Contacts of the helix formed by residues 395 - 413 (chain A) in PDB entry 6FEQ
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 SER 395 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU* 3.8 29.2 - - - +
391A ASN 3.8 8.0 + - - -
392A PRO* 2.7 7.2 + - - -
394A ALA* 1.3 79.8 - - - +
396A ILE* 1.3 66.4 + - - +
397A ALA 3.2 1.6 - - - -
398A GLN* 3.6 7.8 + - - +
399A ILE* 3.5 25.0 + - - +
481A MET* 3.1 30.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A PRO* 2.5 47.6 + - + +
393A GLN* 5.0 5.8 - - - +
395A SER* 1.3 74.2 - - - +
397A ALA* 1.3 56.7 + - - +
399A ILE* 2.9 22.7 + - + +
400A ILE* 2.9 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A PRO 4.0 2.2 + - - -
393A GLN* 3.3 27.5 - - - +
394A ALA* 4.8 3.1 - - - -
395A SER 3.2 0.4 - - - -
396A ILE* 1.3 78.5 - - - +
398A GLN* 1.3 58.1 + - + +
400A ILE* 3.3 6.6 + - - +
401A VAL* 3.0 37.0 + - + +
1002A D6T 5.1 19.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A ALA 4.1 18.4 + - - +
395A SER* 3.6 9.9 + - - +
396A ILE 3.3 0.6 - - - -
397A ALA* 1.3 77.8 - - + +
399A ILE* 1.3 55.9 + - + +
401A VAL* 4.1 5.4 - - - +
402A THR* 2.4 34.1 + - - -
440A SER 4.9 2.6 + - - -
443A SER* 3.0 33.1 + - - -
481A MET* 4.4 14.9 - - - +
482A ARG* 4.0 18.1 + - - +
485A PRO* 5.0 4.3 - - + +
1002A D6T 5.3 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A SER* 3.5 20.4 - - - +
396A ILE* 2.9 25.7 + - + +
398A GLN* 1.3 78.3 - - + +
400A ILE* 1.3 65.9 + - + +
402A THR* 3.1 6.7 + - - -
403A VAL* 2.9 38.2 + - + +
481A MET* 5.5 9.0 - - + -
484A LEU* 5.5 19.3 - - + -
485A PRO* 6.2 1.8 - - + -
488A ILE* 5.4 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ILE* 2.9 34.8 + - + +
397A ALA* 3.3 7.4 + - - +
399A ILE* 1.3 78.6 - - + +
401A VAL* 1.3 63.4 + - + +
403A VAL* 3.3 7.8 + - + +
404A VAL* 3.0 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ALA* 3.0 21.2 + - + +
398A GLN* 4.3 5.4 - - - +
400A ILE* 1.3 76.2 - - + +
402A THR* 1.3 59.3 + - - +
404A VAL* 4.7 4.0 - - - -
405A LEU* 2.9 44.5 + - + +
1002A D6T 5.0 30.1 - - - +
543B ILE* 5.7 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A GLN 2.4 26.8 + - - -
399A ILE* 3.1 8.0 + - - -
401A VAL* 1.3 81.1 - - - +
403A VAL* 1.3 56.3 + - - +
405A LEU 3.8 0.2 - - - -
406A GLY* 2.8 26.2 + - - -
485A PRO* 3.6 40.4 - - + +
488A ILE* 3.8 19.1 - - + +
489A PHE* 3.7 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ILE* 2.9 30.6 + - + +
400A ILE* 3.3 10.1 + - + +
402A THR* 1.3 75.5 - - - +
404A VAL* 1.3 62.1 + - + +
406A GLY* 3.1 1.6 + - - -
407A LEU* 2.8 42.2 + - + +
488A ILE* 3.7 24.5 - - + -
492A ILE* 4.2 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ILE* 3.0 31.7 + - + +
401A VAL* 4.1 3.6 - - - +
403A VAL* 1.3 80.0 - - + +
405A LEU* 1.3 59.1 + - - +
407A LEU* 3.1 10.9 + - + +
408A VAL* 3.0 38.2 + - + +
547B PHE* 5.5 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A VAL* 2.9 28.0 + - + +
402A THR* 4.5 1.1 - - - +
404A VAL* 1.3 75.9 - - - +
406A GLY* 1.3 62.6 + - - +
408A VAL* 4.0 3.6 - - + +
409A ILE* 3.2 34.0 + - + +
432A PHE* 4.2 23.3 - - + -
436A ASN* 3.2 26.7 - - - +
489A PHE* 4.6 9.0 - - + -
1002A D6T 3.7 25.8 - - - -
546B VAL* 5.8 1.8 - - + -
547B PHE* 3.7 34.8 - - + -
550B ILE* 5.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A THR 2.8 22.0 + - - -
403A VAL 3.1 3.1 + - - -
405A LEU* 1.3 78.1 - - - +
407A LEU* 1.3 55.4 + - - +
410A GLY 3.1 20.6 + - - -
488A ILE 5.5 0.7 - - - -
489A PHE* 4.5 8.9 - - - -
492A ILE* 3.7 16.5 - - - +
493A VAL* 3.4 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A VAL* 2.8 37.3 + - + +
404A VAL* 3.1 8.9 + - + +
406A GLY* 1.3 71.4 - - - +
408A VAL* 1.3 56.7 - - + +
410A GLY* 3.1 2.8 + - - +
411A ALA* 2.7 34.9 + - - +
492A ILE* 3.9 22.2 - - + -
496A MET* 4.7 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A VAL* 3.0 25.7 + - + +
405A LEU* 4.4 4.5 - - + +
406A GLY 3.4 0.2 - - - -
407A LEU* 1.3 75.3 - - + +
409A ILE* 1.3 63.3 + - + +
411A ALA* 2.9 7.0 + - + +
412A ILE* 2.8 49.7 + - + +
547B PHE* 4.0 31.9 - - + -
550B ILE* 5.5 0.2 - - + -
551B PHE* 6.1 1.1 - - + -
565B LEU* 6.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A LEU* 3.2 24.0 + - + +
406A GLY 4.2 2.0 - - - +
408A VAL* 1.3 77.7 - - + +
410A GLY* 1.3 62.8 + - - +
412A ILE* 4.8 3.6 - - + -
413A TYR* 3.3 50.9 + - + +
429A VAL* 3.7 22.2 - - + -
432A PHE* 3.6 37.7 - - + -
433A LEU* 5.2 6.3 - - + -
489A PHE* 5.9 1.3 - - + -
493A VAL* 4.6 11.2 - - + -
497A LEU* 3.6 3.8 - - + +
550B ILE* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLY 3.1 17.1 + - - -
407A LEU 3.1 6.0 + - - -
409A ILE* 1.3 77.4 - - - +
411A ALA* 1.3 59.3 + - - +
413A TYR 4.4 0.3 - - - -
414A PHE* 3.9 17.3 + - - +
493A VAL* 4.3 3.7 - - - +
496A MET* 3.4 36.4 - - - +
497A LEU* 4.0 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A LEU 2.7 17.7 + - - +
408A VAL* 2.9 9.1 + - + +
410A GLY* 1.3 75.1 - - - +
412A ILE* 1.3 66.4 + - + +
414A PHE* 3.7 14.3 + - - +
496A MET* 4.7 3.8 - - + -
561B ILE* 5.9 0.2 - - - +
562B ALA* 5.5 5.2 + - - +
564B TRP* 4.9 13.7 - - + -
565B LEU* 4.5 25.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A VAL* 2.8 41.0 + - + +
409A ILE* 4.8 2.5 - - + -
411A ALA* 1.3 74.7 - - + +
413A TYR* 1.3 68.0 + - + +
414A PHE* 3.2 5.8 + - - +
550B ILE* 4.0 23.3 - - + -
551B PHE* 3.8 30.3 - - + -
556B VAL* 3.9 29.0 - - + +
560B THR 5.0 2.3 - - - +
561B ILE* 4.4 35.3 - - + +
562B ALA* 4.9 2.4 + - - +
565B LEU* 4.8 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ILE* 3.3 51.6 + - + +
410A GLY 4.4 2.0 - - - -
412A ILE* 1.3 87.0 - - + +
414A PHE* 1.3 64.9 + - - +
416A LEU* 3.5 19.5 - - + +
425A ASN* 3.8 29.8 - - - +
428A GLY 4.4 0.2 - - - -
429A VAL* 4.0 21.3 + - + -
432A PHE* 5.3 3.6 - - + +
497A LEU* 3.4 30.1 - - + +
550B ILE* 4.0 9.3 - - + +
555B LEU* 3.7 21.1 - - - +
556B VAL* 3.6 39.7 - - + +
----------------------------------------------------------
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