Contacts of the strand formed by residues 153 - 161 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213G LEU* 4.9 0.7 - - - +
145H ILE* 4.3 22.9 - - + -
150H PHE* 4.1 17.3 - - + -
151H GLY 3.8 11.0 - - - +
152H ARG* 1.3 81.2 + - - +
154H TYR* 1.3 67.2 + - - +
156H VAL* 4.1 17.3 - - + -
200H VAL* 4.1 17.9 - - + +
231H HIS* 4.4 16.0 + - + +
232H GLY 4.8 0.5 - - - -
233H ALA* 3.3 23.4 + - + +
254H ILE* 4.0 32.1 - - + -
255H LEU 4.0 4.9 - - - +
256H GLY* 4.0 1.3 - - - -
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Residues in contact with TYR 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213G LEU* 3.7 33.7 - - + +
214G ALA* 3.8 15.7 - - + +
215G ARG* 5.5 0.7 + - - -
222G THR* 3.7 14.4 - - - +
240G THR* 4.7 3.8 - - + +
242G LEU* 3.5 44.6 - - + -
152H ARG* 3.7 22.0 - - + +
153H ILE* 1.3 79.9 - - - +
155H MET* 1.3 62.1 + - + +
233H ALA* 3.5 2.8 - - - -
234H MET 3.0 23.3 + - - +
255H LEU* 2.8 14.6 + - + +
256H GLY* 3.5 16.8 - - - -
257H GLU* 2.9 48.4 + - + +
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Residues in contact with MET 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161G PHE* 3.8 24.7 - - + -
222G THR* 3.7 13.9 - - + -
223G GLY 3.6 14.6 - - - +
224G VAL* 4.0 9.9 - - + -
238G ASN* 4.1 22.0 - - - -
239G VAL 3.5 26.0 - - - +
240G THR* 4.4 9.9 - - + -
153H ILE* 4.5 0.4 - - - +
154H TYR* 1.3 78.8 - - + +
156H VAL* 1.3 77.4 + - - +
234H MET 3.2 16.6 - - - +
235H GLY* 4.3 2.9 - - - -
253H THR* 3.9 0.4 - - + +
254H ILE* 3.6 0.5 - - - -
255H LEU* 2.8 48.6 + - + +
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Residues in contact with VAL 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153H ILE* 4.1 17.7 - - + -
155H MET* 1.3 83.5 - - - +
157H THR* 1.3 64.8 + - - +
196H LEU* 4.5 7.4 - - + -
200H VAL* 3.9 27.6 - - + -
227H LEU* 5.9 0.2 - - + -
229H TRP* 3.7 30.0 - - + -
233H ALA* 4.9 1.3 - - + -
234H MET 3.1 6.6 + - - +
235H GLY* 3.0 23.3 - - - -
236H SER 3.2 4.2 + - - +
252H ILE* 4.2 22.7 - - + -
253H THR 3.2 9.4 - - - +
254H ILE* 4.2 7.2 - - + -
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Residues in contact with THR 157 (chain H).
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* 6.0 0.7 - - + -
159G ASN* 4.3 6.2 + - - +
161G PHE* 3.6 21.1 - - + -
238G ASN* 3.3 29.2 - - + +
155H MET* 4.4 1.7 - - - +
156H VAL* 1.3 76.2 - - - +
158H VAL* 1.3 65.3 + - - +
159H ASN* 4.2 6.9 + - - -
236H SER* 2.9 30.1 - - - +
238H ASN* 4.5 4.0 - - - +
251H SER* 4.0 1.4 + - - +
252H ILE* 3.4 1.6 - - - -
253H THR* 2.8 46.2 + - - -
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Residues in contact with VAL 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H VAL* 4.8 1.3 - - + -
157H THR* 1.3 76.7 - - - +
159H ASN* 1.3 72.9 + - - +
160H VAL* 4.2 0.7 - - + -
192H TYR* 3.9 35.0 - - + +
195H LEU* 5.3 1.1 - - + -
196H LEU* 3.9 22.7 - - + -
236H SER 3.0 7.6 + - - +
237H ILE* 3.4 18.2 - - + -
238H ASN* 2.9 27.5 + - - +
251H SER 3.2 13.9 - - - +
252H ILE* 3.9 29.6 - - + -
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Residues in contact with ASN 159 (chain H).
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* 4.1 12.2 + - - +
159G ASN* 5.2 5.7 - - - +
262G ARG* 4.5 5.1 - - - +
157H THR* 5.2 6.3 + - - -
158H VAL* 1.3 74.9 + - - +
160H VAL* 1.3 63.6 + - - +
161H PHE* 3.4 38.1 - - + -
238H ASN* 3.1 27.7 + - - -
249H GLU* 3.2 20.8 + - - +
250H GLY* 3.2 4.7 - - - -
251H SER* 2.7 46.2 + - - +
262H ARG* 4.6 3.2 - - - +
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Residues in contact with VAL 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158H VAL* 4.1 4.2 + - + -
159H ASN* 1.3 76.9 - - - +
161H PHE* 1.3 60.3 + - - +
162H TRP* 3.7 39.7 - - + -
189H ALA* 3.8 14.4 - - + -
192H TYR* 3.5 42.6 - - + -
238H ASN 2.8 9.3 + - - -
239H VAL* 3.4 14.5 - - + +
240H THR 3.1 27.0 + - - +
241H MET* 4.1 10.5 - - + -
249H GLU 3.6 2.0 - - - -
250H GLY* 5.0 0.2 - - - -
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Residues in contact with PHE 161 (chain H).
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* 3.7 21.8 - - + -
157G THR* 3.4 24.5 - - - -
253G THR* 4.1 18.2 - - + -
255G LEU* 3.6 20.4 - - + -
262G ARG* 4.5 1.3 - - - -
159H ASN* 3.4 28.9 - - + -
160H VAL* 1.3 75.2 - - - +
162H TRP* 1.3 51.9 + - - +
238H ASN* 3.8 19.5 - - + -
240H THR* 3.9 8.5 - - + -
243H THR* 2.8 18.5 + - - +
248H LEU* 2.8 44.1 + - + +
249H GLU* 2.8 39.1 + - + +
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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