Contacts of the strand formed by residues 219 - 225 (chain A) in PDB entry 4BLW
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 ILE 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A LEU* 4.0 28.3 - - + +
216A ILE* 3.4 33.0 - - + +
217A ARG 3.8 9.9 - - - +
218A LYS* 1.3 76.7 - - - +
220A LEU* 1.3 58.8 + - - +
241A ILE* 3.5 32.1 - - + -
242A VAL 3.6 2.2 - - - -
243A ILE* 4.1 14.8 - - + -
276A TRP* 3.4 7.5 - - - -
277A ILE* 2.8 41.7 + - + -
278A VAL* 2.8 30.7 + - + +
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Residues in contact with LEU 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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218A LYS 4.1 0.2 - - - -
219A ILE* 1.3 75.2 - - - +
221A GLN* 1.3 59.7 + - - +
222A ILE* 4.3 12.6 - - + -
240A MET 3.8 0.5 - - - +
241A ILE* 3.3 5.2 - - - +
242A VAL* 2.8 44.3 + - + +
245A PRO* 4.0 30.3 - - + -
249A LEU* 4.2 15.7 - - + -
250A GLU* 4.3 24.2 - - + +
274A VAL* 3.7 21.5 - - + -
275A SER 3.5 16.2 - - - +
276A TRP* 3.6 30.9 - - + +
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Residues in contact with GLN 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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196A TYR* 2.8 30.1 + - - +
201A ARG* 4.9 3.8 - - - +
208A ILE* 3.6 26.4 - - - +
219A ILE 4.1 0.2 + - - -
220A LEU* 1.3 74.1 - - - +
222A ILE* 1.3 66.2 + - - +
223A GLU* 3.7 12.6 + - + +
240A MET 3.6 2.2 - - - +
241A ILE* 4.2 9.2 - - + +
273A THR* 3.8 2.2 + - - +
274A VAL* 3.2 5.2 - - - +
275A SER* 2.7 51.0 + - - +
277A ILE* 3.6 24.8 - - + +
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Residues in contact with ILE 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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17A LEU* 3.9 16.7 - - + +
21A VAL* 3.9 17.0 - - + -
196A TYR* 4.3 0.5 + - - -
220A LEU* 4.4 7.9 - - + -
221A GLN* 1.3 78.5 - - - +
223A GLU* 1.3 62.9 + - - +
239A GLY* 3.1 3.5 - - - -
240A MET* 2.8 40.5 + - + +
242A VAL* 4.1 22.7 - - + -
249A LEU* 4.3 10.3 - - + -
253A MET* 3.8 45.5 - - + -
257A LEU* 4.0 14.4 - - + -
273A THR 3.4 3.6 - - - -
274A VAL* 4.4 10.3 - - + -
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Residues in contact with GLU 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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17A LEU* 4.3 1.6 - - - -
196A TYR* 2.6 29.6 + - - +
198A VAL* 4.2 5.4 - - - -
201A ARG* 2.8 44.3 + - - -
221A GLN* 3.7 9.1 + - + +
222A ILE* 1.3 74.2 - - - +
224A LEU* 1.3 67.0 + - - +
225A ALA 4.2 0.2 - - - -
237A ALA* 4.4 3.6 - - + +
238A SER 3.4 14.6 - - - +
257A LEU* 4.5 2.1 - - - +
271A HIS* 2.9 23.1 + - - +
272A ALA* 3.2 5.2 - - - +
273A THR* 2.9 45.8 + - - +
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Residues in contact with LEU 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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13A HIS* 4.5 12.8 + - - +
17A LEU* 3.8 21.8 - - + +
223A GLU* 1.3 75.2 - - - +
225A ALA* 1.3 61.2 + - - +
226A VAL* 4.1 21.7 + - + -
237A ALA* 3.5 3.6 - - - -
238A SER* 3.0 29.5 + - - +
257A LEU* 4.2 19.5 - - + -
260A LEU* 4.3 6.1 - - + -
261A HIS* 3.9 42.0 - - + +
264A LEU* 4.1 29.2 - - + -
265A VAL* 4.4 2.0 - - + -
271A HIS 3.7 1.6 - - - -
272A ALA* 4.2 2.7 - - + -
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Residues in contact with ALA 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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223A GLU 4.2 0.6 - - - -
224A LEU* 1.3 73.1 - - - +
226A VAL* 1.3 62.3 + - - +
227A LEU 3.5 14.1 - - - +
229A ASP* 5.7 0.2 - - - +
237A ALA* 3.4 20.4 - - + -
261A HIS* 3.2 10.9 + - - -
270A GLY* 3.4 0.5 - - - -
271A HIS* 2.8 64.5 + - + +
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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