Contacts of the helix formed by residues 329 - 340 (chain A) in PDB entry 3FPL
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 HIS 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A TYR* 3.6 32.4 - + + -
325A HIS 3.0 31.3 + - - -
326A GLY* 3.0 12.2 + - - +
328A ASP* 1.3 75.5 + - + +
330A ILE* 1.3 65.5 + - - +
331A GLU 3.1 2.0 - - - -
332A GLU* 3.2 32.0 + - + +
333A ALA* 2.9 24.4 + - - +
349A VAL* 4.0 3.6 - - + -
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Residues in contact with ILE 330 (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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4A PHE* 4.0 15.0 - - + -
14A TRP* 4.2 5.2 - - + -
31A PRO* 6.3 0.4 - - + -
34A VAL* 4.0 22.2 - - + -
36A PRO* 5.5 0.2 - - - +
119A VAL 5.2 0.2 - - - +
120A PHE* 3.5 55.1 - - + -
326A GLY 4.3 0.2 + - - -
327A PHE* 3.1 53.2 + - + +
329A HIS* 1.3 77.3 - - - +
331A GLU* 1.3 62.7 + - - +
333A ALA* 3.3 2.2 + - - +
334A LEU* 2.9 23.2 + - - +
349A VAL* 4.0 13.7 - - + +
351A LEU* 5.2 1.1 - - + -
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Residues in contact with GLU 331 (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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4A PHE* 3.5 41.2 - - + -
14A TRP* 3.1 22.6 + - + +
328A ASP 3.5 11.3 + - - +
329A HIS 3.1 0.8 - - - -
330A ILE* 1.3 81.5 - - - +
332A GLU* 1.3 65.6 + - - +
334A LEU* 3.2 2.1 + - - +
335A LEU* 3.2 37.2 + - + +
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Residues in contact with GLU 332 (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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324A TYR* 3.7 28.7 + - + +
328A ASP 4.6 0.4 + - - -
329A HIS* 3.2 36.6 + - - +
331A GLU* 1.3 80.0 - - - +
333A ALA* 1.3 64.6 + - - +
335A LEU* 3.4 9.8 + - - +
336A LEU* 3.1 23.8 + - + +
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Residues in contact with ALA 333 (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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36A PRO* 3.6 25.8 - - + +
120A PHE* 6.5 0.2 - - + -
324A TYR* 4.1 18.8 - - + -
329A HIS 2.9 17.2 + - - +
330A ILE* 3.5 5.4 - - - +
332A GLU* 1.3 77.0 - - - +
334A LEU* 1.3 63.2 + - - +
336A LEU* 3.1 23.8 + - - +
337A MET 3.5 2.6 + - - -
347A ALA* 4.6 2.7 - - + -
349A VAL* 3.7 21.3 - - + -
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 3.7 22.7 - - + -
12A LEU* 4.2 11.4 - - + -
36A PRO* 3.6 25.9 - - + +
37A CYS 4.2 5.8 - - - +
40A ASP* 4.2 18.2 - - + +
41A ILE* 3.9 21.9 - - + +
44A VAL* 5.8 0.7 - - + -
57A LEU* 3.7 29.6 - - + -
120A PHE* 4.6 11.0 - - + -
330A ILE 2.9 16.2 + - - +
331A GLU 3.8 3.1 - - - +
333A ALA* 1.3 75.5 - - - +
335A LEU* 1.3 60.0 + - + +
337A MET* 3.0 25.7 + - + +
338A LYS 3.3 4.0 + - - -
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Residues in contact with LEU 335 (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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4A PHE* 5.8 0.2 - - + -
12A LEU* 4.0 28.0 - - + -
41A ILE* 6.3 0.2 - - + -
45A PHE* 5.2 0.4 - - + -
331A GLU* 3.2 34.8 + - + +
332A GLU* 3.7 10.3 - - - +
334A LEU* 1.3 74.4 - - + +
336A LEU* 1.3 59.8 + - - +
338A LYS* 3.1 24.9 + - + +
339A ASP* 3.0 42.5 + - - +
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Residues in contact with LEU 336 (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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322A HIS* 3.7 29.2 - - + +
324A TYR* 3.3 28.5 - - + +
332A GLU* 3.1 15.4 + - + +
333A ALA 3.1 10.0 + - - +
335A LEU* 1.3 76.2 - - - +
337A MET* 1.3 57.1 + - - +
339A ASP* 4.6 3.4 - - + -
340A LYS* 2.8 28.6 + - - -
341A PRO* 3.5 29.0 - - + +
344A LEU* 3.7 16.2 - - + +
347A ALA* 4.1 17.9 - - + -
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Residues in contact with MET 337 (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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36A PRO* 3.7 50.5 - - + +
37A CYS* 4.2 6.1 - - - +
38A THR* 3.9 28.0 + - + +
41A ILE* 3.9 20.2 - - + +
177A PRO* 5.5 4.0 - - + -
333A ALA 4.6 1.3 - - - +
334A LEU* 3.0 12.0 + - + +
336A LEU* 1.3 78.1 - - - +
338A LYS* 1.3 61.2 + - - +
340A LYS* 3.5 17.0 - - - +
344A LEU* 3.7 25.4 - - + -
345A ILE 4.2 15.7 - - - +
346A LYS* 4.4 9.2 - - + +
347A ALA* 5.2 4.5 - - - -
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Residues in contact with LYS 338 (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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41A ILE* 3.8 30.8 - - + +
45A PHE* 3.7 43.9 - - + -
334A LEU 3.3 2.4 + - - -
335A LEU* 3.1 26.9 + - + +
337A MET* 1.3 83.2 - - - +
339A ASP* 1.3 71.4 + - - +
340A LYS* 3.5 16.1 - - - -
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Residues in contact with ASP 339 (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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335A LEU* 3.0 28.3 + - - +
336A LEU* 4.1 4.7 - - + +
338A LYS* 1.3 92.3 - - - +
340A LYS* 1.3 70.6 + - - +
341A PRO* 3.7 5.0 - - + +
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Residues in contact with LYS 340 (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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38A THR* 5.9 2.2 - - - -
41A ILE* 5.9 4.5 - - - -
200A ARG* 5.8 2.8 - - - -
336A LEU 2.8 17.2 + - - -
337A MET* 3.5 18.4 - - - +
338A LYS* 3.5 14.6 - - - +
339A ASP* 1.3 76.0 - - - +
341A PRO* 1.3 71.1 - - - +
342A LYS* 3.7 2.4 + - - +
344A LEU* 4.8 4.3 - - - -
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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