Contacts of the helix formed by residues 343 - 353 (chain B) in PDB entry 4FDI
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 MET 343 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B ALA* 4.1 9.9 - - + -
85B ALA* 3.4 37.2 - - + +
86B LEU* 4.6 0.2 - - - +
89B GLY* 3.7 2.5 - - - -
90B ARG 3.5 4.5 - - - +
91B LEU* 3.4 56.3 - - + -
341B SER* 2.9 26.5 + - - +
342B ILE* 1.3 78.6 - - - +
344B ASP* 1.3 60.3 + - - +
346B PHE* 3.1 22.5 + - - +
364B ASP* 3.6 18.2 - - + +
365B GLY* 3.3 21.9 - - - +
380B ARG* 5.6 1.1 - - - +
383B PHE 5.9 0.7 - - - +
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Residues in contact with ASP 344 (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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340B GLY* 3.7 0.5 - - - -
341B SER* 2.8 29.7 + - - +
343B MET* 1.3 71.2 - - - +
345B LEU* 1.3 55.4 + - - +
347B THR 3.3 1.1 + - - -
348B THR* 2.8 37.8 + - - -
365B GLY* 3.4 1.2 - - - -
366B LEU* 2.6 43.7 + - - +
368B LEU* 3.6 29.5 - - + +
380B ARG* 2.7 39.5 + - - -
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Residues in contact with LEU 345 (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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35B LEU* 4.3 26.2 - - + -
72B PHE* 4.6 4.5 - - + -
86B LEU* 4.3 14.1 - - + -
124B LEU* 4.2 3.0 - - - +
282B PHE* 5.3 4.3 - - + -
284B PHE* 3.5 52.9 - - + -
286B THR* 4.0 20.2 - - + -
341B SER 4.7 0.2 - - - +
342B ILE* 3.5 25.6 - - + +
343B MET 3.1 1.0 - - - -
344B ASP* 1.3 75.3 - - - +
346B PHE* 1.3 60.9 + - - +
348B THR* 4.4 6.3 - - + -
349B SER* 2.7 34.7 + - - -
368B LEU* 5.1 5.4 - - + -
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Residues in contact with PHE 346 (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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86B LEU 3.4 16.0 + - - +
87B LEU 3.5 26.2 - - - -
88B THR 3.5 16.6 - - - -
89B GLY* 3.4 17.0 - - - -
122B GLN 3.8 8.5 - - - -
124B LEU* 3.6 31.1 - - + +
127B LEU* 3.6 25.4 - - + -
343B MET 3.1 12.9 + - - +
345B LEU* 1.3 78.8 - - - +
347B THR* 1.3 67.3 + - - +
350B LEU* 3.1 47.2 + - + +
357B PRO* 4.3 2.0 - - + -
358B PRO* 3.8 17.3 - - + -
363B ILE* 4.2 11.9 - - + -
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Residues in contact with THR 347 (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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344B ASP 3.3 2.6 + - - -
346B PHE* 1.3 78.7 - - - +
348B THR* 1.3 60.4 + - - +
350B LEU* 3.3 8.2 + - - +
351B ALA* 2.9 27.3 + - - +
355B LEU 5.1 0.2 - - - +
357B PRO* 4.2 23.3 - - + +
363B ILE* 3.6 13.5 - - - +
365B GLY* 2.6 37.7 + - - +
366B LEU* 3.7 3.4 - - - -
367B ASN* 3.5 27.4 - - + +
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Residues in contact with THR 348 (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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282B PHE* 4.5 12.3 - - + -
344B ASP 2.8 25.0 + - - -
345B LEU* 4.4 6.7 - - + -
347B THR* 1.3 74.5 - - - +
349B SER* 1.3 59.1 + - - +
351B ALA* 3.2 3.8 + - - +
352B LEU* 2.9 30.1 + - + +
366B LEU 3.2 1.6 + - - -
367B ASN* 4.1 8.1 - - - -
368B LEU* 2.8 30.5 + - + +
369B LEU* 3.9 16.8 - - + +
372B LEU* 3.8 28.0 - - + -
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Residues in contact with SER 349 (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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33B ILE* 3.6 40.3 - - - +
35B LEU* 4.3 6.8 - - - +
124B LEU* 3.7 22.5 - - - +
128B LEU* 4.0 2.4 - - - +
282B PHE* 5.5 2.1 - - - -
345B LEU* 2.7 25.9 + - - -
346B PHE 3.7 3.1 - - - -
348B THR* 1.3 73.3 - - - +
350B LEU* 1.3 66.3 + - - +
352B LEU* 3.3 10.8 + - - +
353B ALA* 3.2 18.5 + - - +
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Residues in contact with LEU 350 (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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124B LEU* 3.9 14.1 - - + -
127B LEU* 3.8 30.3 - - + -
128B LEU* 4.0 13.0 - - + -
346B PHE* 3.1 43.1 + - + +
347B THR* 3.6 7.4 - - - +
348B THR 3.3 0.2 - - - -
349B SER* 1.3 76.2 - - - +
351B ALA* 1.3 57.2 + - - +
353B ALA* 3.1 3.5 + - - -
354B GLY 3.1 5.0 + - - -
355B LEU* 2.7 55.7 + - + +
356B THR 4.2 3.8 - - - +
357B PRO* 3.7 31.2 - - + -
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Residues in contact with ALA 351 (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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347B THR* 2.9 14.9 + - + +
348B THR 3.5 8.1 - - - +
350B LEU* 1.3 75.1 - - - +
352B LEU* 1.3 58.1 + - - +
354B GLY* 3.0 18.5 + - - +
355B LEU 3.5 9.8 + - - +
367B ASN* 3.5 33.7 - - + +
369B LEU* 3.9 12.7 - - + +
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Residues in contact with LEU 352 (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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30B PRO* 4.4 0.7 - - - +
31B PRO* 3.5 31.8 - - + +
33B ILE* 4.1 13.7 - - + -
133B TYR* 4.4 0.2 - - - -
282B PHE* 3.5 41.7 - - + -
326B TRP* 3.5 40.2 - - + -
348B THR* 2.9 20.1 + - + +
349B SER* 3.4 16.6 - - - +
350B LEU 3.2 0.2 - - - -
351B ALA* 1.3 77.2 - - - +
353B ALA* 1.3 57.1 + - - +
354B GLY* 3.1 3.5 + - - -
369B LEU* 3.7 20.2 - - + +
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Residues in contact with ALA 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PRO* 4.2 9.9 - - - +
128B LEU* 3.8 19.3 - - + -
131B ALA* 4.1 9.9 - - + +
133B TYR* 3.5 34.7 + - + +
349B SER 3.2 2.0 + - - +
350B LEU 3.1 9.2 + - - +
352B LEU* 1.3 76.2 - - - +
354B GLY* 1.3 60.8 + - - +
355B LEU* 3.7 17.1 + - + +
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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