Contacts of the helix formed by residues 71 - 84 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B CYS* 3.3 24.2 - - + +
69B THR 3.2 8.5 + - - +
70B TYR* 1.3 72.3 - - + +
72B HIS* 1.3 60.6 + - + +
74B LEU* 3.4 5.3 - - - +
75B ALA* 3.1 21.3 + - - +
100B MET* 3.6 34.8 - - + -
103B GLN* 4.1 6.7 - - + -
459B VAL* 3.9 3.0 - - + +
461B ALA* 3.9 7.2 - - + -
462B PRO* 3.8 24.7 - - + -
466B LEU* 3.6 13.4 - - + +
537B FCO 3.6 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B THR* 3.3 30.5 + - - +
62B GLN* 3.8 6.3 - - + -
64B ALA* 4.1 11.7 - - + +
65B CYS* 4.6 5.4 - - + -
68B CYS* 4.1 11.4 + - - -
70B TYR 3.2 1.2 - - - +
71B VAL* 1.3 82.2 - - + +
73B ALA* 1.3 66.7 + - - +
74B LEU 3.2 0.2 - - - -
75B ALA 3.9 0.2 - - - -
76B SER* 3.2 20.1 + - - -
466B LEU* 3.7 23.5 - - + +
468B HIS* 2.9 35.4 + - + -
482B LEU* 3.9 9.4 - - + +
484B VAL* 4.0 15.5 - - + -
533B CYS* 3.5 22.7 - - - -
537B FCO 3.6 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLN* 3.9 29.3 - - - +
62B GLN* 3.7 32.1 - - + +
70B TYR* 2.8 18.2 + - + +
72B HIS* 1.3 78.8 - - - +
74B LEU* 1.3 56.3 + - - +
76B SER* 3.2 2.4 + - - -
77B VAL* 2.9 34.4 + - - +
220B THR* 4.6 2.0 - - - +
223B THR* 4.2 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B TYR* 3.1 40.1 + - + +
71B VAL* 3.4 9.2 - - - +
73B ALA* 1.3 73.8 - - - +
75B ALA* 1.3 59.4 + - - +
77B VAL* 3.4 7.3 + - + +
78B ARG* 2.8 79.5 + - + +
96B ARG* 4.1 22.4 - - + +
100B MET* 3.6 31.0 - - + -
223B THR* 5.2 0.9 + - + -
285B GLU* 4.4 1.3 - - - +
459B VAL* 3.8 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL 3.1 11.8 + - - +
74B LEU* 1.3 78.2 - - - +
76B SER* 1.3 58.5 + - - +
78B ARG* 3.4 2.9 + - - -
79B ALA* 3.0 28.9 + - - +
457B GLY* 3.6 12.7 - - - +
459B VAL* 3.5 22.4 - - + +
466B LEU* 4.1 9.2 - - + -
468B HIS* 3.5 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA* 4.3 2.1 + - - -
58B GLN* 3.8 16.1 - - - -
61B THR* 3.0 18.4 + - - +
72B HIS 3.2 15.8 + - - -
73B ALA 3.5 2.9 - - - -
74B LEU 3.1 1.0 - - - -
75B ALA* 1.3 73.9 - - - +
77B VAL* 1.3 60.2 + - - +
78B ARG 3.1 1.1 - - - -
79B ALA* 3.2 2.4 + - - +
80B VAL* 3.0 35.6 + - - +
468B HIS* 2.8 20.9 + - - -
480B PHE* 3.1 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLN* 3.5 41.7 - - + +
73B ALA 2.9 14.7 + - - +
74B LEU* 3.5 15.7 - - + +
76B SER* 1.3 75.2 - - - +
78B ARG* 1.3 59.2 + - - +
80B VAL* 4.3 0.4 - - - +
81B ASP* 2.9 37.5 + - - +
96B ARG* 3.5 30.5 - - - +
223B THR* 4.2 7.4 - - - +
224B VAL* 3.8 23.6 - - - +
225B VAL* 4.0 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 2.8 53.2 + - + +
75B ALA 3.8 4.3 - - - +
76B SER 3.1 0.2 - - - -
77B VAL* 1.3 78.4 - - - +
79B ALA* 1.3 55.9 + - - +
81B ASP* 3.9 5.6 - - - +
82B ASN* 3.2 28.2 + - - +
96B ARG* 4.1 12.5 + - - +
97B ASN* 4.2 7.9 + - - -
285B GLU* 3.0 29.9 + - - -
287B PRO* 3.6 19.6 - - - +
290B GLU* 3.7 19.9 + - - +
296B ARG* 3.6 14.5 - - - +
456B VAL 4.0 1.6 - - - +
457B GLY* 3.8 11.0 - - - -
458B PHE 3.0 29.7 + - - +
459B VAL* 3.6 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ALA 3.0 16.1 + - - +
76B SER* 3.2 5.4 + - - +
78B ARG* 1.3 77.0 - - - +
80B VAL* 1.3 59.1 + - + +
83B CYS* 3.1 26.5 + - - +
455B GLY* 3.7 3.6 - - - -
456B VAL* 3.7 6.7 - - - -
457B GLY* 3.6 9.2 - - - +
468B HIS* 3.3 33.7 - - + +
470B ILE* 3.5 16.8 - - + +
480B PHE* 5.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PRO* 3.9 35.2 - - + +
55B ARG 5.2 0.2 - - - +
57B ALA* 5.1 1.3 - - + -
76B SER 3.0 19.3 + - - +
79B ALA* 1.3 75.6 - - - +
81B ASP* 1.3 66.2 + - - +
83B CYS* 4.0 10.2 - - - +
84B VAL* 3.1 28.8 + - + +
225B VAL* 3.8 30.5 - - + -
447B TRP* 5.3 1.3 - - + -
449B TYR* 4.8 10.8 - - + -
470B ILE* 4.2 18.6 - - + -
480B PHE* 4.7 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL 2.9 24.9 + - - +
78B ARG* 3.9 5.5 - - - +
79B ALA 3.4 0.2 - - - -
80B VAL* 1.3 76.7 - - - +
82B ASN* 1.3 62.1 + - - +
84B VAL* 3.6 1.0 - - - +
85B GLY 3.0 19.2 + - - -
86B VAL* 3.2 27.9 + - + +
88B ILE* 3.3 17.5 - - + +
96B ARG* 2.8 30.5 + - - -
224B VAL 4.0 0.5 - - - +
225B VAL* 3.1 11.6 - - - -
226B GLY 2.9 27.3 + - - -
290B GLU* 5.3 0.7 - - - +
291B TYR* 3.7 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG 3.2 18.7 + - - +
79B ALA 3.8 4.0 - - - +
81B ASP* 1.3 76.1 - - - +
83B CYS* 1.3 62.3 + - - +
84B VAL 3.3 0.7 + - - -
85B GLY* 3.6 9.2 + - - -
290B GLU 5.6 0.9 - - - +
291B TYR* 3.4 34.0 + - + -
337B TYR* 4.7 1.4 + - - -
454B GLN 4.4 2.5 + - - +
455B GLY* 3.3 9.5 - - - -
456B VAL* 3.0 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA 3.1 8.2 + - - +
80B VAL* 3.4 13.2 + - - -
81B ASP 3.3 0.6 - - - -
82B ASN* 1.3 80.1 - - - +
84B VAL* 1.3 61.7 + - - +
85B GLY 3.6 0.2 - - - -
449B TYR* 5.7 0.7 - - - -
450B PRO* 3.4 3.5 - - - +
453B SER* 2.6 45.5 + - - +
454B GLN 3.2 33.9 - - - +
455B GLY* 3.3 6.1 - - - +
470B ILE* 4.0 15.7 - - + -
472B GLN* 3.7 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 3.1 15.7 - - + +
81B ASP 3.6 8.1 - - - +
82B ASN 3.2 0.2 - - - -
83B CYS* 1.3 78.1 - - - +
85B GLY* 1.3 58.2 + - - +
86B VAL* 3.4 22.5 + - + +
225B VAL* 4.8 0.9 - - + -
447B TRP* 3.6 47.5 - - + +
448B GLN 3.7 19.2 + - - +
449B TYR* 3.9 11.9 - - + -
450B PRO* 3.8 18.9 - - + +
128H ASN* 5.6 2.8 - - - +
----------------------------------------------------------
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