Contacts of the strand formed by residues 249 - 256 (chain M) 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 GLU 249 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159M ASN* 3.4 21.6 + - + -
160M VAL* 3.6 1.6 - - - -
161M PHE* 2.8 47.7 + - + +
162M TRP* 3.7 3.3 - - - -
247M ASN 3.9 0.4 - - - -
248M LEU* 1.3 91.0 - - + +
250M GLY* 1.3 60.7 + - - +
251M SER* 2.2 40.8 + - - +
262M ARG* 3.0 22.4 + - - +
264M GLY* 5.4 0.2 - - - -
265M GLY 3.3 12.3 - - - +
266M VAL* 3.7 6.2 - - - +
253N THR* 5.9 0.5 - - - +
262N ARG* 5.0 10.4 + - - -
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Residues in contact with GLY 250 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159M ASN 3.3 6.7 - - - -
160M VAL* 4.6 1.3 - - - -
162M TRP* 4.3 4.0 - - - -
192M TYR* 4.1 13.2 - - - -
249M GLU* 1.3 72.5 - - - +
251M SER* 1.3 59.7 + - - -
264M GLY 3.9 1.7 - - - +
265M GLY 3.0 11.9 + - - +
266M VAL 3.1 15.4 + - - -
267M ALA 4.0 0.4 - - - -
268M VAL* 2.6 33.6 + - - -
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Residues in contact with SER 251 (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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157M THR 5.1 1.0 + - - -
158M VAL* 3.2 12.9 - - - +
159M ASN* 2.9 41.4 + - - +
192M TYR* 4.5 0.8 - - - -
249M GLU* 2.2 36.2 + - - -
250M GLY* 1.3 74.6 - - - +
252M ILE* 1.3 63.0 + - - +
253M THR* 5.0 3.1 + - - -
262M ARG* 4.4 5.9 + - - -
263M VAL 3.3 13.5 - - - -
264M GLY* 4.0 7.6 - - - -
268M VAL* 3.9 4.5 - - - +
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Residues in contact with ILE 252 (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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138M LEU* 4.1 10.5 - - + -
141M VAL* 5.9 0.4 - - + -
156M VAL* 4.4 8.1 - - + -
157M THR 3.4 3.8 - - - +
158M VAL* 4.1 20.0 - - + -
195M LEU* 4.0 24.9 - - + +
196M LEU* 5.3 0.9 - - + -
199M LEU* 4.0 23.6 - - + -
200M VAL* 5.2 1.6 - - + -
251M SER* 1.3 76.2 - - - +
253M THR* 1.3 65.8 + - - +
254M ILE* 3.9 22.9 - - + -
261M VAL 4.1 0.3 - - - +
262M ARG* 3.5 1.6 - - - -
263M VAL* 2.8 58.2 + - + +
268M VAL* 3.9 11.4 - - + -
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Residues in contact with THR 253 (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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155M MET* 3.8 0.9 - - + +
156M VAL* 3.3 5.5 - - - +
157M THR* 2.9 41.6 + - - +
251M SER* 5.0 3.1 + - - -
252M ILE* 1.3 72.5 + - - +
254M ILE* 1.3 64.5 + - - +
255M LEU* 4.5 15.5 - - + -
261M VAL 3.3 10.3 - - - +
262M ARG* 3.2 37.1 + - + +
161N PHE* 4.0 27.4 - - + -
248N LEU* 5.0 4.3 - - + -
249N GLU* 5.1 0.8 + - - +
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Residues in contact with ILE 254 (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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141M VAL* 4.0 27.1 - - + -
145M ILE* 4.3 8.1 - - + -
150M PHE* 3.4 27.5 - - + -
153M ILE* 4.0 29.2 - - + -
155M MET 3.6 2.5 - - - -
156M VAL* 4.3 10.1 - - + -
199M LEU* 4.3 3.4 - - + -
200M VAL* 4.2 16.6 - - + -
252M ILE* 3.9 26.0 - - + -
253M THR* 1.3 80.1 - - - +
255M LEU* 1.3 64.8 + - - +
260M THR* 3.7 0.2 - - - -
261M VAL* 2.8 38.0 + - + +
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Residues in contact with LEU 255 (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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150M PHE* 4.6 1.3 - - - -
153M ILE* 4.0 1.4 - - - +
154M TYR* 3.0 27.5 + - + +
155M MET* 2.9 29.8 + - + +
253M THR* 4.5 11.0 - - + -
254M ILE* 1.3 83.4 - - - +
256M GLY* 1.3 58.3 + - - +
259M GLY 3.7 1.3 - - - -
260M THR* 3.7 30.3 - - + +
261M VAL 4.8 0.2 - - - +
161N PHE* 3.7 38.4 - - + -
240N THR* 3.8 19.7 - - + -
243N THR* 4.1 13.2 - - + +
248N LEU* 4.2 12.6 - - + -
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Residues in contact with GLY 256 (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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150M PHE* 3.9 12.5 - - - -
152M ARG 3.3 11.4 - - - -
153M ILE* 4.1 4.5 - - - -
154M TYR* 3.7 11.5 - - - -
255M LEU* 1.3 74.6 - - - +
257M GLU* 1.3 69.0 + - - +
258M LYS 3.3 3.4 + - - -
259M GLY 2.6 22.8 + - - +
260M THR* 4.9 0.2 + - - -
242N LEU 4.1 3.8 - - - +
244N TYR* 3.7 9.5 + - - +
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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