Contacts of the strand formed by residues 249 - 256 (chain A) in PDB entry 4PIM
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 ARG 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A THR* 3.5 27.9 - - - +
169A PRO* 5.7 2.0 - - - +
243A TRP* 3.4 8.8 - - - -
244A ASN* 2.8 35.6 + - + +
247A GLU* 3.8 27.0 + - + +
248A GLU* 1.3 78.6 - - - +
250A ILE* 1.3 62.1 + - - +
251A GLU* 2.7 38.5 + - + +
280A LEU* 4.2 13.3 - - - +
283A VAL* 3.9 22.9 - - - +
284A SER 3.4 14.1 - - - +
285A CYS* 3.7 20.9 - - - -
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Residues in contact with ILE 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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202A LEU* 3.7 29.8 - - + +
203A VAL* 3.9 15.3 - - + +
206A TYR* 3.7 47.3 - - + -
241A ALA* 5.0 2.2 - - + -
242A LYS 3.3 13.7 - - - +
243A TRP* 3.7 21.2 - - + -
249A ARG* 1.3 73.3 - - - +
251A GLU* 1.3 72.2 + - - +
252A MSE 4.5 3.8 - - + -
282A GLU 5.7 0.2 - - - +
283A VAL* 3.3 5.1 - - - +
284A SER* 2.8 43.9 + - - +
286A LYS* 4.5 3.6 - - - -
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Residues in contact with GLU 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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241A ALA* 3.5 2.6 - - - -
242A LYS* 2.8 40.0 + - + +
244A ASN* 2.9 30.9 + - + +
249A ARG* 2.7 46.3 + - + +
250A ILE* 1.3 78.2 - - - +
252A MSE 1.3 63.7 + - - +
253A TRP* 3.4 38.6 + - - +
280A LEU* 3.9 6.5 - - + -
282A GLU 3.7 3.8 - - - -
283A VAL* 4.2 5.6 - - + -
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Residues in contact with MSE 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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206A TYR* 4.0 28.3 - - + -
213A THR* 4.0 14.1 - - + -
216A PHE* 4.0 29.2 - - + -
217A ASN* 3.9 25.6 - - - +
239A HIS* 3.9 16.2 - - + -
240A VAL 3.4 4.5 - - - +
241A ALA* 4.6 1.8 - - + -
250A ILE* 4.5 9.6 - - + -
251A GLU* 1.3 77.5 - - - +
253A TRP* 1.3 60.8 + - - +
280A LEU* 3.6 7.8 - - - +
281A THR* 2.9 33.6 + - - +
282A GLU* 2.8 30.4 + - + +
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Residues in contact with TRP 253 (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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30A GLN* 3.5 37.7 - - + -
217A ASN* 3.1 12.2 - - - +
238A GLU 3.6 0.5 - - - +
240A VAL* 2.8 43.5 + - + +
242A LYS* 3.8 29.9 - - + +
251A GLU* 3.4 45.2 + - - +
252A MSE 1.3 77.5 - - - +
254A LEU* 1.3 63.0 + - - +
278A GLU* 3.7 29.8 - - + +
279A MSE 3.2 9.0 - - - -
280A LEU* 3.5 39.7 - - + -
281A THR* 4.5 0.9 - - - -
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Residues in contact with LEU 254 (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 ASN* 3.5 50.3 - - + +
218A ARG* 4.1 22.9 - - + -
220A VAL* 3.9 8.3 - - + -
221A LEU* 3.9 30.7 - - + -
237A PHE* 4.2 20.8 - - + -
238A GLU 3.4 12.6 - - - +
239A HIS* 4.5 1.3 - - - -
253A TRP* 1.3 71.7 - - - +
255A ARG* 1.3 60.9 + - - +
256A ALA 4.1 0.3 + - - -
277A GLU 3.8 1.2 - - - +
278A GLU* 3.4 2.3 - - - -
279A MSE 2.9 43.6 + - + +
281A THR* 3.9 7.2 - - + -
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Residues in contact with ARG 255 (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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237A PHE* 3.3 4.6 - - - -
238A GLU* 2.8 61.4 + - + +
240A VAL* 4.1 14.1 - - + -
254A LEU* 1.3 73.6 - - - +
256A ALA* 1.3 69.3 + - - +
257A ARG* 3.3 1.5 + - - -
276A GLY* 3.1 42.8 + - - +
277A GLU 3.4 3.6 - - - -
278A GLU* 3.0 34.9 + - + -
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Residues in contact with ALA 256 (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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236A ALA 3.6 6.5 - - - +
237A PHE* 3.9 21.4 - - + -
255A ARG* 1.3 74.4 + - - +
257A ARG* 1.3 59.7 + - - +
258A THR 3.5 16.8 - - - +
260A GLN* 4.5 2.2 - - + -
273A PHE* 4.0 11.4 - - + -
274A ALA 3.7 16.8 - - - +
276A GLY* 2.8 31.0 + - - -
277A GLU 2.9 13.2 + - - +
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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