Contacts of the strand formed by residues 219 - 227 (chain A) in PDB entry 3ANX
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 TYR 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A PHE 3.3 0.2 - - - -
218A ARG* 1.3 119.3 + - + +
220A VAL* 1.3 60.4 + - - +
221A ARG* 4.1 8.7 - - - +
238A LEU 3.5 1.9 - - - +
239A ALA* 3.3 4.3 - - - -
240A SER 2.8 46.5 + - - +
241A ASP 3.9 7.4 - - - -
242A ALA 4.9 0.4 - - - -
243A PHE* 3.4 28.3 - - - +
244A ASP* 3.7 28.0 - - + -
245A PRO* 3.7 20.8 - - + +
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Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A HIS* 3.3 31.6 + - + +
213A VAL* 3.5 22.4 - - + +
214A ARG* 3.3 45.6 - - - +
217A PHE* 3.9 9.4 - - + -
218A ARG 3.8 2.2 + - - -
219A TYR* 1.3 73.1 - - - +
221A ARG* 1.3 76.5 + - - +
237A LEU* 3.4 35.2 - - + -
238A LEU 3.4 4.7 - - - +
239A ALA* 4.4 0.4 - - + -
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Residues in contact with ARG 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ARG* 5.7 1.8 - - - +
219A TYR* 4.7 9.2 - - - +
220A VAL* 1.3 90.7 + - - +
222A SER* 1.3 62.9 + - - +
223A TYR 3.7 0.7 + - - -
237A LEU* 3.4 1.8 - - - +
238A LEU* 2.8 39.2 + - + +
244A ASP* 2.8 45.1 + - - -
245A PRO* 3.8 15.5 - - + -
246A ALA* 3.7 22.9 - - + +
276A PHE* 4.2 9.1 - - + -
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Residues in contact with SER 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A HIS* 2.7 30.9 + - - -
210A HIS* 3.2 31.6 - - - -
221A ARG* 1.3 74.4 - - - +
223A TYR* 1.3 60.5 + - - +
236A PHE 3.7 4.2 + - - -
237A LEU* 3.9 2.5 - - - -
276A PHE* 4.2 8.0 - - - +
278A LEU* 3.3 23.8 - - - +
282A LEU* 5.0 2.4 - - - +
286A LEU* 4.0 14.3 - - - +
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Residues in contact with TYR 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A THR* 3.0 38.4 + - + -
67A LEU* 4.1 9.7 + - - -
70A PRO* 3.7 13.2 - - + +
192A GLY* 5.6 0.2 - - - -
193A MET 4.8 2.9 + - - -
206A HIS* 5.4 0.2 + - - -
222A SER* 1.3 74.7 + - - +
224A LYS* 1.3 64.6 + - - +
235A GLY* 4.0 0.5 - - - -
236A PHE* 2.8 63.6 + + + +
237A LEU* 3.6 21.1 + - - -
238A LEU* 4.0 9.7 - - + +
275A MET* 3.4 40.2 - - + +
276A PHE* 3.3 37.7 - + + -
278A LEU* 4.7 1.3 - - - -
282A LEU* 6.1 0.4 - - - -
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Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ILE* 4.1 16.6 - - + -
223A TYR* 1.3 77.9 - - - +
225A ASN* 1.3 66.3 + - - +
233A ASN* 3.8 29.4 - - - +
234A PHE 3.7 11.4 - - - +
236A PHE* 4.5 2.5 - - - -
271A TYR* 5.4 0.3 + - - -
274A ALA 5.5 0.4 + - - -
275A MET* 3.0 32.5 + - - +
277A VAL 4.2 7.5 + - - -
278A LEU* 3.7 16.2 - - + -
279A PRO* 4.4 7.4 - - + -
282A LEU* 4.2 18.2 - - + -
225B ASN* 5.4 0.4 - - - -
226B HIS* 6.0 2.0 - - - -
271B TYR* 3.5 39.0 + - - -
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Residues in contact with ASN 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ILE* 3.6 9.5 - - - +
66A THR* 2.6 44.0 + - + +
224A LYS* 1.3 81.4 - - - +
226A HIS* 1.4 69.4 + - - +
227A ILE* 3.5 10.2 + - + +
233A ASN* 3.6 7.3 + - - -
234A PHE* 3.0 28.5 + - - +
236A PHE* 4.6 0.7 - - + -
266A HIS* 3.2 23.2 + - - -
271A TYR* 2.6 29.5 + - - -
275A MET* 3.9 8.3 - - - -
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Residues in contact with HIS 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ILE* 4.5 7.1 - - - +
225A ASN* 1.4 75.7 + - - +
227A ILE* 1.3 60.6 + - - +
228A PRO* 3.4 38.3 + - + +
231A PHE* 4.2 2.5 - - - -
232A LEU 3.8 20.5 + - - -
233A ASN* 3.8 7.2 + - - +
266A HIS* 5.7 0.7 + - - -
198B ILE 4.9 3.3 + - - -
199B LEU* 5.3 2.0 - - - +
224B LYS* 6.0 1.6 - - - +
226B HIS* 2.7 43.8 + + + +
231B PHE 4.3 0.7 - - - -
232B LEU* 3.8 5.2 - - - +
233B ASN* 3.4 48.8 + - + +
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Residues in contact with ILE 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASP* 3.4 18.4 - - - +
62A ILE* 4.4 10.1 - - + -
63A TYR* 4.1 36.1 - - + +
66A THR* 4.8 0.2 - - - +
225A ASN* 3.8 22.0 - - - +
226A HIS* 1.3 74.6 - - - +
228A PRO* 1.4 68.1 - - + +
230A PHE* 2.9 51.4 + - + +
231A PHE 3.3 7.1 + - - -
232A LEU 3.3 10.3 + - - +
234A PHE* 3.9 18.2 - - + -
236A PHE* 4.3 15.3 - - + -
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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