Contacts of the strand formed by residues 267 - 274 (chain A) in PDB entry 3AS2
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 LYS 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A THR 3.0 18.0 + - - +
187A HIS* 3.3 28.8 - - + +
188A ILE* 2.8 27.9 + - - +
260A LYS* 5.0 1.3 - - - +
264A PRO 5.8 0.2 - - - -
265A ASP* 3.5 22.4 - - - +
266A LEU* 1.3 75.0 - - - +
268A ILE* 1.3 62.5 + - - +
269A ILE* 4.1 10.9 - - + +
308A ASP* 3.4 20.4 - - + +
357A THR* 5.3 12.0 + - - +
359A GLU* 3.2 26.0 + - - +
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Residues in contact with ILE 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 3.4 22.7 - - + +
190A TYR* 5.2 3.4 - - + -
256A LEU* 3.7 39.7 - - + +
259A LEU* 4.3 11.0 - - + -
260A LYS* 3.4 35.7 - - + -
266A LEU* 4.3 3.8 - - + +
267A LYS* 1.3 78.7 - - - +
269A ILE* 1.3 61.7 + - - +
306A PHE* 4.0 17.3 - - + +
307A TYR* 3.3 26.1 - - + -
308A ASP* 2.8 33.1 + - - -
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Residues in contact with ILE 269 (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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187A HIS* 3.9 28.5 - - + -
188A ILE 2.8 7.0 + - - +
189A LEU* 3.3 18.2 - - + -
190A TYR 2.8 22.3 + - - -
267A LYS* 4.3 6.3 - - + -
268A ILE* 1.3 83.5 - - - +
270A PRO* 1.3 65.3 - - - +
307A TYR* 3.9 2.9 - - - -
308A ASP 4.3 2.9 - - - +
309A GLY* 4.3 12.1 - - - +
310A VAL 3.6 12.3 - - - +
311A ASP* 3.5 37.0 - - + +
359A GLU* 3.9 25.1 - - + +
361A THR* 4.4 10.1 - - + +
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Residues in contact with PRO 270 (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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190A TYR 3.8 5.4 - - - +
193A ILE* 3.8 20.2 - - + -
269A ILE* 1.3 80.9 - - + +
271A SER* 1.3 60.6 + - - +
272A ILE* 3.8 3.9 + - + -
297A VAL* 6.3 0.4 - - + -
300A PHE* 4.3 7.4 - - + -
301A LEU* 4.4 6.3 - - + -
307A TYR* 3.3 45.2 - - + -
309A GLY 3.0 28.9 - - - +
310A VAL* 3.9 9.1 - - + +
311A ASP* 2.9 26.8 + - - +
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Residues in contact with SER 271 (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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164A TYR* 3.8 15.7 - - - -
189A LEU* 4.6 4.0 - - - -
190A TYR 2.9 19.3 + - - -
192A PHE* 3.4 16.9 - - - -
193A ILE* 2.8 24.3 + - - -
269A ILE 3.5 0.6 + - - -
270A PRO* 1.3 72.6 - - - +
272A ILE* 1.3 60.8 + - - +
311A ASP* 2.8 19.6 + - - -
313A ASP* 2.7 31.4 + - - -
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Residues in contact with ILE 272 (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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193A ILE* 3.3 25.6 - - + +
195A ILE* 3.7 27.1 - - + -
225A VAL* 3.9 9.9 - - + -
270A PRO* 4.3 7.4 - - + +
271A SER* 1.3 75.0 + - - +
273A GLY* 1.3 61.6 + - - +
281A PHE* 3.7 6.1 - - + -
293A PHE* 3.8 28.5 - - + -
297A VAL* 3.8 14.8 - - + -
300A PHE* 6.3 2.5 - - + -
310A VAL* 3.3 27.6 - - + -
311A ASP 2.8 14.6 + - - +
312A ILE* 4.2 4.7 - - + -
313A ASP* 2.9 28.1 + - - +
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Residues in contact with GLY 273 (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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192A PHE* 3.3 24.6 - - - +
193A ILE 3.0 12.9 + - - -
195A ILE* 5.5 1.1 - - - -
271A SER 3.8 0.8 + - - -
272A ILE* 1.3 74.6 - - - +
274A GLY* 1.3 61.5 + - - -
277A LEU* 3.3 36.8 - - - +
281A PHE* 3.9 8.1 - - - -
313A ASP 3.8 3.1 - - - -
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Residues in contact with GLY 274 (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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192A PHE* 3.9 22.2 - - - -
273A GLY* 1.3 74.6 - - - -
275A GLY* 1.3 63.2 + - - -
276A THR 3.4 2.5 - - - -
277A LEU 4.0 0.2 - - - -
278A SER* 2.7 26.4 + - - -
313A ASP* 2.8 18.0 + - - +
315A GLU* 3.5 16.6 - - - -
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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