Contacts of the helix formed by residues 61 - 70 (chain B) in PDB entry 3MYV
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 ALA 61 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER* 3.5 9.8 + - - +
58B TYR 3.8 0.2 - - - -
59B TYR 3.3 2.2 - - - -
60B GLY* 1.3 80.6 - - - +
62B ALA* 1.3 68.8 + - - +
63B MSE 3.3 2.7 - - - -
64B PHE* 3.1 11.3 + - - +
65B ALA* 3.0 20.6 + - - +
82B VAL* 5.3 2.9 - - + -
289B ASP 3.3 21.8 - - - +
291B TRP* 3.7 22.3 - - + +
294B LEU* 4.2 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER 3.0 13.7 + - - +
57B GLY 3.4 26.5 - - - +
58B TYR 3.2 1.4 + - - -
61B ALA* 1.3 75.1 - - - +
63B MSE 1.3 56.4 + - - +
65B ALA* 3.4 9.3 + - - +
66B TYR* 2.9 30.1 + - - +
82B VAL* 4.4 11.7 - - + -
86B CYS* 5.0 1.7 - - - -
98B ALA 4.3 0.9 - - - +
99B GLY* 4.0 18.4 - - - -
101B LEU* 4.0 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 2.9 43.7 + - + +
59B TYR* 3.8 23.8 - - + +
62B ALA* 1.3 75.7 - - - +
64B PHE* 1.3 59.4 + - + +
66B TYR* 3.5 5.1 + - - +
67B GLY* 3.1 23.0 + - - -
101B LEU* 3.5 17.9 - - + -
149B ASP* 3.6 20.0 - - + +
152B ARG* 3.5 34.5 - - - +
153B CYS* 4.2 15.9 - - - -
421B GLY* 4.4 3.3 - - - +
425B PHE* 4.1 14.1 - - + -
513B EDO 4.4 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TYR* 3.3 47.6 - + - -
61B ALA* 3.1 14.2 + - - +
63B MSE 1.3 74.3 - - - +
65B ALA* 1.3 66.2 + - - +
66B TYR 3.1 1.1 - - - -
67B GLY 3.3 0.2 + - - -
68B ASP* 2.9 30.4 + - - +
291B TRP* 3.3 41.5 - + + +
355B ASN* 3.6 15.9 - - + -
356B VAL 3.6 16.6 - - - -
357B VAL* 4.7 1.1 - - + -
420B GLU* 3.4 28.0 - - - -
421B GLY* 4.1 5.4 - - - -
504B EDO 3.3 21.1 - - - -
513B EDO 4.1 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ALA 3.0 12.8 + - - +
62B ALA 3.7 7.4 - - - +
64B PHE* 1.3 75.5 - - - +
66B TYR* 1.3 58.4 + - - +
69B MSE 2.9 36.9 + - - +
82B VAL* 4.0 39.5 - - + +
83B CYS* 4.2 7.2 - - - -
86B CYS* 3.7 3.6 - - - +
291B TRP* 3.5 20.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA 2.9 18.1 + - - +
63B MSE 3.5 7.2 - - - +
65B ALA* 1.3 76.6 - - - +
67B GLY* 1.3 61.5 + - - +
68B ASP 3.5 0.2 + - - -
70B LYS* 3.2 54.5 + - + +
86B CYS* 3.9 15.2 - - - -
98B ALA* 4.7 1.3 - - + -
101B LEU* 3.7 23.1 - - + -
152B ARG 4.8 0.2 + - - -
153B CYS* 3.5 31.9 + - - -
424B PHE* 3.8 17.8 - + - +
425B PHE* 3.6 32.1 - + - -
455B LYS 5.2 0.9 + - - -
456B CYS 4.1 11.4 + - - -
457B VAL 4.3 0.9 - - - -
458B LEU* 3.5 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B MSE 3.1 8.4 + - - -
66B TYR* 1.3 80.1 - - - +
68B ASP* 1.3 62.2 + - - +
421B GLY 3.6 26.2 - - - -
423B ARG* 3.6 3.8 + - - -
424B PHE* 3.0 35.4 + - - +
425B PHE* 4.0 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE 2.9 17.1 + - - +
67B GLY* 1.3 75.6 - - - +
69B MSE 1.3 64.6 + - + +
70B LYS 3.2 2.2 - - - -
71B GLY* 3.2 13.7 + - - -
73B ASP* 4.9 1.6 + - - +
74B MSE 3.7 38.0 + - + +
291B TRP* 3.9 7.3 - - + -
417B LEU 4.3 1.0 - - - +
418B VAL* 3.9 5.5 - - - +
419B GLY* 2.9 39.2 + - - +
421B GLY* 2.7 30.7 + - - -
422B HIS 4.6 2.1 + - - -
423B ARG* 4.8 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA* 2.9 30.2 + - - +
68B ASP* 1.3 71.7 - - - +
70B LYS* 1.3 59.0 + - - +
71B GLY 3.4 0.4 - - - +
74B MSE 3.8 40.4 - - + +
75B GLN* 3.2 38.6 - - - +
76B SER* 3.5 3.8 - - - -
83B CYS* 3.6 44.6 - - + +
86B CYS* 4.1 0.7 - - + -
87B TYR* 3.4 20.3 - - - +
291B TRP* 4.1 10.3 - - + -
295B LEU* 4.0 16.6 - - + -
303B GLY* 4.2 4.0 - - - -
436B ARG* 2.9 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TYR* 3.2 65.5 + - + +
68B ASP 3.2 0.6 - - - -
69B MSE 1.3 77.4 - - - +
71B GLY* 1.3 61.8 - - - +
86B CYS* 3.0 29.6 + - + +
89B PHE* 3.4 34.6 - - + -
91B HIS* 2.7 30.7 + - - -
424B PHE* 3.5 32.0 - - + -
434B ILE* 3.8 7.1 - - - +
436B ARG* 3.5 16.8 + - - +
449B VAL* 5.3 0.3 - - - +
455B LYS 4.7 1.2 + - - -
----------------------------------------------------------
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