Contacts of the strand formed by residues 219 - 229 (chain O) in PDB entry 2AXT
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 219 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173O ASN* 3.6 7.4 + - - -
174O VAL* 2.7 55.2 + - - +
217O SER* 4.7 9.0 + - - +
218O LEU* 1.3 84.7 - - - +
220O LYS* 1.3 65.5 + - - +
246O LEU* 4.3 31.6 + - + +
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Residues in contact with LYS 220 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150O ASN 5.9 0.4 + - - -
171O GLU* 4.1 42.0 + - + +
172O PHE* 3.4 14.2 + - - +
173O ASN* 3.4 26.4 + - - +
174O VAL* 4.2 3.7 - - - +
219O THR* 1.3 80.7 + - - +
221O GLY* 1.3 58.5 + - - +
244O GLU 4.9 0.7 - - - +
245O GLN* 5.0 4.3 - - - -
246O LEU* 5.5 2.8 + - - +
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Residues in contact with GLY 221 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171O GLU* 3.1 8.1 - - - +
172O PHE* 2.9 58.7 + - - -
174O VAL* 4.0 4.8 - - - +
220O LYS* 1.3 75.0 - - - +
222O GLN* 1.3 59.4 + - - -
244O GLU 3.6 9.6 - - - -
245O GLN* 4.6 0.7 - - - -
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Residues in contact with GLN 222 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170O GLY 3.4 8.7 - - - +
171O GLU* 4.5 6.1 - - + +
172O PHE* 3.4 1.1 - - - -
221O GLY* 1.3 73.8 - - - +
223O ILE* 1.3 63.0 + - - +
243O SER* 2.9 4.7 - - - -
244O GLU* 2.9 40.3 + - + +
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Residues in contact with ILE 223 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71O LEU* 5.2 2.5 - - + -
148O VAL* 3.7 22.0 - - + -
151O LEU* 3.0 45.8 - - + -
153O ALA* 5.7 0.9 - - + -
169O LYS* 3.7 2.3 - - - +
170O GLY 3.1 22.0 + - - +
172O PHE* 3.3 16.8 - - + -
222O GLN* 1.3 72.9 - - - +
224O SER* 1.3 71.9 + - - +
225O LEU* 4.2 18.2 - - + -
241O PHE* 4.2 11.7 - - + -
242O GLU 3.2 13.5 - - - +
243O SER* 3.2 23.6 - - - -
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Residues in contact with SER 224 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167O ASP* 5.7 0.2 - - - -
168O PHE 3.0 15.9 - - - -
169O LYS* 3.5 25.3 - - - +
223O ILE* 1.3 83.9 - - - +
225O LEU* 1.3 64.4 + - - +
226O ASN* 3.7 3.3 + - - +
240O THR 4.1 0.2 - - - +
241O PHE* 3.6 3.6 - - - -
242O GLU* 3.2 29.6 + - - +
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Residues in contact with LEU 225 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69O LEU* 3.9 36.3 - - + -
71O LEU* 4.3 8.1 - - + -
151O LEU* 5.1 4.7 - - + -
153O ALA* 5.4 3.4 - - + -
167O ASP* 3.2 4.6 - - - +
168O PHE* 2.7 55.8 + - + +
223O ILE* 4.2 25.4 - - + -
224O SER* 1.3 82.2 - - - +
226O ASN* 1.3 59.8 - - - +
240O THR 3.8 4.9 - - - -
241O PHE* 4.2 7.9 - - + -
265O PHE* 3.5 33.0 - - + -
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Residues in contact with ASN 226 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166O THR 5.1 0.4 - - - +
167O ASP* 3.7 12.6 - - + -
224O SER 3.7 4.1 + - - +
225O LEU* 1.3 70.8 - - - +
227O VAL* 1.3 66.2 + - - +
228O ALA* 3.4 2.3 + - - +
239O GLY* 3.6 0.7 - - - -
240O THR* 3.0 41.6 + - - +
265O PHE* 4.1 2.0 - - - -
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Residues in contact with VAL 227 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162O ILE* 4.4 0.4 - - + -
163O THR 4.1 5.8 - - - +
164O THR* 3.0 28.2 - - - +
166O THR* 3.4 34.9 + - - +
167O ASP* 4.3 0.7 - - - +
168O PHE* 4.2 13.7 - - + -
226O ASN* 1.3 70.6 - - - +
228O ALA* 1.3 61.2 + - - +
229O LYS 3.3 22.7 - - - +
230O VAL* 3.9 14.4 - - + -
237O ILE* 3.8 33.7 - - + -
238O ALA 3.5 8.7 - - - +
265O PHE* 4.4 5.8 - - + -
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Residues in contact with ALA 228 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52O ALA* 5.2 0.5 - - - +
53O ARG* 5.3 1.0 + - - -
164O THR* 3.8 19.6 + - - +
226O ASN 3.4 1.9 + - - +
227O VAL* 1.3 75.3 - - - +
229O LYS* 1.3 58.8 + - + +
238O ALA 2.7 9.6 + - - -
239O GLY* 3.7 19.7 - - - -
240O THR* 4.8 7.4 - - + +
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Residues in contact with LYS 229 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48O LEU* 3.7 23.8 - - + +
52O ALA* 3.2 23.8 - - + -
53O ARG 4.4 2.0 - - - +
164O THR* 4.5 0.9 - - - -
227O VAL* 3.3 3.0 - - - +
228O ALA* 1.3 80.0 - - + +
230O VAL* 1.3 66.6 + - - +
237O ILE* 3.3 3.5 - - - -
238O ALA* 2.9 33.6 + - + -
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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