Contacts of the strand formed by residues 167 - 174 (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 ASP 167 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154O SER 3.6 0.3 - - - +
155O THR* 2.8 26.2 - - - +
156O GLN* 3.8 26.2 + - - +
165O SER 3.8 4.4 - - - +
166O THR* 1.3 84.8 + - - +
168O PHE* 1.3 70.4 + - - +
169O LYS* 3.7 27.7 - - - +
224O SER* 5.7 0.3 - - - -
225O LEU 3.2 15.0 - - - +
226O ASN* 3.7 14.8 - - + +
227O VAL* 4.3 2.0 - - - +
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Residues in contact with PHE 168 (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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66O ILE* 5.5 5.8 - - + -
111O LEU* 4.1 26.2 - - + -
119O LEU* 4.5 5.8 - - + -
121O PHE* 4.7 7.4 - - + -
153O ALA* 3.5 32.8 - - + -
154O SER* 3.0 7.4 - - - +
155O THR* 3.4 23.1 - - + -
162O ILE* 4.8 14.8 - - + -
166O THR* 5.0 2.2 - - - -
167O ASP* 1.3 79.9 - - - +
169O LYS* 1.3 66.5 + - - +
224O SER* 3.0 5.0 - - - -
225O LEU* 2.7 50.7 + - + +
227O VAL* 4.2 10.5 - - + -
237O ILE* 4.1 26.7 - - + -
265O PHE* 5.8 0.7 - + - -
269O ILE* 5.5 1.1 - - + -
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Residues in contact with LYS 169 (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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152O VAL 4.0 0.2 - - - +
153O ALA* 3.0 6.2 - - - -
154O SER* 2.8 35.9 + - - +
156O GLN* 6.0 3.1 - - - +
167O ASP* 3.7 20.2 - - - +
168O PHE* 1.3 82.1 - - - +
170O GLY* 1.3 58.9 + - - +
223O ILE 3.7 10.1 - - - +
224O SER* 3.5 18.2 - - - +
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Residues in contact with GLY 170 (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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151O LEU* 4.4 2.7 - - - -
152O VAL 3.5 12.8 - - - -
153O ALA* 4.2 3.3 - - - +
169O LYS* 1.3 77.8 - - - +
171O GLU* 1.3 66.0 + - - -
222O GLN* 3.4 4.5 - - - +
223O ILE* 3.1 34.1 + - - +
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Residues in contact with GLU 171 (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 4.9 0.2 - - - -
151O LEU* 3.1 19.1 - - - +
152O VAL* 3.4 21.9 + - + +
170O GLY* 1.3 74.3 - - - +
172O PHE* 1.3 61.8 + - - +
220O LYS* 4.1 40.1 + - + +
221O GLY 3.1 13.9 - - - +
222O GLN* 5.3 4.9 - - + -
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Residues in contact with PHE 172 (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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147O THR 3.1 26.7 - - - -
148O VAL* 3.8 7.4 - - + -
149O LYS 3.2 14.6 - - - +
150O ASN 4.0 6.3 - - - -
151O LEU* 3.8 9.2 - - - -
171O GLU* 1.3 77.0 - - - +
173O ASN* 1.3 75.3 + - - +
174O VAL* 3.5 23.6 - - + -
220O LYS* 3.4 11.3 - - - +
221O GLY* 2.9 56.4 + - - -
222O GLN 3.4 7.6 - - - -
223O ILE* 3.3 39.7 - - + -
243O SER* 4.3 9.0 - - - -
244O GLU 4.4 4.0 - - - -
245O GLN* 4.2 9.9 - - - -
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Residues in contact with ASN 173 (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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147O THR* 3.9 1.0 - - - +
149O LYS* 2.9 23.4 + - + +
150O ASN* 2.8 37.9 + - - +
172O PHE* 1.3 79.9 - - - +
174O VAL* 1.3 61.5 + - - +
175O PRO* 3.3 11.7 - - + +
218O LEU* 4.3 20.5 - - + +
219O THR 3.6 5.6 + - - -
220O LYS* 3.4 34.4 + - - +
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Residues in contact with VAL 174 (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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145O LEU* 4.7 7.9 - - + +
147O THR* 4.1 6.1 - - + -
172O PHE* 3.5 29.2 - - + -
173O ASN* 1.3 70.8 - - - +
175O PRO* 1.3 77.4 - - + +
176O SER* 5.2 1.6 - - - +
218O LEU* 3.5 1.7 - - - +
219O THR* 2.7 44.2 + - - +
220O LYS 4.2 2.2 - - - +
221O GLY 4.0 7.4 - - - +
245O GLN* 3.9 32.5 - - + +
246O LEU* 4.5 12.1 - - + +
247O SER 5.8 0.7 - - - +
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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