Contacts of the helix formed by residues 359 - 364 (chain A) in PDB entry 3FFN
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 THR 359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A VAL* 4.4 9.0 - - + -
119A HIS* 5.7 3.4 - - + -
316A PHE* 4.3 6.2 - - - -
353A LEU* 4.0 23.1 - - + +
358A GLU* 1.3 73.0 - - - +
360A PRO* 1.4 68.2 - - - +
361A LEU* 4.0 17.6 - - + +
362A PHE* 2.9 34.5 + - - +
363A LYS* 3.1 14.0 + - - +
382A TYR* 3.7 36.6 - - + +
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Residues in contact with PRO 360 (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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358A GLU 4.2 0.4 - - - +
359A THR* 1.4 84.7 - - - +
361A LEU* 1.3 63.6 + - + +
363A LYS* 3.3 17.0 + - - +
364A GLN* 3.1 33.0 + - - +
382A TYR* 3.5 26.9 - - + +
384A SER* 3.6 22.9 - - - +
636A ASP 4.4 6.3 - - - +
637A ALA* 3.4 23.6 - - - +
639A PRO* 4.1 13.2 - - + -
641A ARG* 4.2 9.2 - - - +
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Residues in contact with LEU 361 (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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129A THR* 5.7 4.9 - - - +
314A LYS* 5.6 11.7 - - + -
316A PHE* 4.6 12.8 - - + -
359A THR* 3.2 22.3 - - + +
360A PRO* 1.3 79.5 - - + +
362A PHE* 1.3 62.6 + - - +
364A GLN* 3.7 15.5 + - - +
365A PHE* 3.2 23.4 - - + -
382A TYR* 6.0 1.3 - - + -
384A SER* 5.4 1.6 - - - +
641A ARG* 3.6 36.1 - - - +
656A GLU* 5.2 9.0 - - - +
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Residues in contact with PHE 362 (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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273A LEU* 5.6 0.9 - - + -
299A LEU* 3.9 10.3 - - + -
307A LEU* 4.0 22.4 - - + -
316A PHE* 3.8 33.3 - + + -
318A TRP* 3.5 39.9 - + + -
353A LEU* 3.5 27.1 - - + -
358A GLU* 3.7 20.2 - - + -
359A THR* 2.9 16.3 + - - +
361A LEU* 1.3 79.5 - - - +
363A LYS* 1.3 67.0 + - - +
365A PHE* 3.1 26.3 + - - +
366A PHE* 3.6 32.1 - + - -
369A TRP* 4.1 2.9 - + - -
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Residues in contact with LYS 363 (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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358A GLU* 3.7 27.5 + - + -
359A THR 3.1 9.5 + - - +
360A PRO* 3.3 21.1 + - - +
362A PHE* 1.3 75.9 - - - +
364A GLN* 1.3 56.8 + - + +
365A PHE 3.1 0.2 - - - -
366A PHE* 3.1 29.0 + - - +
369A TRP* 3.4 58.3 - - + +
371A ASP* 3.9 7.9 + - - -
380A LEU* 4.2 20.1 - - - +
381A SER* 3.4 27.7 + - - +
382A TYR 4.8 2.6 + - - +
636A ASP 5.8 0.4 + - - -
637A ALA* 5.4 6.7 - - - +
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Residues in contact with GLN 364 (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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293A PRO* 5.5 0.3 - - - +
360A PRO* 3.1 21.8 + - - +
361A LEU* 4.0 11.8 - - - +
362A PHE 3.1 1.0 + - - -
363A LYS* 1.3 73.9 - - + +
365A PHE* 1.3 58.5 + - + +
366A PHE 3.1 11.4 + - - +
637A ALA 3.6 10.2 + - - +
638A HIS* 2.8 45.4 - - + +
639A PRO* 5.3 0.6 - - - +
641A ARG* 5.5 8.2 + - - +
677A TRP* 4.0 19.2 - - + -
707A ASP* 5.1 3.6 - - - +
708A PRO* 5.4 0.4 - - - -
709A ALA* 3.3 36.5 - - + +
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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