Contacts of the strand formed by residues 222 - 229 (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 THR 222 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184M ALA* 5.5 0.2 - - - -
210M THR* 3.4 3.3 - - - -
211M ALA 2.9 26.2 + - - +
213M LEU* 4.1 7.3 - - + +
220M GLU* 3.6 5.3 - - - +
221M ASP* 1.3 89.9 + - - +
223M GLY* 1.3 59.2 + - - +
239M VAL 3.3 5.8 - - - -
240M THR* 2.9 22.2 + - - +
242M LEU* 3.1 12.3 - - - +
154N TYR 3.5 26.7 - - - +
155N MET* 3.5 21.1 - - + -
234N MET* 3.8 16.9 - - + +
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Residues in contact with GLY 223 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185M PHE* 3.6 18.5 - - - -
209M TYR 3.2 13.0 - - - -
210M THR* 3.9 1.3 - - - -
222M THR* 1.3 77.6 - - - +
224M VAL* 1.3 72.6 + - - +
239M VAL 2.8 29.4 + - - +
155N MET* 3.3 0.9 - - - +
234N MET* 4.1 6.5 - - - -
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Residues in contact with VAL 224 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185M PHE* 3.7 4.7 - - - -
207M TYR 4.2 0.2 - - - +
208M ALA* 3.2 3.7 - - - +
209M TYR* 2.8 37.5 + - + +
223M GLY* 1.3 84.3 - - - +
225M ALA* 1.3 65.5 + - - +
236M SER* 5.0 0.4 - - - -
237M ILE 3.4 7.6 - - - +
238M ASN* 3.3 27.6 - - - +
155N MET* 3.5 21.8 - - + -
226N ALA* 4.2 13.8 - - + +
234N MET* 4.2 4.5 - - + -
235N GLY 3.5 33.9 - - - +
236N SER* 4.0 7.6 - - - -
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Residues in contact with ALA 225 (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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185M PHE* 4.4 1.3 - - + -
206M VAL* 4.9 0.9 - - + -
207M TYR 3.3 7.2 - - - +
208M ALA* 3.9 14.4 - - + -
224M VAL* 1.3 76.7 - - - +
226M ALA* 1.3 64.1 + - - +
227M LEU* 3.9 6.5 - - + +
236M SER* 3.1 8.0 - - - -
237M ILE* 3.0 48.3 + - + +
335M ILE* 3.9 20.9 - - + -
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Residues in contact with ALA 226 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206M VAL* 3.1 7.8 - - - +
207M TYR 2.7 36.0 + - - +
224M VAL 4.3 0.2 - - - -
225M ALA* 1.3 74.7 - - - +
227M LEU* 1.3 61.6 + - - +
235M GLY 3.6 4.5 - - - -
236M SER* 4.5 1.3 - - - +
207N TYR* 4.7 8.5 - - + +
209N TYR* 3.5 22.6 - - + -
224N VAL* 4.1 17.9 - - + +
226N ALA* 4.3 20.9 - - + +
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Residues in contact with LEU 227 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156M VAL 5.3 0.2 - - - +
196M LEU* 3.8 33.9 - - + -
203M VAL* 4.5 8.5 - - + -
205M SER 3.7 3.1 - - - +
206M VAL* 3.4 28.9 - - + -
225M ALA* 3.9 13.9 - - + +
226M ALA* 1.3 81.8 - - - +
228M ARG* 1.3 60.5 + - - +
229M TRP* 3.9 24.0 - - + -
234M MET* 3.4 6.2 - - - +
235M GLY 2.9 29.2 + - - +
236M SER 3.8 27.8 - - - +
237M ILE* 4.2 2.9 - - + +
331M LEU* 4.9 2.5 - - + -
335M ILE* 5.7 1.8 - - + -
209N TYR* 3.7 8.8 - - - -
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Residues in contact with ARG 228 (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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203M VAL* 3.6 3.0 - - - +
204M GLU* 2.8 57.3 + - - +
205M SER* 3.1 18.7 + - - +
227M LEU* 1.3 76.2 - - - +
229M TRP* 1.3 68.6 + - - +
232M GLY* 4.9 6.7 - - - +
233M ALA 3.6 9.0 - - - +
234M MET* 4.5 11.6 - - + +
344M ARG* 4.3 15.2 - - - +
207N TYR* 5.5 0.2 + - - -
209N TYR* 3.5 48.2 - - + +
210N THR 5.3 5.5 + - - -
339N ALA 5.6 3.4 + - - -
204O GLU* 5.6 3.4 + - - -
228O ARG* 6.1 1.4 - - - +
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Residues in contact with TRP 229 (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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156M VAL* 3.6 23.6 - - + -
196M LEU* 3.2 34.2 + - + -
200M VAL* 3.5 25.6 - - + +
201M GLY 3.1 32.7 + - - -
202M PRO 3.4 14.1 - - - -
203M VAL* 3.7 11.1 - - + +
204M GLU* 3.8 4.1 - - - +
227M LEU* 3.9 24.2 - - + -
228M ARG* 1.3 85.2 - - - +
230M ARG* 1.3 59.2 + - - +
231M HIS* 3.3 26.9 - + + +
232M GLY* 2.9 20.4 + - - -
233M ALA* 2.9 28.2 + - + +
234M MET 3.7 24.2 - - - -
235M GLY* 3.8 5.4 - - - -
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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