Contacts of the helix formed by residues 403 - 409 (chain F) in PDB entry 1FFT
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 VAL 403 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353F MET* 4.0 5.4 - - - -
399F VAL 4.8 3.4 - - - +
400F LEU* 3.2 6.7 + - - +
401F LEU 3.2 12.3 - - - +
402F ALA* 1.3 78.2 - - + +
404F PRO* 1.3 81.7 - - + +
405F GLY 4.2 2.5 - - - +
406F ALA* 3.3 19.9 + - + +
407F ASP 3.7 1.0 + - - -
45G LEU* 3.9 32.3 - - + -
103G LEU* 4.5 10.1 - - + +
106G LEU* 6.1 0.9 - - + -
107G THR* 3.5 38.8 - - + +
110G THR* 4.9 3.1 - - + -
111G THR* 4.4 2.0 - - - +
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Residues in contact with PRO 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336F PHE* 3.2 39.3 - - + -
345F ASN* 3.8 12.6 - - + +
346F ALA* 5.1 1.1 - - - +
349F GLY* 5.3 1.8 - - - -
402F ALA 3.6 4.0 - - - +
403F VAL* 1.3 91.4 - - + +
405F GLY* 1.3 61.1 + - - +
407F ASP* 3.2 11.4 + - - +
408F PHE* 2.9 21.7 + - + -
107G THR* 3.4 10.1 - - + -
111G THR* 3.0 47.1 - - + +
115G GLU* 5.0 1.1 - - - +
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Residues in contact with GLY 405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403F VAL* 3.6 3.6 - - - +
404F PRO* 1.3 74.4 - - - +
406F ALA* 1.3 55.2 + - - +
407F ASP 2.6 17.4 + - - -
408F PHE* 2.8 32.1 + - - +
409F VAL* 4.2 3.3 + - - +
42G SER* 4.1 18.0 + - - +
45G LEU* 4.2 9.6 - - - +
110G THR* 5.8 2.0 - - - +
111G THR* 5.5 3.0 - - - +
115G GLU* 5.7 0.6 + - - -
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Residues in contact with ALA 406 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400F LEU* 3.3 27.4 - - + +
401F LEU* 4.4 2.3 - - - +
403F VAL* 3.3 9.9 + - + +
405F GLY* 1.3 74.0 - - - +
407F ASP* 1.3 57.5 + - - +
409F VAL* 4.8 4.0 + - - +
410F LEU* 3.3 23.7 + - - +
42G SER 4.4 3.8 - - - +
45G LEU* 3.2 39.0 - - + +
46G THR* 3.6 17.5 - - + +
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Residues in contact with ASP 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333F HIS 5.3 1.6 - - - +
336F PHE* 5.1 14.9 - - + +
401F LEU* 3.8 39.3 - - + +
403F VAL 3.7 0.2 + - - -
404F PRO 3.2 8.6 + - - +
405F GLY 2.6 5.3 + - - -
406F ALA* 1.3 76.1 - - - +
408F PHE* 1.3 52.8 + - - +
409F VAL 2.6 8.4 + - - -
410F LEU* 2.6 32.2 + - - +
411F HIS* 2.7 62.8 + - - +
416F LEU* 5.9 0.2 - - - +
1002F HEO 3.8 9.2 - - + +
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Residues in contact with PHE 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336F PHE* 4.4 28.7 - + + -
337F THR* 5.2 9.4 - - - -
345F ASN* 4.8 4.7 - - - -
404F PRO* 2.9 43.5 - - + -
405F GLY* 2.8 19.3 + - - +
407F ASP* 1.3 77.0 - - - +
409F VAL* 1.3 56.9 + - + +
411F HIS* 5.0 1.3 - - - -
42G SER* 5.1 4.0 - - - +
114G LEU* 3.4 34.1 - - + -
115G GLU* 3.7 23.8 - - - -
175G PHE* 3.8 1.3 - - - -
180G GLY 5.1 4.7 - - - +
182G GLN* 2.4 57.0 + - + +
183G ILE* 5.4 6.3 - - + -
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Residues in contact with VAL 409 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405F GLY 4.3 12.1 - - - +
406F ALA 4.9 3.4 - - - +
407F ASP 2.6 4.8 + - - -
408F PHE* 1.3 79.5 - - + +
410F LEU* 1.3 66.1 + - + +
411F HIS 3.7 0.4 - - - -
413F SER* 4.2 7.3 + - - -
475F GLY 4.7 3.8 - - - +
476F PHE 5.7 1.6 - - - +
478F GLY* 5.2 1.7 - - - -
32G PRO* 4.7 6.5 - - + -
42G SER* 4.7 9.0 - - - +
43G LEU* 3.5 32.3 - - + -
46G THR* 6.6 0.2 - - + -
175G PHE* 3.2 44.4 - - + -
177G PRO* 3.8 10.1 - - + +
180G GLY* 3.4 24.7 - - - -
182G GLN* 4.4 0.9 + - - -
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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