Contacts of the helix formed by residues 405 - 417 (chain A) in PDB entry 2FWN
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 PHE 405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A GLY* 4.8 6.2 - - - -
55A ASP* 3.7 28.7 - - + -
56A GLY* 4.8 2.2 - - - -
59A GLN* 3.7 21.3 - - - -
84A ASN* 3.7 29.4 - - + +
373A LEU* 4.2 3.6 - - + -
375A GLU* 3.0 6.6 + - - +
396A TYR* 4.0 27.6 - + + -
397A PHE* 4.1 3.8 - - - -
398A CYS* 3.6 31.2 - - + -
399A ALA 5.8 0.7 - - - -
402A GLY 3.9 0.2 + - - -
403A LEU 3.5 1.6 - - - -
404A GLY* 1.3 79.0 - - - +
406A ALA* 1.3 68.7 + - + +
407A LEU 3.3 1.0 + - - -
408A PRO* 3.3 5.2 - - - +
409A ALA* 2.8 56.1 + - + +
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Residues in contact with ALA 406 (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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373A LEU* 3.8 24.0 - - + +
374A ASN 4.3 3.1 - - - +
375A GLU* 2.9 42.0 + - + +
405A PHE* 1.3 84.9 - - + +
407A LEU* 1.3 57.5 + - - +
410A ALA* 2.9 33.1 + - - +
424A ALA* 4.3 0.5 - - - +
426A ILE* 4.2 12.1 - - + -
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Residues in contact with LEU 407 (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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375A GLU* 5.1 1.8 + - - +
404A GLY* 5.0 1.3 - - - -
405A PHE 4.8 0.2 - - - +
406A ALA* 1.3 80.9 - - - +
408A PRO* 1.3 70.1 - - + +
410A ALA 3.4 4.5 + - - -
411A ILE* 3.6 12.0 + - + +
426A ILE* 3.7 23.1 - - + +
430A SER 5.9 0.7 - - - +
431A ALA* 3.8 30.5 - - + +
434A SER* 3.9 10.3 - - - +
435A ILE* 4.3 14.1 - - + -
437A ALA* 3.8 22.2 - - + -
438A LEU* 3.8 24.0 - - + +
450A PHE* 3.6 30.1 - - + -
452A ILE* 5.2 4.9 - - + -
518A LEU* 5.8 0.4 - - + -
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Residues in contact with PRO 408 (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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48A ALA 4.3 0.2 - - - +
49A CYS* 3.6 26.5 - - - +
52A GLY* 4.0 9.4 - - - -
53A ILE* 3.3 19.4 - - + +
404A GLY 3.2 25.4 - - - +
405A PHE 3.3 9.9 - - - +
407A LEU* 1.3 95.2 - - + +
409A ALA* 1.3 60.0 + - - +
411A ILE* 3.0 12.4 + - + +
412A GLY 3.2 8.7 + - - -
434A SER* 3.6 17.9 - - - +
437A ALA* 3.7 18.4 - - + -
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Residues in contact with ALA 409 (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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52A GLY 3.2 15.8 + - - +
56A GLY* 3.7 7.6 - - - -
373A LEU* 3.8 10.8 - - + -
405A PHE* 2.8 59.2 + - + +
408A PRO* 1.3 74.6 - - - +
410A ALA* 1.3 57.7 + - - +
412A GLY* 3.1 2.1 + - - +
413A VAL* 2.8 31.9 + - - +
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Residues in contact with ALA 410 (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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373A LEU* 3.6 20.4 - - + +
406A ALA 2.9 20.1 + - - +
407A LEU 3.7 4.7 - - - +
408A PRO 3.1 0.2 - - - -
409A ALA* 1.3 76.5 - - - +
411A ILE* 1.3 59.3 + - - +
413A VAL* 3.9 0.7 - - - -
414A GLN* 3.0 21.7 + - - +
422A VAL* 3.6 5.7 - - + +
424A ALA* 3.7 18.4 - - + -
448A THR* 3.2 30.9 + - + -
450A PHE* 4.4 0.4 - - + -
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Residues in contact with ILE 411 (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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53A ILE* 4.3 8.5 - - + -
407A LEU* 3.6 17.3 - - + +
408A PRO* 3.0 7.7 + - + +
410A ALA* 1.3 76.1 - - - +
412A GLY* 1.3 59.8 + - - +
414A GLN 3.3 0.5 + - - -
415A LEU* 3.0 28.1 + - - +
437A ALA* 3.1 40.2 - - + +
440A THR* 4.3 15.7 - - + -
441A ALA* 3.8 17.9 - - + +
446A ILE* 3.6 32.8 - - + +
448A THR* 3.7 6.5 - - - +
450A PHE* 3.8 19.7 - - + -
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Residues in contact with GLY 412 (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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53A ILE* 3.3 32.9 - - - +
57A TYR* 3.5 20.7 - - - -
408A PRO 3.2 7.3 + - - -
409A ALA 3.1 5.1 + - - -
411A ILE* 1.3 75.5 - - - +
413A VAL* 1.3 59.3 + - - +
415A LEU* 3.3 6.3 + - - +
416A ALA 2.9 23.0 + - - -
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Residues in contact with VAL 413 (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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56A GLY* 3.5 25.3 - - - +
60A ALA* 4.0 12.6 - - + -
371A ILE* 3.7 39.0 - - + -
373A LEU* 4.5 6.7 - - + -
396A TYR* 4.0 24.5 - - + -
409A ALA 2.8 26.1 + - - +
410A ALA* 4.0 5.6 - - - +
412A GLY* 1.3 71.4 - - - +
414A GLN* 1.3 59.7 + - - +
416A ALA* 3.0 3.5 + - - +
417A GLU* 2.9 27.0 + - - +
422A VAL* 3.8 8.3 - - + -
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Residues in contact with GLN 414 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A ALA 3.0 10.4 + - - +
413A VAL* 1.3 77.1 - - - +
415A LEU* 1.3 63.4 + - - +
417A GLU 3.0 29.1 + - - -
418A PRO* 3.4 15.2 + - - +
420A ARG 2.8 22.5 + - - +
421A GLN* 3.4 14.8 + - - +
422A VAL* 2.9 31.4 + - + +
446A ILE* 3.5 20.0 - - + -
447A PRO* 3.6 24.3 - - + +
448A THR* 3.2 23.1 - - - +
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Residues in contact with LEU 415 (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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19A THR* 5.1 2.7 - - + -
21A PHE* 3.9 24.0 - - + -
40A ARG* 3.8 28.3 - - + +
42A ILE* 4.2 16.4 - - + -
53A ILE* 5.3 1.6 - - + -
57A TYR* 3.9 24.5 - - + -
411A ILE 3.0 16.8 + - - +
412A GLY* 3.5 6.7 - - - +
413A VAL 3.2 0.2 - - - -
414A GLN* 1.3 76.6 - - - +
416A ALA* 1.3 61.5 + - - +
418A PRO* 3.7 11.0 - - - +
446A ILE* 4.0 28.4 - - + +
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Residues in contact with ALA 416 (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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57A TYR* 3.6 27.6 - - + +
60A ALA* 3.7 23.1 - - + -
61A SER* 4.2 9.5 - - - +
412A GLY 2.9 14.3 + - - +
413A VAL 3.0 8.0 + - - +
415A LEU* 1.3 79.0 - - - +
417A GLU* 1.3 63.3 + - + +
418A PRO* 3.4 3.2 - - - +
534A CA 2.3 30.8 - - - -
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Residues in contact with GLU 417 (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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60A ALA* 4.1 25.3 - - + +
62A ARG* 5.2 4.3 + - - -
371A ILE* 3.9 25.8 - - + -
413A VAL 2.9 13.3 + - - +
414A GLN* 3.0 18.5 + - - -
415A LEU 3.3 0.2 - - - -
416A ALA* 1.3 86.5 - - + +
418A PRO* 1.3 66.5 - - - +
419A GLU* 3.0 5.6 + - - +
420A ARG* 3.1 34.9 + - + +
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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