Contacts of the strand formed by residues 241 - 248 (chain A) in PDB entry 3LMK
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 SER 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A THR 3.0 16.6 + - - -
213A TYR* 3.4 9.7 - - - -
214A VAL 3.2 23.7 + - - +
239A GLY 4.0 3.0 + - - -
240A ILE* 1.3 76.8 - - - +
242A ILE* 1.3 64.6 + - - +
243A ALA 3.9 0.4 + - - -
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Residues in contact with ILE 242 (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 VAL* 3.4 31.6 - - + +
216A ALA* 3.8 17.7 - - + -
231A PHE* 4.0 16.6 - - + -
232A LYS* 4.7 16.6 - - + +
235A SER* 4.0 21.3 - - - +
236A ALA* 6.5 0.4 - - + -
240A ILE* 4.1 5.8 + - + +
241A SER* 1.3 76.7 - - - +
243A ALA* 1.3 71.4 + - - +
244A HIS* 3.8 23.7 - - - +
245A SER* 4.3 5.4 - - - +
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Residues in contact with ALA 243 (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 TYR* 5.6 3.9 - - + +
214A VAL 3.2 11.1 + - - +
215A SER* 4.3 15.3 - - - +
241A SER* 3.9 2.0 + - - -
242A ILE* 1.3 74.6 - - - +
244A HIS* 1.3 67.7 + - + +
267A HIS* 4.9 9.0 - - + +
271A ALA* 4.4 12.1 - - + -
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Residues in contact with HIS 244 (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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215A SER* 4.1 2.6 + - - +
216A ALA 3.3 23.0 + - - +
242A ILE* 3.4 6.9 - - - +
243A ALA* 1.3 83.0 + - + +
245A SER* 1.3 84.9 + - - +
246A TYR* 3.7 42.3 + + + +
263A LYS* 5.6 5.0 + - - -
267A HIS* 5.8 2.7 - - + -
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Residues in contact with SER 245 (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 ALA* 3.6 13.4 + - - -
218A HIS* 4.5 11.3 + - - -
228A MET* 4.7 2.9 - - - +
232A LYS* 4.4 23.2 - - - +
242A ILE* 4.3 4.2 - - - +
244A HIS* 1.3 91.0 - - - +
246A TYR* 1.3 67.4 + - - +
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Residues in contact with TYR 246 (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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215A SER* 5.0 2.7 - - - -
216A ALA 2.8 19.9 + - - +
217A VAL* 3.7 4.5 - - + -
218A HIS* 3.3 28.6 + - - -
244A HIS* 3.7 44.1 + + + +
245A SER* 1.3 78.8 + - - +
247A LYS* 1.3 68.5 + - - +
260A LEU* 3.6 24.9 - - + -
263A LYS* 3.5 62.5 + - + +
264A LEU* 4.0 30.3 - - + -
266A SER* 4.8 1.2 + - - -
267A HIS* 4.8 5.3 - - + +
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Residues in contact with LYS 247 (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 VAL* 5.1 0.9 - - - -
218A HIS* 3.1 37.2 - - + +
220A GLU* 3.5 35.1 + - + +
225A GLU* 6.0 3.1 - - + +
246A TYR* 1.3 81.4 - - - +
248A ILE* 1.3 66.2 + - - +
260A LEU* 4.9 4.6 - - - +
229B GLU* 5.1 13.1 - - - +
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Residues in contact with ILE 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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217A VAL* 4.8 2.0 - - + -
218A HIS 3.2 5.6 + - - +
219A THR* 3.3 7.1 - - - +
220A GLU* 2.7 33.1 + - - +
247A LYS* 1.3 77.4 - - - +
249A TYR* 1.3 69.4 + - - +
252A ALA* 3.7 12.6 - - + -
256A SER* 4.0 9.0 - - - +
257A PHE* 3.6 53.2 - - + +
260A LEU* 3.7 23.8 - - + -
282A THR* 4.0 24.9 - - + -
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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