Contacts of the helix formed by residues 343 - 354 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ALA* 4.1 9.6 - - + -
85A ALA* 3.5 35.4 - - + +
86A LEU* 4.6 0.9 - - - +
89A GLY* 3.7 6.6 - - - -
90A ARG 3.4 4.7 - - - +
91A LEU* 3.4 56.1 - - + -
341A SER* 3.0 23.0 - - - +
342A ILE* 1.3 75.3 - - - +
344A ASP* 1.3 61.6 + - - +
345A LEU 3.1 0.4 - - - -
346A PHE* 3.2 20.4 + - - +
347A THR 3.8 0.3 + - - -
364A ASP* 3.7 18.4 - - + +
365A GLY* 3.3 21.9 - - - -
380A ARG* 5.5 1.1 - - - +
383A PHE 6.0 0.4 - - - +
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Residues in contact with ASP 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A PHE* 5.3 0.2 - - + -
340A GLY* 3.7 0.2 - - - -
341A SER* 2.8 25.4 + - - +
343A MET* 1.3 73.6 - - - +
345A LEU* 1.3 57.9 + - - +
346A PHE 3.2 0.2 - - - -
347A THR 3.3 0.7 + - - -
348A THR* 2.7 37.7 + - - -
365A GLY* 3.3 1.4 - - - -
366A LEU* 2.6 42.8 + - - +
368A LEU* 3.6 28.9 - - + +
380A ARG* 2.7 41.0 + - - -
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Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 4.4 25.4 - - + -
72A PHE* 4.5 4.0 - - + -
86A LEU* 4.2 17.9 - - + -
124A LEU* 4.4 2.9 - - - +
282A PHE* 5.6 3.1 - - + -
284A PHE* 3.6 46.7 - - + +
286A THR* 3.9 28.0 - - + -
341A SER 4.5 0.7 - - - +
342A ILE* 3.4 21.8 - - + +
343A MET 3.1 0.6 - - - -
344A ASP* 1.3 76.2 - - - +
346A PHE* 1.3 61.4 + - - +
348A THR* 4.5 5.6 - - + -
349A SER* 2.6 32.6 + - - -
368A LEU* 5.0 5.4 - - + -
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Residues in contact with PHE 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU 3.4 16.7 + - - +
87A LEU 3.4 20.6 - - - -
88A THR 3.5 16.2 - - - -
89A GLY* 3.4 14.8 - - - -
122A GLN 3.6 20.6 - - - -
124A LEU* 3.7 27.5 - - + +
127A LEU* 3.5 26.5 - - + -
343A MET 3.2 13.2 + - - +
345A LEU* 1.3 79.7 - - - +
347A THR* 1.3 73.6 + - - +
350A LEU* 3.2 41.1 + - + +
357A PRO* 4.3 4.3 - - + -
358A PRO* 3.9 17.5 - - + -
363A ILE* 4.2 7.6 - - + -
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Residues in contact with THR 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A MET 3.8 0.6 + - - -
344A ASP 3.3 1.6 + - - -
346A PHE* 1.3 81.1 - - - +
348A THR* 1.3 60.1 + - - +
350A LEU* 3.5 6.7 + - - +
351A ALA* 3.1 26.2 + - - +
357A PRO* 4.3 24.2 - - + +
363A ILE* 3.4 15.2 - - + +
365A GLY* 2.7 35.9 + - - +
366A LEU* 3.8 3.6 - - - -
367A ASN* 3.6 23.8 - - + +
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Residues in contact with THR 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A PHE* 4.7 6.5 - - + -
344A ASP 2.7 25.0 + - - -
345A LEU* 4.3 6.7 - - + -
347A THR* 1.3 74.9 - - - +
349A SER* 1.3 57.6 + - - +
351A ALA* 3.1 3.8 + - - +
352A LEU* 2.9 37.0 + - + +
366A LEU 3.3 1.2 + - - -
367A ASN* 4.2 7.9 - - - -
368A LEU* 2.9 31.2 + - + +
369A LEU* 3.9 15.5 - - + -
372A LEU* 3.8 27.8 - - + -
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Residues in contact with SER 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 3.5 44.6 - - - +
35A LEU* 4.4 7.3 - - - +
124A LEU* 3.7 27.9 - - - +
128A LEU* 3.9 2.4 - - - +
282A PHE* 5.7 1.7 - - - -
345A LEU* 2.6 25.0 + - - -
348A THR* 1.3 76.0 - - - +
350A LEU* 1.3 62.5 + - - +
352A LEU* 3.4 6.1 + - - +
353A ALA* 3.1 19.2 + - - +
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Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 3.7 17.9 - - + -
127A LEU* 3.8 28.7 - - + -
128A LEU* 4.1 4.7 - - + -
346A PHE* 3.2 49.4 + - + +
347A THR* 3.7 7.9 - - - +
349A SER* 1.3 75.3 - - - +
351A ALA* 1.3 56.8 + - - +
353A ALA* 3.1 6.1 + - - +
354A GLY 3.1 3.8 + - - -
355A LEU* 2.7 58.9 + - + +
356A THR 4.2 4.3 - - - +
357A PRO* 3.7 26.2 - - + -
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Residues in contact with ALA 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A THR 3.1 12.6 + - - +
348A THR 3.1 8.5 + - - +
350A LEU* 1.3 73.6 - - - +
352A LEU* 1.3 63.8 + - - +
354A GLY* 3.0 14.2 + - - -
355A LEU 3.8 8.9 + - - +
357A PRO* 6.2 0.2 - - - +
367A ASN* 3.5 34.8 - - + +
369A LEU* 3.9 12.5 - - + +
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PRO* 4.2 1.4 - - - +
31A PRO* 3.3 33.8 - - + +
33A ILE* 4.3 11.7 - - + -
133A TYR* 4.5 0.4 - - - -
282A PHE* 3.5 40.8 - - + -
326A TRP* 3.4 41.5 - - + -
348A THR* 2.9 24.7 + - + +
349A SER* 3.6 13.9 - - - +
351A ALA* 1.3 76.4 - - - +
353A ALA* 1.3 60.1 + - - +
354A GLY 3.4 0.5 + - - -
369A LEU* 3.7 21.7 - - + +
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Residues in contact with ALA 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PRO* 4.2 9.0 - - - +
128A LEU* 3.6 23.6 - - + -
131A ALA* 3.6 16.9 - - + +
133A TYR* 3.8 22.6 + - + +
349A SER 3.1 13.5 + - - +
350A LEU 3.1 11.0 + - - +
352A LEU* 1.3 76.3 - - - +
354A GLY* 1.3 58.8 + - - +
355A LEU* 3.9 12.9 - - + +
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Residues in contact with GLY 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A ALA 3.0 14.8 + - - -
352A LEU 3.2 2.0 + - - -
353A ALA* 1.3 78.9 - - - +
355A LEU* 1.3 65.7 + - - +
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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