Contacts of the strand formed by residues 153 - 161 (chain G) in PDB entry 3Q2K
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 ILE 153 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145G ILE* 4.4 23.6 - - + -
150G PHE* 4.0 22.9 - - + -
151G GLY 3.8 12.1 - - - +
152G ARG* 1.3 82.4 - - - +
154G TYR* 1.3 67.3 + - - +
156G VAL* 4.1 18.4 - - + -
200G VAL* 4.5 15.5 - - + +
231G HIS* 4.5 14.1 + - + +
233G ALA* 3.3 22.1 + - + +
254G ILE* 3.9 31.4 - - + -
255G LEU 4.0 3.1 - - - +
256G GLY* 3.8 3.6 - - - -
213H LEU* 4.8 0.5 - - - +
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Residues in contact with TYR 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G ARG* 3.7 24.4 - - + +
153G ILE* 1.3 82.2 - - - +
155G MET* 1.3 63.7 + - + +
233G ALA* 4.0 5.4 - - - -
234G MET 3.2 16.5 + - - -
255G LEU* 2.6 16.5 + - + +
256G GLY* 3.6 16.2 - - - -
257G GLU* 3.2 44.5 + - + +
213H LEU* 3.6 28.8 - - + +
214H ALA* 3.6 19.5 - - + +
215H ARG* 5.8 0.2 + - - -
222H THR* 3.5 15.6 - - + +
240H THR* 4.7 2.9 - - + +
242H LEU* 3.6 50.3 - - + -
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Residues in contact with MET 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153G ILE* 4.3 1.3 - - - +
154G TYR* 1.3 80.0 - - + +
156G VAL* 1.3 75.5 + - - +
157G THR* 4.4 1.6 - - - -
234G MET 3.2 15.7 - - - +
235G GLY* 4.2 8.1 - - - -
253G THR 3.9 0.8 - - - +
254G ILE* 3.7 0.5 - - - -
255G LEU* 3.0 43.0 + - + +
161H PHE* 3.7 23.8 - - + -
222H THR* 3.5 23.1 - - + -
223H GLY 3.4 29.2 - - - +
224H VAL* 4.2 3.4 - - + -
238H ASN* 4.0 22.2 - - - +
239H VAL 3.6 7.9 - - - +
240H THR* 4.4 10.5 - - + -
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Residues in contact with VAL 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153G ILE* 4.1 15.7 - - + -
155G MET* 1.3 82.6 - - - +
157G THR* 1.3 67.1 + - - +
158G VAL* 4.5 5.4 - - + -
196G LEU* 4.6 2.5 - - + -
200G VAL* 4.0 24.9 - - + -
229G TRP* 3.8 32.0 - - + -
233G ALA* 4.9 0.9 - - + -
234G MET 3.0 5.4 + - - +
235G GLY* 2.7 30.9 - - - -
236G SER 2.9 3.8 + - - +
252G ILE* 4.1 24.0 - - + -
253G THR 3.2 10.8 - - - +
254G ILE* 4.3 7.4 - - + -
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Residues in contact with THR 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155G MET* 4.4 1.2 - - - -
156G VAL* 1.3 75.7 + - - +
158G VAL* 1.3 67.4 + - - +
159G ASN* 4.0 24.0 - - - +
236G SER* 3.5 6.5 - - - +
238G ASN* 4.5 7.2 - - - +
251G SER* 3.9 1.7 + - - +
252G ILE* 3.4 3.1 - - - -
253G THR* 3.0 45.9 + - - +
262G ARG* 6.2 0.2 - - - +
157H THR* 6.0 1.1 - - + -
159H ASN* 4.3 16.6 - - - +
161H PHE* 3.4 22.9 - - - -
238H ASN* 4.0 13.9 - - - +
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Residues in contact with VAL 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G VAL* 4.5 2.0 - - + -
157G THR* 1.3 80.7 - - - +
159G ASN* 1.3 61.6 + - - +
160G VAL* 4.4 3.1 - - + -
192G TYR* 3.9 37.0 - - + +
195G LEU* 5.7 1.1 - - + -
196G LEU* 4.0 20.6 - - + -
236G SER 2.9 10.2 + - - +
237G ILE* 3.1 16.2 - - + -
238G ASN* 2.8 31.5 + - - +
251G SER 3.2 11.7 - - - +
252G ILE* 3.5 31.4 - - + -
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Residues in contact with ASN 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157G THR* 4.0 14.2 - - - +
158G VAL* 1.3 72.5 - - - +
160G VAL* 1.3 66.2 + - - +
161G PHE* 3.4 30.9 - - + -
238G ASN* 3.1 34.0 + - - +
249G GLU* 3.1 28.7 + - - +
250G GLY* 3.1 6.8 - - - -
251G SER* 2.9 34.5 + - - +
262G ARG* 5.9 1.0 - - - +
157H THR* 4.3 6.8 + - - +
159H ASN* 5.2 6.1 - - - +
262H ARG* 6.1 1.0 - - - +
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Residues in contact with VAL 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158G VAL* 4.4 4.0 - - + -
159G ASN* 1.3 78.1 - - - +
161G PHE* 1.3 53.5 + - - +
162G TRP* 3.6 42.8 - - + -
189G ALA* 4.4 13.7 - - + -
192G TYR* 3.4 42.6 - - + -
237G ILE* 5.1 0.2 - - + -
238G ASN 3.0 6.6 + - - +
239G VAL* 3.2 17.5 - - + -
240G THR 2.9 32.2 + - - +
241G MET* 4.3 10.3 - - + -
249G GLU 3.6 2.7 - - - -
250G GLY* 4.5 0.4 - - - -
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Residues in contact with PHE 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159G ASN* 3.4 36.1 - - + -
160G VAL* 1.3 76.3 - - - +
162G TRP* 1.3 57.5 + - - +
238G ASN* 3.5 24.9 - - + -
239G VAL 4.4 0.2 - - - -
240G THR* 3.8 8.1 - - + -
243G THR* 3.0 15.9 + - - +
248G LEU* 2.9 37.2 + - + -
249G GLU* 2.9 39.6 + - + +
155H MET* 3.8 21.1 - - + -
157H THR* 3.6 19.3 - - - -
253H THR* 4.3 11.2 - - + -
255H LEU* 3.6 23.6 - - + -
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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