Contacts of the strand formed by residues 211 - 215 (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 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B THR* 4.0 9.2 - - + -
182B LEU* 3.8 45.1 - - + -
198B PHE* 3.8 30.7 - + + -
210B LEU* 1.3 81.0 - - - +
212B SER* 1.3 63.3 + - - +
213B LEU* 4.1 13.7 - - + -
235B MET* 4.9 6.1 - - + -
236B ILE 3.2 14.4 - - - +
237B ILE* 4.3 7.9 - - + -
260B TYR* 3.4 22.2 - + - -
405B VAL 3.8 0.2 - - - -
406B PHE* 2.8 67.5 + + + +
408B ARG* 4.1 8.3 - - - -
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Residues in contact with SER 212 (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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211B PHE* 1.3 77.1 - - - +
213B LEU* 1.3 64.0 + - - +
234B SER 3.7 0.9 - - - +
235B MET* 3.3 5.4 - - - +
236B ILE* 2.9 34.8 + - - +
239B GLY 2.9 17.0 + - - -
240B ILE* 4.9 0.4 - - - -
403B TYR* 2.6 35.8 + - - -
404B VAL 3.2 11.9 - - - -
405B VAL* 4.0 14.6 - - - -
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Residues in contact with LEU 213 (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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67B LEU* 4.3 8.5 - - + -
92B VAL* 3.9 22.9 - - + -
94B THR* 3.6 30.7 - - + -
211B PHE* 4.1 9.0 - - + -
212B SER* 1.3 74.9 - - - +
214B GLN* 1.3 60.1 + - - +
215B LEU* 3.9 9.3 + - + +
234B SER 3.5 2.5 - - - +
235B MET* 3.6 38.6 - - + -
290B SER* 4.4 4.9 - - - +
399B MET* 3.9 20.4 - - + +
402B PHE 3.9 2.8 - - - +
403B TYR* 3.4 5.4 - - - -
404B VAL* 2.8 37.4 + - - +
406B PHE* 3.8 10.3 - - + -
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Residues in contact with GLN 214 (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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65B ASP* 4.8 3.5 - - - +
213B LEU* 1.3 73.2 - - - +
215B LEU* 1.3 62.0 + - - +
216B CYS* 3.6 16.4 - - - -
233B GLY* 3.1 7.4 - - - -
234B SER* 2.8 47.9 + - - +
243B SER 5.2 0.2 + - - -
244B LEU* 3.3 56.2 + - + +
402B PHE 4.5 3.1 - - - -
403B TYR* 3.9 14.1 - - + -
418B SER* 3.7 10.1 + - - +
419B ALA* 4.2 3.8 - - - +
420B CYS* 3.7 30.5 - - - +
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.7 27.4 - - + -
75B TYR* 3.9 39.7 - - + -
92B VAL* 5.9 1.8 - - + -
213B LEU* 3.9 19.8 + - + -
214B GLN* 1.3 72.8 - - - +
216B CYS* 1.3 60.8 + - - +
217B GLY 4.0 0.4 - - - -
232B GLY 3.9 2.0 - - - -
290B SER* 4.2 23.3 - - - +
396B ALA* 4.4 10.5 - - + -
399B MET* 4.0 25.9 + - + +
400B GLU* 3.3 36.1 - - + +
402B PHE 4.6 4.7 + - - +
418B SER* 4.9 0.5 + - - -
420B CYS* 3.9 3.5 - - - -
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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