Contacts of the strand formed by residues 402 - 407 (chain B) in PDB entry 3LPJ
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 PHE 402 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B LEU 3.9 5.0 - - - +
214B GLN* 4.5 4.3 - - - -
215B LEU 4.6 0.7 + - - -
359B ILE* 3.8 23.8 - - + -
360B THR 3.5 24.0 - - - -
361B ILE* 4.1 14.6 - - + -
365B GLN* 5.9 0.4 - - + -
398B ILE* 3.2 26.2 - - + -
399B MET* 2.8 21.3 + - - +
400B GLU 3.3 1.0 + - - -
401B GLY* 1.3 90.8 - - - +
403B TYR* 1.3 66.6 + - - +
404B VAL* 3.7 14.0 + - + +
415B PHE* 4.3 16.4 - + + -
416B ALA 3.2 10.8 - - - +
417B VAL* 4.3 1.1 - - - -
418B SER* 3.6 11.1 + - - -
429B ALA* 4.3 7.4 - - + -
430B ALA 3.5 22.4 - - - -
431B VAL* 3.5 22.9 - - + -
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Residues in contact with TYR 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B SER* 2.6 37.7 + - - -
213B LEU 3.4 22.4 - - - -
214B GLN* 3.9 9.9 - - + +
236B ILE* 3.8 6.1 - - - +
240B ILE* 3.6 14.7 - - + -
241B ASP 3.0 26.6 + - - -
244B LEU* 3.6 30.2 - - + +
245B TYR* 3.2 51.6 - + + -
249B LEU* 4.4 3.7 - - + +
402B PHE* 1.3 72.4 - - - +
404B VAL* 1.3 60.1 + - - +
405B VAL* 4.1 10.0 + - + -
414B GLY 3.6 0.9 - - - +
415B PHE* 3.5 5.0 - - - -
416B ALA* 2.8 27.9 + - + +
418B SER* 3.9 2.9 - - - -
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Residues in contact with VAL 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B SER* 3.2 2.5 - - - -
213B LEU 2.8 40.0 + - - +
288B VAL* 4.5 4.5 - - + -
399B MET* 4.3 25.1 - - + +
402B PHE* 3.9 17.3 - - + +
403B TYR* 1.3 77.4 - - - +
405B VAL* 1.3 63.6 + - - +
406B PHE* 3.5 30.5 - - + -
413B ILE* 3.6 23.6 - - + -
414B GLY 3.3 3.8 - - - +
415B PHE* 4.2 21.3 - - + -
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Residues in contact with VAL 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 3.9 31.0 - - + -
211B PHE 4.0 2.7 - - - +
212B SER* 4.0 11.7 - - - -
240B ILE* 3.9 24.2 - - + -
249B LEU* 3.8 29.4 - - + -
251B TYR* 4.3 4.9 - - + +
403B TYR* 4.3 9.2 - - + -
404B VAL* 1.3 75.1 - - - +
406B PHE* 1.3 62.1 + - - +
407B ASP* 3.2 10.2 + - + +
413B ILE* 3.2 9.9 - - - +
414B GLY* 2.8 42.2 + - - +
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Residues in contact with PHE 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B THR* 3.7 17.7 - - + -
210B LEU* 3.5 3.0 - - - -
211B PHE* 2.8 63.9 + + + +
213B LEU* 3.8 18.2 - - + -
254B ILE* 5.6 0.4 - - - -
260B TYR* 3.6 50.7 - + + -
288B VAL* 3.8 22.2 - - + -
399B MET* 3.9 4.5 - - + -
404B VAL* 3.5 39.3 - - + -
405B VAL* 1.3 69.2 - - - +
407B ASP* 1.3 58.8 + - - +
408B ARG* 3.0 12.6 + - - +
412B ARG 4.3 2.5 - - - -
413B ILE* 4.6 8.3 - - + -
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Residues in contact with ASP 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B LEU* 3.6 28.5 - - + +
251B TYR* 4.4 3.8 + - + -
254B ILE* 4.9 1.1 - - - -
405B VAL* 3.2 8.6 + - + -
406B PHE* 1.3 68.9 - - - +
408B ARG* 1.3 61.7 + - - +
409B ALA* 3.5 10.4 + - - +
410B ARG* 3.1 29.1 + - - +
411B LYS 3.0 17.5 + - - -
412B ARG* 2.9 61.0 + - + +
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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
------------------------------------------------------------
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