Contacts of the strand formed by residues 237 - 246 (chain D) 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 237 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C ARG* 2.9 31.3 + - - +
31C TYR* 2.8 29.0 + - - +
33C SER* 3.0 21.5 + - - +
235D THR* 3.4 0.6 - - - +
236D ILE* 1.3 85.9 - - - +
238D ASP* 1.3 69.4 + - - +
256D LEU* 3.8 29.7 - - + +
257D ASP 3.5 8.3 - - - +
258D THR* 4.8 4.3 - - + +
267D MET* 3.6 19.8 - - + +
271D TYR* 5.4 5.6 - - + +
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Residues in contact with ASP 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C TYR* 3.8 7.4 - - - +
32C LYS* 3.2 38.7 + - - +
33C SER 3.3 4.0 + - - -
52C LYS* 4.3 10.4 - - - -
217D SER* 4.5 1.2 + - - -
235D THR* 3.6 20.9 + - - +
237D GLU* 1.3 81.9 + - - +
239D SER* 1.3 59.4 + - - +
240D TYR* 3.7 19.9 + - + -
256D LEU* 3.5 7.4 - - - +
257D ASP* 2.7 53.1 + - + +
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Residues in contact with SER 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASN* 3.1 8.1 - - - +
30C MET* 2.7 40.8 + - - +
31C TYR* 3.1 45.8 + - - -
238D ASP* 1.3 74.9 - - - +
240D TYR* 1.3 61.4 + - - +
254D ASP* 5.9 1.0 - - - +
255D ILE 3.4 7.3 + - - -
256D LEU* 4.3 7.4 - - - +
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Residues in contact with TYR 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLY 3.2 9.0 - - - +
29C ASN* 3.4 35.7 - - + -
30C MET* 4.0 3.8 - - - +
32C LYS* 3.2 25.9 - - - -
217D SER* 5.6 0.2 - - - -
220D THR* 3.6 24.9 - - + -
221D ILE* 3.6 29.9 - - + +
224D ILE* 3.8 28.5 - - + -
225D GLN* 4.3 11.9 - - - -
238D ASP* 3.7 25.8 + - + -
239D SER* 1.3 82.7 + - - +
241D ARG* 1.3 63.2 + - - +
254D ASP* 3.7 3.3 - - - -
255D ILE* 2.8 36.5 + - + +
257D ASP* 4.1 9.8 + - + -
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Residues in contact with ARG 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLY* 2.6 31.8 + - - +
30C MET* 3.9 40.3 - - - +
224D ILE* 4.1 4.0 - - - +
240D TYR* 1.3 75.1 - - - +
242D LYS* 1.3 64.9 + - - +
252D LEU* 3.6 32.4 - - + +
253D LEU 3.1 14.1 - - - +
254D ASP* 3.7 20.2 - - - +
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Residues in contact with LYS 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D LEU* 3.3 31.9 + - + +
224D ILE* 3.6 30.7 - - + +
241D ARG* 1.3 78.9 - - - +
243D GLN* 1.3 67.3 + - - +
244D VAL* 3.5 23.4 + - + +
252D LEU* 4.8 2.9 - - - -
253D LEU* 2.8 45.2 + - + +
349D ARG* 5.1 2.6 - - - +
353D GLU* 4.9 4.4 + - - -
357D TYR* 3.2 21.5 + - - +
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Residues in contact with GLN 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D MET* 3.5 32.7 - - - +
242D LYS* 1.3 75.9 - - - +
244D VAL* 1.3 64.6 + - - +
250D THR* 5.0 9.8 - - - +
251D CYS 3.1 15.5 - - - +
252D LEU* 4.7 7.1 - - + +
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Residues in contact with VAL 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D LYS* 3.5 39.9 + - + +
243D GLN* 1.3 81.0 - - - +
245D VAL* 1.3 74.5 + - - +
246D ILE* 3.9 11.9 - - + -
250D THR* 4.3 1.1 - - - -
251D CYS* 2.6 44.8 + - - +
253D LEU* 4.2 11.0 - - + -
357D TYR* 3.7 30.7 - - + +
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Residues in contact with VAL 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D VAL* 1.3 80.4 - - - +
246D ILE* 1.3 65.7 + - - +
247D ASP 4.2 0.6 + - - -
248D GLY* 3.6 33.7 - - - +
249D GLU 3.4 4.5 - - - +
250D THR* 3.7 24.7 - - + -
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Residues in contact with ILE 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D VAL* 3.6 12.3 + - + -
245D VAL* 1.3 78.4 - - - +
247D ASP* 1.3 81.8 + - - +
248D GLY 3.3 0.7 + - - -
249D GLU* 2.8 15.6 + - - +
251D CYS* 4.0 11.9 - - + -
253D LEU* 4.2 9.2 - - + -
357D TYR* 3.8 48.2 - - + +
360D VAL* 3.9 28.5 - - + -
361D ARG* 4.9 6.1 - - + +
364D ARG* 2.9 37.5 + - - +
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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