Contacts of the helix formed by residues 71 - 84 (chain H) in PDB entry 2FRV
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 71 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H CYS* 3.3 24.7 - - + +
69H THR 3.2 8.6 + - - +
70H TYR* 1.3 73.2 - - + +
72H HIS* 1.3 61.7 + - + +
74H LEU* 3.4 4.8 - - - +
75H ALA* 3.1 20.8 + - - +
100H MET* 3.6 34.5 - - + -
103H GLN* 4.1 7.2 - - + -
459H VAL* 3.9 3.2 - - + +
461H ALA* 3.9 7.6 - - + -
462H PRO* 3.8 24.2 - - + -
466H LEU* 3.6 13.8 - - + +
537H FCO 3.6 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 72 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H THR* 3.3 30.6 + - - +
62H GLN* 3.8 6.3 - - - -
64H ALA* 4.1 11.5 - - + +
65H CYS* 4.6 5.2 - - + -
68H CYS* 4.1 11.2 + - - -
70H TYR 3.2 1.0 - - - +
71H VAL* 1.3 83.2 - - + +
73H ALA* 1.3 66.6 + - - +
74H LEU 3.2 0.4 - - - -
76H SER* 3.2 21.0 + - - -
466H LEU* 3.7 23.0 - - + +
468H HIS* 2.9 34.7 + - + -
482H LEU* 3.9 10.1 - - + +
484H VAL* 4.0 15.7 - - + -
533H CYS* 3.5 22.6 - - - -
537H FCO 3.6 6.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H GLN* 3.9 28.9 - - - +
62H GLN* 3.7 31.1 - - + +
70H TYR* 2.8 17.4 + - + +
72H HIS* 1.3 79.5 - - - +
74H LEU* 1.3 57.4 + - - +
76H SER* 3.2 1.9 + - - -
77H VAL* 2.9 34.8 + - - +
220H THR* 4.6 2.2 - - - +
223H THR* 4.2 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H TYR* 3.1 39.2 + - + +
71H VAL* 3.4 9.4 - - - +
73H ALA* 1.3 74.0 - - - +
75H ALA* 1.3 60.0 + - - +
77H VAL* 3.4 7.2 + - + +
78H ARG* 2.8 80.6 + - + +
96H ARG* 4.1 22.9 - - + +
100H MET* 3.6 30.5 - - + -
223H THR* 5.4 0.9 - - + -
285H GLU* 4.4 1.6 - - - +
459H VAL* 3.8 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H VAL 3.1 11.4 + - - +
73H ALA 3.5 0.4 - - - -
74H LEU* 1.3 79.1 - - - +
76H SER* 1.3 56.1 + - - +
78H ARG* 3.4 2.6 + - - -
79H ALA* 3.0 29.5 + - - +
457H GLY* 3.6 14.2 - - - +
459H VAL* 3.5 23.3 - - + +
466H LEU* 4.1 9.2 - - + -
468H HIS* 3.5 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 76 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H ALA* 4.3 1.7 + - - -
58H GLN* 3.8 16.7 - - - -
61H THR* 3.0 18.7 + - - +
72H HIS 3.2 15.1 + - - -
73H ALA 3.5 3.6 - - - -
74H LEU 3.1 0.4 - - - -
75H ALA* 1.3 73.4 - - - +
77H VAL* 1.3 60.1 + - - +
78H ARG 3.1 1.3 - - - -
79H ALA* 3.2 2.6 + - - +
80H VAL* 3.0 35.5 + - - +
468H HIS* 2.8 20.7 + - - -
480H PHE* 3.1 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H GLN* 3.5 41.5 - - + +
73H ALA 2.9 14.8 + - - +
74H LEU* 3.5 17.0 - - + +
76H SER* 1.3 75.3 - - - +
78H ARG* 1.3 59.5 + - - +
80H VAL* 3.9 1.0 - - - +
81H ASP* 2.9 35.5 + - - +
96H ARG* 3.5 29.6 - - - +
223H THR* 4.2 6.7 - - - +
224H VAL* 3.8 24.0 - - - +
225H VAL* 4.0 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74H LEU* 2.8 53.6 + - + +
75H ALA 3.8 4.5 - - - +
76H SER 3.1 0.2 - - - -
77H VAL* 1.3 78.2 - - - +
79H ALA* 1.3 55.2 + - - +
81H ASP* 3.9 6.6 - - - +
82H ASN* 3.2 27.7 + - - +
96H ARG* 4.1 13.1 + - - +
97H ASN* 4.2 7.9 + - - -
285H GLU* 3.0 30.3 + - - -
287H PRO* 3.6 19.2 - - - +
290H GLU* 3.7 20.1 + - - +
296H ARG* 3.6 15.8 - - - +
456H VAL 4.0 1.4 - - - +
457H GLY* 3.8 10.8 - - - -
458H PHE 3.0 28.9 + - - +
459H VAL* 3.6 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H ALA 3.0 15.3 + - - +
76H SER* 3.2 5.6 + - - +
78H ARG* 1.3 76.2 - - - +
80H VAL* 1.3 60.7 + - + +
82H ASN* 3.8 0.2 - - - +
83H CYS* 3.1 26.9 + - - +
455H GLY* 3.7 3.3 - - - -
456H VAL* 3.7 6.3 - - - -
457H GLY* 3.6 9.6 - - - +
468H HIS* 3.3 33.0 - - + +
470H ILE* 3.5 17.3 - - + +
480H PHE* 5.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H PRO* 3.9 35.7 - - + +
57H ALA* 5.1 1.3 - - + -
76H SER 3.0 20.4 + - - +
79H ALA* 1.3 76.0 - - - +
81H ASP* 1.3 65.0 + - - +
82H ASN 3.3 0.2 - - - -
83H CYS* 3.4 9.7 + - - +
84H VAL* 3.1 28.6 + - + +
225H VAL* 3.8 30.3 - - + -
447H TRP* 5.3 1.6 - - + -
449H TYR* 4.8 10.5 - - + -
470H ILE* 4.2 18.8 - - + -
480H PHE* 4.7 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H VAL 2.9 25.0 + - - +
78H ARG* 3.9 5.9 - - - +
80H VAL* 1.3 76.7 - - - +
82H ASN* 1.3 62.2 + - - +
84H VAL* 3.2 1.0 + - - +
85H GLY 3.0 18.7 + - - -
86H VAL* 3.2 28.7 + - + +
88H ILE* 3.3 17.7 - - + +
96H ARG* 2.8 29.8 + - - -
224H VAL 4.0 0.7 - - - +
225H VAL* 3.1 11.6 - - - -
226H GLY 2.9 28.7 + - - -
290H GLU* 5.3 0.7 - - - +
291H TYR* 3.7 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H ARG 3.2 18.3 + - - +
79H ALA 3.8 4.3 - - - +
81H ASP* 1.3 77.0 - - - +
83H CYS* 1.3 61.2 + - - +
84H VAL 3.3 0.7 + - - -
85H GLY* 3.6 8.8 + - - -
290H GLU 5.6 0.5 - - - +
291H TYR* 3.4 34.0 + - + -
337H TYR* 4.7 1.6 + - - -
454H GLN 4.4 2.8 + - - +
455H GLY* 3.3 9.3 - - - -
456H VAL* 3.0 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 83 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H ALA 3.1 8.6 + - - +
80H VAL* 3.4 13.0 + - - -
81H ASP 3.3 0.8 - - - -
82H ASN* 1.3 79.9 - - - +
84H VAL* 1.3 61.5 + - - +
85H GLY 3.6 0.4 - - - -
449H TYR* 5.7 0.2 - - - -
450H PRO* 3.4 3.6 - - - +
453H SER* 2.6 46.0 + - - +
454H GLN 3.2 33.2 - - - +
455H GLY* 3.3 6.5 - - - +
470H ILE* 4.0 15.9 - - + -
472H GLN* 3.7 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H VAL* 3.1 15.0 - - + +
81H ASP* 3.6 8.5 - - - +
82H ASN 3.2 0.6 - - - -
83H CYS* 1.3 76.5 - - - +
85H GLY* 1.3 58.3 + - - +
86H VAL* 3.4 21.8 + - + +
225H VAL* 4.8 0.7 - - + -
447H TRP* 3.6 47.6 - - + +
448H GLN 3.7 17.9 + - - +
449H TYR* 3.9 11.7 - - + -
450H PRO* 3.8 18.9 - - + +
----------------------------------------------------------
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