Contacts of the helix formed by residues 247 - 252 (chain A) in PDB entry 3LSG
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 THR 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A ILE* 4.8 11.0 - - + -
240A PHE* 3.8 1.6 - - - -
241A LYS* 4.0 17.9 - - + -
246A ILE* 1.3 75.0 - - - +
248A PRO* 1.3 70.8 - - + +
249A LYS* 3.6 7.8 + - - +
250A GLN* 2.9 46.2 + - - +
251A TYR* 2.8 28.1 + - - +
162E GLU* 3.7 25.6 - - - +
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Residues in contact with PRO 248 (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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214A LEU* 3.9 24.6 - - + +
221A ASN* 3.3 22.9 - - - +
236A PHE* 3.7 21.3 - - + -
237A ILE* 4.1 22.9 - - + +
240A PHE* 3.5 37.9 - - + -
247A THR* 1.3 88.0 - - - +
249A LYS* 1.3 63.8 + - - +
251A TYR* 3.1 14.7 + - - +
252A ARG* 3.3 5.7 + - - +
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Residues in contact with LYS 249 (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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221A ASN* 4.4 13.3 - - - +
247A THR* 3.3 7.9 + - - +
248A PRO* 1.3 77.9 - - - +
250A GLN* 1.3 65.4 + - + +
252A ARG* 3.0 40.4 + - - +
253A GLU* 3.5 29.5 + - - +
204E GLN* 5.6 6.7 - - - +
208E GLU* 4.9 12.6 - - - +
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Residues in contact with GLN 250 (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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241A LYS* 5.3 1.7 - - - -
246A ILE* 3.4 16.4 - - + +
247A THR* 2.9 47.3 + - - +
249A LYS* 1.3 78.2 - - + +
251A TYR* 1.3 58.7 + - - +
253A GLU* 2.9 40.1 + - - +
158E GLN* 3.0 59.9 + - - +
159E ASN* 5.0 1.9 - - - +
162E GLU* 3.3 22.7 + - - +
201E TYR* 4.2 3.9 + - - +
205E LYS* 3.5 15.0 - - + +
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Residues in contact with TYR 251 (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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211A LYS* 3.2 49.5 + - + +
214A LEU* 4.2 14.6 - - + -
215A LEU* 4.0 31.8 - - + +
240A PHE* 3.7 21.5 - + + -
244A TYR* 4.1 24.7 - + + -
246A ILE* 3.7 23.5 - - + +
247A THR 2.8 12.6 + - - +
248A PRO 3.2 12.1 - - - +
249A LYS 3.1 0.2 - - - -
250A GLN* 1.3 78.6 - - - +
252A ARG* 1.3 57.3 + - - +
253A GLU 3.5 4.7 + - - +
155E GLU* 5.6 2.7 - - - -
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Residues in contact with ARG 252 (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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213A LEU 3.9 3.0 + - - -
214A LEU* 3.1 51.2 + - + +
215A LEU* 5.3 4.7 - - + -
217A THR* 2.8 31.1 + - - -
218A GLU* 3.5 7.0 + - - -
219A LEU 2.7 37.2 + - - +
220A LYS* 4.6 2.8 - - - +
221A ASN* 4.5 7.5 + - - +
224A ILE* 4.1 2.2 - - - +
248A PRO 3.9 7.9 - - - +
249A LYS* 3.0 32.3 + - - +
251A TYR* 1.3 77.4 - - - +
253A GLU* 1.3 61.8 + - - +
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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