS 3.3 2.7 - - - -
184M ILE* 3.8 26.9 - - + -
188M GLY* 3.8 10.5 - - - +
189M ASN* 1.3 77.0 - - - +
191M TYR* 1.3 62.1 + - - +
192M LEU* 4.9 3.1 - - + +
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Residues in contact with TYR 191 (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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153M GLU* 5.0 3.6 - - - -
161M ARG* 3.6 27.4 - - - +
162M ILE 3.8 2.0 - - - -
163M PHE* 3.6 31.2 - + + -
182M CYS* 2.6 36.3 - - - +
183M LYS* 2.9 60.2 + - + +
185M ALA* 5.6 0.4 - - + -
189M ASN* 4.9 5.2 - - + -
190M VAL* 1.3 74.9 - - - +
192M LEU* 1.3 58.8 + - - +
193M ASP* 4.2 7.2 - - - +
17N C 3.2 53.3 + + - +
18N T 3.6 24.7 + - - +
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Residues in contact with LEU 192 (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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161M ARG* 3.1 8.9 - - - +
162M ILE* 2.8 62.3 + - + +
167M MET* 3.7 28.5 - - + -
172M ILE* 4.6 17.3 - - + +
175M PHE* 4.2 32.5 - - + -
176M THR* 5.8 0.9 - - + -
180M MET* 3.5 16.3 - - + +
181M SER 2.7 18.4 - - - +
182M CYS* 3.8 13.0 - - + -
190M VAL* 4.9 3.6 - - + +
191M TYR* 1.3 78.0 - - - +
193M ASP* 1.3 63.7 + - - +
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Residues in contact with ASP 193 (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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159M ASN* 5.4 7.8 - - + +
160M MET 4.1 2.5 - - - -
161M ARG* 2.5 46.9 + - - -
179M GLY 4.3 0.5 - - - +
180M MET* 3.1 9.7 - - - -
181M SER* 2.9 51.3 + - - -
182M CYS 5.8 0.5 - - - -
183M LYS* 6.1 0.9 - - - +
191M TYR* 4.7 5.4 - - - +
192M LEU* 1.3 74.1 + - - +
194M ILE* 1.3 60.3 - - - +
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Residues in contact with ILE 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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159M ASN* 3.1 9.4 - - - +
160M MET* 2.9 65.3 + - + +
178M ILE* 3.9 18.2 - - + +
179M GLY 4.2 7.4 - - - +
180M MET* 3.7 30.5 - - + -
192M LEU 3.8 0.2 + - - -
193M ASP* 1.3 73.9 - - - +
195M LYS* 1.3 75.6 + - - +
200M ASN* 3.4 31.2 - - + +
203M ALA* 5.4 0.9 - - + -
204M VAL* 3.7 13.7 - - + -
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Residues in contact with LYS 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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158M GLY* 3.3 14.8 - - - +
159M ASN* 4.2 0.9 - - - +
160M MET* 4.1 0.4 - - - +
194M ILE* 1.3 80.4 - - - +
196M ARG* 1.3 87.5 + - - +
197M SER* 3.1 17.4 + - - -
200M ASN* 2.9 35.7 + - - +
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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