Contacts of the strand formed by residues 233 - 241 (chain A) in PDB entry 4LG8
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 233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A CYS* 3.1 19.1 + - - +
231A PRO 3.4 1.0 + - - -
232A SER* 1.3 82.7 + - - +
234A THR* 1.3 59.3 + - - +
235A ASN* 3.0 27.1 + - - +
236A LYS* 3.1 47.2 + - + +
276A GLN* 3.7 17.6 + - - +
485A HIS* 4.0 4.0 - - - -
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Residues in contact with THR 234 (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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229A LEU* 4.0 20.8 - - + +
230A CYS 3.4 16.2 - - - +
231A PRO* 4.7 2.2 - - + +
233A ASP* 1.3 69.3 + - - +
235A ASN* 1.3 60.9 + - - +
236A LYS 3.2 7.4 - - - +
237A ILE* 3.5 11.3 - - - +
445A GLN* 4.2 9.4 - - - +
483A PHE 4.2 2.2 - - - +
484A GLY* 3.6 8.3 - - - -
485A HIS* 2.9 59.6 + - + +
489A PHE* 3.4 19.3 - - - -
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Residues in contact with ASN 235 (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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233A ASP* 3.0 15.6 + - - +
234A THR* 1.3 77.9 + - - +
236A LYS* 1.3 61.4 + - + +
237A ILE* 3.5 3.1 - - - +
250A ASP* 3.6 7.1 - - - +
251A LYS* 2.9 57.8 + - + +
252A SER* 3.1 26.9 + - - +
489A PHE* 3.9 9.4 - - - -
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Residues in contact with LYS 236 (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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229A LEU* 3.5 3.6 - - - -
230A CYS* 3.0 32.3 + - + -
233A ASP* 3.1 34.9 + - + +
234A THR 4.1 0.9 - - - +
235A ASN* 1.3 77.4 - - - +
237A ILE* 1.3 62.4 + - - +
248A VAL* 5.1 1.3 - - + -
249A PHE 3.6 2.2 - - - +
250A ASP* 3.5 28.0 - - + +
257A LEU* 4.1 24.6 - - + +
272A PHE* 3.6 24.9 - - + -
276A GLN* 3.6 24.4 + - + +
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Residues in contact with ILE 237 (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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227A LEU* 3.6 28.0 - - + -
228A ASP 3.8 2.9 - - - +
229A LEU* 3.7 12.1 - - + -
234A THR 3.5 24.5 - - - +
235A ASN 3.5 9.4 - - - +
236A LYS* 1.3 76.5 - - - +
238A LEU* 1.3 63.1 + - - +
239A THR* 4.2 7.6 - - + -
247A VAL 3.6 0.9 - - - +
248A VAL* 3.2 7.1 - - - +
249A PHE* 2.8 55.2 + - + +
251A LYS* 4.1 3.6 - - + -
272A PHE* 4.0 1.8 - - - -
499A LEU* 4.0 17.7 - - + -
501A PHE* 3.8 29.6 - - + -
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Residues in contact with LEU 238 (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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227A LEU* 3.4 2.8 - - - +
228A ASP* 2.9 36.5 + - + +
237A ILE* 1.3 74.4 - - - +
239A THR* 1.3 66.1 + - - +
246A VAL* 3.4 30.3 - - + -
247A VAL 3.2 9.2 - - - +
248A VAL* 4.0 9.4 - - + -
270A VAL* 3.6 13.9 - - + +
271A VAL 3.2 47.3 - - - +
272A PHE* 3.5 18.8 - - + +
279A VAL* 3.8 24.2 - - + -
280A PHE 4.0 1.3 - - - +
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Residues in contact with THR 239 (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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216A LEU* 3.8 20.3 - - + +
217A HIS* 2.7 29.5 + - - -
224A ILE* 3.7 16.4 - - + -
226A ALA 3.3 11.7 - - - +
237A ILE* 4.2 11.9 - - + -
238A LEU* 1.3 81.0 - - - +
240A GLY* 1.3 60.6 + - - +
246A VAL* 3.4 8.0 - - - +
247A VAL* 2.8 43.1 + - - +
270A VAL* 4.0 4.9 - - - -
493A THR* 4.1 13.5 - - + -
499A LEU* 4.9 1.1 - - + -
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Residues in contact with GLY 240 (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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217A HIS* 3.8 2.0 - - - -
224A ILE* 3.6 5.0 - - - +
225A LEU 2.8 25.8 + - - -
226A ALA* 3.0 12.3 + - - -
239A THR* 1.3 74.1 - - - +
241A GLY* 1.3 59.1 + - - -
245A ASN 3.8 1.8 - - - -
267A VAL* 3.7 33.0 - - - -
270A VAL* 3.8 6.5 - - - +
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Residues in contact with GLY 241 (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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217A HIS* 3.3 22.4 - - - -
223A GLY 3.6 7.2 - - - -
225A LEU* 4.2 3.4 - - - -
240A GLY* 1.3 74.4 - - - -
242A ALA* 1.3 66.4 + - - -
243A ASP* 3.0 3.8 - - - -
244A LYS* 3.1 6.9 + - - -
245A ASN 3.0 12.7 + - - -
267A VAL* 3.0 24.4 + - - +
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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