Contacts of the strand formed by residues 203 - 210 (chain B) in PDB entry 1LFD
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 GLU 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B MET 3.6 2.3 + - - +
202B THR* 1.3 85.1 - - - +
204B TYR* 1.3 67.7 + - - +
205B LYS* 4.0 18.0 + - + +
241B ARG* 3.1 20.6 + - - -
252B LEU* 3.3 31.1 - - + +
254B ASP* 3.1 28.0 - - - +
276B GLU* 3.8 9.9 - - - +
367B LYS* 5.3 2.3 - - - -
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Residues in contact with TYR 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B THR* 3.9 25.0 - - + +
203B GLU* 1.3 77.0 - - - +
205B LYS* 1.3 59.4 + - - +
206B LEU* 3.5 18.6 - - + +
249B GLU* 5.3 0.9 + - - -
251B CYS* 3.6 39.3 - - + -
252B LEU 2.7 8.7 + - - -
253B LEU* 3.9 8.1 - - + -
254B ASP* 2.7 34.1 + - - +
276B GLU* 3.8 2.0 - - - -
360B VAL* 3.7 33.8 - - + +
363B ILE* 3.8 30.7 - - + -
364B ARG* 3.6 33.7 + - + +
367B LYS* 4.4 8.3 + - - -
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Residues in contact with LYS 205 (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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203B GLU* 4.0 21.9 + - + +
204B TYR* 1.3 73.4 - - - +
206B LEU* 1.3 61.6 + - - +
207B VAL* 4.9 1.6 - - + -
254B ASP* 3.5 14.6 - - + +
274B THR* 3.3 31.2 - - - +
275B GLY* 4.0 3.4 - - - -
276B GLU* 3.0 60.2 + - + +
277B GLY 3.3 7.1 + - - -
363B ILE* 4.8 1.3 - - - +
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Residues in contact with LEU 206 (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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204B TYR* 3.5 34.8 - - + +
205B LYS* 1.3 75.4 - - - +
207B VAL* 1.3 63.6 + - - +
208B VAL* 4.3 0.4 - - + -
253B LEU* 4.0 15.7 - - + -
254B ASP 2.7 16.5 + - - +
255B ILE* 3.4 12.5 - - + -
256B LEU* 2.8 25.8 + - - +
277B GLY 3.4 4.7 - - - -
279B LEU* 6.3 0.2 - - + -
356B PHE* 3.7 47.8 - - + +
359B LEU* 3.9 22.0 - - + -
360B VAL* 4.1 8.5 - - + -
363B ILE* 4.3 6.3 - - + -
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Residues in contact with VAL 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LYS* 4.6 1.1 - - + +
206B LEU* 1.3 81.2 - - - +
208B VAL* 1.3 59.2 + - - +
209B VAL* 3.7 7.8 + - + -
256B LEU* 3.5 16.8 - - + +
258B THR* 3.6 27.8 - - + -
271B TYR* 3.7 24.7 - - + +
275B GLY* 3.7 29.4 - - - -
277B GLY 2.8 9.4 + - - +
278B PHE* 3.2 19.5 - - + +
279B LEU* 2.7 32.2 + - - -
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Residues in contact with VAL 208 (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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206B LEU* 5.4 0.4 - - + -
207B VAL* 1.3 72.1 - - - +
209B VAL* 1.3 61.2 + - - +
216B LYS* 3.5 36.7 - - + +
219B LEU* 5.3 0.9 - - + -
220B THR* 3.5 20.0 - - - +
255B ILE* 3.7 20.2 - - + -
256B LEU 3.0 9.6 + - - +
257B ASP* 4.6 4.9 - - - +
258B THR* 2.8 24.6 + - - -
279B LEU* 3.6 13.0 - - + +
281B VAL* 3.8 21.8 - - + -
356B PHE* 3.9 16.8 - - + -
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Residues in contact with VAL 209 (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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207B VAL* 3.8 10.1 - - + +
208B VAL* 1.3 78.5 - - - +
210B GLY* 1.3 58.9 + - - +
216B LYS* 3.5 7.2 - - - -
258B THR* 3.8 2.7 - - - +
271B TYR* 3.7 36.3 - - + +
272B MET* 5.2 0.2 - - + -
278B PHE* 4.2 10.3 - - + -
279B LEU 2.9 16.5 + - - +
280B CYS* 3.8 25.4 - - + -
281B VAL* 2.8 31.2 + - - +
296B TYR* 3.8 22.4 - - + -
300B ILE* 4.4 8.7 - - + -
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Residues in contact with GLY 210 (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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209B VAL* 1.3 79.3 - - - +
211B ALA* 1.3 63.3 + - - -
214B VAL* 4.5 0.2 - - - -
216B LYS* 2.8 21.6 + - - +
258B THR* 4.9 0.6 + - - -
259B ALA 4.5 0.2 - - - +
260B GLY* 3.3 10.6 - - - -
281B VAL 3.4 15.0 - - - -
293B ILE* 4.2 2.2 - - - -
296B TYR* 3.4 25.6 + - - -
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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