Contacts of the helix formed by residues 387 - 407 (chain A) in PDB entry 5FN2
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 ASN 387 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL 3.5 5.4 + - - +
384A SER 3.0 14.3 + - - +
385A GLN 3.0 4.9 - - - +
386A LYS* 1.3 75.3 - - - +
388A GLU* 1.3 69.5 + - - +
389A SER* 3.8 5.0 + - - -
390A VAL* 4.2 21.9 - - + +
391A ARG 2.9 23.9 + - - -
435A ASN* 5.0 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLN 4.9 1.7 - - - +
386A LYS 5.0 5.3 - - - +
387A ASN* 1.3 80.4 + - - +
389A SER* 1.3 60.8 + - - +
391A ARG* 3.2 20.8 + - - +
392A ASN* 2.9 50.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ASN* 4.4 3.4 + - - -
388A GLU* 1.3 77.3 - - - +
390A VAL* 1.3 60.4 + - - +
392A ASN* 3.2 9.4 + - - +
393A GLN* 2.9 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A SER* 3.6 35.2 - - - +
387A ASN* 3.7 23.1 + - + +
388A GLU 3.2 0.2 - - - -
389A SER* 1.3 77.5 - - - +
391A ARG* 1.3 58.3 + - - +
393A GLN* 3.2 17.8 + - - +
394A VAL* 2.9 34.9 + - + +
435A ASN* 4.4 18.8 - - + -
436A ILE 4.2 20.2 - - - +
437A SER* 4.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A SER 4.1 0.7 - - - -
385A GLN* 3.0 59.3 - - + +
387A ASN 2.9 10.3 + - - +
388A GLU* 3.2 22.3 + - - +
390A VAL* 1.3 77.0 - - - +
392A ASN* 1.3 70.4 + - - +
394A VAL* 3.2 3.6 + - - +
395A GLU* 2.9 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLU* 2.9 29.4 + - - +
389A SER* 3.5 11.6 - - - +
391A ARG* 1.3 93.8 + - - +
393A GLN* 1.3 57.7 + - - +
395A GLU* 3.2 9.8 + - - +
396A ASP* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ARG* 4.0 16.4 + - - +
360A ASP* 3.9 15.2 - - - +
389A SER* 2.9 26.6 + - - +
390A VAL* 3.2 17.6 + - - +
392A ASN* 1.3 74.7 - - - +
394A VAL* 1.3 58.6 - - - +
396A ASP* 3.2 9.9 + - - +
397A LEU* 2.9 28.5 + - - +
437A SER* 2.8 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A THR* 3.5 26.9 - - + -
384A SER* 4.7 5.2 - - - -
385A GLN* 3.3 35.2 - - - +
390A VAL* 2.9 24.9 + - + +
391A ARG 3.3 7.6 - - - +
393A GLN* 1.3 77.5 - - - +
395A GLU* 1.3 56.1 + - - +
397A LEU* 3.2 10.9 + - - +
398A LEU* 2.9 32.1 + - + +
436A ILE 4.6 1.8 - - - +
437A SER* 4.2 19.7 + - - -
438A GLY 4.3 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLN* 3.9 14.1 + - - +
391A ARG* 2.9 54.0 + - + +
392A ASN* 3.2 11.6 + - - +
394A VAL* 1.3 76.1 - - - +
396A ASP* 1.3 58.0 + - - +
398A LEU* 3.2 9.9 + - - +
399A ALA* 2.9 29.2 + - - +
415A ARG* 3.2 35.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ASN 2.9 12.8 + - - +
393A GLN* 3.4 12.8 - - - +
395A GLU* 1.3 76.4 - - - +
397A LEU* 1.3 57.2 + - - +
399A ALA* 3.2 11.2 + - - +
400A THR* 2.9 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A SER* 4.6 9.2 - - - -
362A PHE 4.3 3.6 - - - +
363A VAL* 4.8 6.1 - - + -
393A GLN 2.9 12.6 + - - +
394A VAL* 3.3 9.9 - - - +
396A ASP* 1.3 75.7 - - - +
398A LEU* 1.3 58.0 + - - +
400A THR* 2.3 26.6 + - - -
401A LEU* 2.9 24.5 + - + +
437A SER* 4.2 11.9 - - - +
438A GLY* 4.0 24.2 - - - +
439A VAL* 3.3 29.4 - - + -
501A LEU* 3.4 40.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A MET* 3.2 49.0 - - + +
380A THR* 3.8 22.7 - - + +
385A GLN* 4.7 1.1 - - - +
394A VAL* 2.9 38.2 + - + +
395A GLU* 3.4 15.0 - - - +
397A LEU* 1.3 75.7 - - - +
399A ALA* 1.3 57.4 + - - +
401A LEU* 3.2 10.0 + - + -
402A GLU* 2.9 29.2 + - - +
415A ARG* 3.8 32.5 - - - +
439A VAL* 4.6 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLU 2.9 12.6 + - - +
396A ASP* 3.2 15.5 + - - +
398A LEU* 1.3 77.3 - - - +
400A THR* 1.3 56.7 + - + +
402A GLU* 3.2 17.9 + - - +
403A LYS* 2.9 29.0 + - - +
415A ARG* 5.4 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ASP* 2.9 31.3 + - - +
397A LEU* 2.3 30.8 + - - +
399A ALA* 1.3 77.2 - - + +
401A LEU* 1.3 56.1 + - - +
403A LYS* 3.2 3.4 + - - -
404A SER* 2.9 28.3 + - - -
497A ALA* 5.5 1.3 - - - -
500A GLU* 3.2 44.4 - - + +
501A LEU* 3.6 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A VAL* 5.0 8.1 - - + -
378A MET* 3.3 24.7 - - + -
397A LEU* 2.9 27.5 + - + +
398A LEU* 3.2 2.9 + - + +
400A THR* 1.3 76.7 + - - +
402A GLU* 1.3 55.6 + - - +
404A SER* 2.4 25.6 + - - +
405A GLY 2.9 11.6 + - - -
413A LEU* 3.2 21.2 - - + +
439A VAL* 3.5 38.6 - - + -
441A LEU* 4.4 20.9 - - + -
493A VAL* 5.6 1.8 - - + +
494A LEU* 5.7 0.9 - - - -
497A ALA* 3.5 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A MET* 3.9 11.3 - - + +
398A LEU 2.9 18.3 + - - +
399A ALA* 3.2 21.1 + - - +
401A LEU* 1.3 75.5 - - - +
403A LYS* 1.3 57.9 + - - +
405A GLY* 3.2 2.9 + - - -
406A ALA* 2.9 27.4 + - - +
413A LEU* 4.3 23.7 - - - +
414A ARG* 5.4 0.3 - - - -
415A ARG* 4.0 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ALA 2.9 13.8 + - - +
400A THR* 3.3 9.6 - - - +
402A GLU* 1.3 75.2 - - - +
404A SER* 1.3 64.2 + - - +
406A ALA* 3.0 23.9 - - + +
407A GLY 3.8 1.7 + - - -
500A GLU* 3.8 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A THR 2.9 12.3 + - - -
401A LEU* 2.4 29.6 + - - -
403A LYS* 1.3 77.9 - - - +
405A GLY* 1.3 61.4 + - - +
407A GLY* 3.3 14.2 + - - -
408A VAL* 4.6 1.4 + - - +
493A VAL* 3.6 21.8 + - - +
496A ARG* 3.7 42.5 + - - +
497A ALA* 3.9 11.0 - - - +
500A GLU* 4.5 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A LEU 2.9 7.3 + - - -
402A GLU 3.2 4.5 + - - -
404A SER* 1.3 79.8 + - - +
406A ALA* 1.3 61.6 + - - +
407A GLY 3.2 0.4 - - - -
408A VAL 2.9 27.9 + - - +
409A PRO* 4.9 0.3 - - - +
411A VAL 3.7 11.1 - - - +
412A ILE* 5.4 0.9 - - - -
413A LEU* 4.4 9.4 - - - -
493A VAL* 3.9 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A GLU 2.9 11.8 + - - +
403A LYS* 3.0 21.1 - - + +
405A GLY* 1.3 76.9 - - - +
407A GLY* 1.3 60.0 + - - +
408A VAL* 3.0 5.7 + - - -
409A PRO* 4.4 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A LYS 3.8 2.0 + - - -
404A SER 3.3 6.0 + - - -
405A GLY 3.2 1.6 - - - -
406A ALA* 1.3 77.4 - - - +
408A VAL* 1.3 58.7 + - - +
409A PRO* 4.5 2.6 - - - +
496A ARG* 3.7 26.7 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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