Contacts of the helix formed by residues 71 - 84 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D CYS* 3.3 23.1 - - + +
69D THR 3.2 9.1 + - - +
70D TYR* 1.3 72.2 - - + +
72D HIS* 1.3 60.5 + - + +
74D LEU* 3.4 4.6 - - - +
75D ALA* 3.1 20.8 + - - +
100D MET* 3.6 34.3 - - + -
103D GLN* 4.1 6.7 - - + -
459D VAL* 3.9 3.3 - - + +
461D ALA* 3.9 7.4 - - + -
462D PRO* 3.8 24.2 - - + -
466D LEU* 3.6 13.0 - - + +
537D FCO 3.6 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D THR* 3.3 30.7 + - - +
62D GLN* 3.8 6.3 - - - +
64D ALA* 4.1 10.9 - - + +
65D CYS* 4.6 5.6 - - + -
68D CYS* 4.1 11.0 + - - -
70D TYR 3.1 1.0 + - - -
71D VAL* 1.3 83.0 - - + +
73D ALA* 1.3 67.0 + - - +
74D LEU 3.2 0.2 - - - -
76D SER* 3.2 20.1 + - - -
466D LEU* 3.7 23.7 - - + +
468D HIS* 2.9 35.3 + - + -
482D LEU* 3.9 9.6 - - + +
484D VAL* 4.0 15.9 - - + -
533D CYS* 3.5 22.9 - - + -
537D FCO 3.6 6.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D GLN* 3.9 29.1 - - - +
62D GLN* 3.7 31.5 - - + +
70D TYR* 2.8 17.8 + - + +
72D HIS* 1.3 79.1 - - - +
74D LEU* 1.3 55.8 + - - +
76D SER* 3.2 2.8 + - - -
77D VAL* 2.9 34.1 + - - +
220D THR* 4.6 2.2 - - - +
223D THR* 4.2 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D TYR* 3.1 37.7 + - + +
71D VAL* 3.4 9.4 - - - +
73D ALA* 1.3 74.2 - - - +
75D ALA* 1.3 61.3 + - - +
77D VAL* 3.4 6.4 + - + +
78D ARG* 2.8 79.0 + - + +
96D ARG* 4.1 23.3 - - + +
100D MET* 3.6 30.7 - - + -
223D THR* 5.2 0.6 + - + -
285D GLU* 4.4 1.6 - - - +
459D VAL* 3.8 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D VAL 3.1 11.3 + - - +
73D ALA 3.5 0.2 - - - -
74D LEU* 1.3 77.4 - - - +
76D SER* 1.3 57.5 + - - +
78D ARG* 3.4 3.3 + - - -
79D ALA* 3.0 29.1 + - - +
457D GLY* 3.6 13.5 - - - +
459D VAL* 3.5 22.6 - - + +
466D LEU* 4.1 8.5 - - + -
468D HIS* 3.5 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ALA* 4.3 1.5 + - - -
58D GLN* 3.8 16.8 - - - -
61D THR* 3.0 17.7 + - - +
72D HIS 3.2 15.0 + - - -
73D ALA 3.5 3.4 - - - -
74D LEU 3.1 0.6 - - - -
75D ALA* 1.3 72.9 - - - +
77D VAL* 1.3 61.0 - - - +
78D ARG 3.1 0.9 - - - -
79D ALA* 3.2 2.6 + - - +
80D VAL* 3.0 35.6 + - - +
468D HIS* 2.8 20.5 + - - -
480D PHE* 3.1 21.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D GLN* 3.5 42.6 - - + +
73D ALA 2.9 15.1 + - - +
74D LEU* 3.5 16.8 - - + +
76D SER* 1.3 74.5 - - - +
78D ARG* 1.3 59.5 + - - +
80D VAL* 4.3 0.2 - - - +
81D ASP* 2.9 37.0 + - - +
96D ARG* 3.5 30.5 - - - +
223D THR* 4.2 6.1 - - - +
224D VAL* 3.8 22.7 - - - +
225D VAL* 4.0 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D LEU* 2.8 55.3 + - + +
75D ALA 3.8 4.0 - - - +
77D VAL* 1.3 79.2 - - - +
79D ALA* 1.3 56.4 + - - +
81D ASP* 3.9 6.4 - - - +
82D ASN* 3.2 27.9 + - - +
96D ARG* 4.1 12.7 + - - +
97D ASN* 4.2 7.9 + - - -
285D GLU* 3.0 30.3 + - - -
287D PRO* 3.6 18.2 - - - +
290D GLU* 3.7 19.7 + - - +
296D ARG* 3.6 15.1 - - - +
456D VAL 4.0 1.7 - - - +
457D GLY* 3.8 10.8 - - - -
458D PHE 3.0 28.5 + - - +
459D VAL* 3.6 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ALA 3.0 16.0 + - - +
76D SER* 3.2 5.6 + - - +
78D ARG* 1.3 75.9 - - - +
80D VAL* 1.3 59.1 + - + +
82D ASN* 3.8 0.2 - - - +
83D CYS* 3.1 26.2 + - - +
455D GLY* 3.7 3.3 - - - -
456D VAL* 3.7 6.3 - - - -
457D GLY* 3.6 9.8 - - - +
468D HIS* 3.3 33.4 - - + +
470D ILE* 3.5 17.2 - - + +
480D PHE* 5.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D PRO* 3.9 36.3 - - + +
57D ALA* 5.1 1.3 - - + -
76D SER 3.0 19.5 + - - +
77D VAL 4.3 0.2 - - - +
79D ALA* 1.3 76.2 - - - +
81D ASP* 1.3 64.4 + - - +
83D CYS* 4.0 9.1 - - - +
84D VAL* 3.1 29.3 + - + +
225D VAL* 3.8 30.9 - - + +
447D TRP* 5.3 1.8 - - + -
449D TYR* 4.8 10.5 - - + -
470D ILE* 4.2 18.8 - - + -
480D PHE* 4.7 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D VAL 2.9 25.3 + - - +
78D ARG* 3.9 5.9 - - - +
80D VAL* 1.3 76.3 - - - +
82D ASN* 1.3 60.3 + - - +
84D VAL* 3.2 0.7 + - - +
85D GLY 3.0 18.9 + - - -
86D VAL* 3.2 29.8 + - + +
88D ILE* 3.3 17.8 - - + +
96D ARG* 2.8 30.7 + - - -
224D VAL 4.0 0.7 - - - +
225D VAL* 3.1 11.8 - - - -
226D GLY 2.9 28.2 + - - -
290D GLU* 5.3 0.9 - - - +
291D TYR* 3.7 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ARG 3.2 19.1 + - - +
79D ALA 3.8 4.0 - - - +
81D ASP* 1.3 76.4 - - - +
83D CYS* 1.3 62.2 + - - +
84D VAL 3.3 0.9 + - - -
85D GLY* 3.6 8.7 + - - -
290D GLU 5.6 0.7 - - - +
291D TYR* 3.4 34.1 + - + -
337D TYR* 4.7 1.4 + - - -
454D GLN 4.4 2.3 + - - +
455D GLY* 3.3 9.7 - - - -
456D VAL* 3.0 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ALA 3.1 8.4 + - - +
80D VAL* 3.4 12.9 + - - -
81D ASP 3.3 0.6 - - - -
82D ASN* 1.3 80.6 - - - +
84D VAL* 1.3 60.7 + - - +
85D GLY 3.6 0.2 - - - -
449D TYR* 5.7 0.2 - - - -
450D PRO* 3.4 3.6 - - - +
453D SER* 2.6 45.2 + - - +
454D GLN 3.2 33.9 - - - +
455D GLY* 3.3 6.3 - - - +
470D ILE* 4.0 16.2 - - + -
472D GLN* 3.7 19.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D VAL* 3.1 15.7 - - + +
81D ASP 3.6 7.6 - - - +
82D ASN 3.2 0.2 - - - -
83D CYS* 1.3 77.9 - - - +
85D GLY* 1.3 58.0 + - - +
86D VAL* 3.6 22.3 - - + +
225D VAL* 4.8 0.7 - - + -
447D TRP* 3.6 47.8 - - + +
448D GLN 3.7 17.7 + - - +
449D TYR* 3.9 12.1 - - + -
450D PRO* 3.8 19.7 - - + +
----------------------------------------------------------
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