Contacts of the helix formed by residues 67 - 79 (chain B) in PDB entry 3M5B
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 67 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 3.8 1.6 - - - -
65B GLY 4.0 2.6 + - - -
66B ILE* 1.3 77.7 - - - +
68B PRO* 1.4 68.4 - - - +
69B SER* 3.5 10.3 + - - -
70B THR* 3.1 29.1 + - - -
71B PHE* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 3.7 37.7 - - + +
36B GLY* 5.6 0.7 - - - -
38B GLN* 4.1 26.5 - - + -
40B PHE* 3.8 10.2 - - + -
67B SER* 1.4 87.3 - - - +
69B SER* 1.3 57.4 + - - +
71B PHE* 3.4 0.8 + - + -
72B ALA* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B SER* 3.3 9.7 + - - -
68B PRO* 1.3 80.0 - - - +
70B THR* 1.3 64.5 + - - +
72B ALA* 3.5 6.4 + - - +
73B GLN* 3.3 31.6 + - - +
89B GLU* 5.1 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 3.9 8.1 - - + -
67B SER* 3.1 22.4 + - - -
69B SER* 1.3 77.7 + - - +
71B PHE* 1.3 63.4 + - - +
73B GLN* 3.3 16.1 + - - +
74B LEU* 3.2 16.5 + - + +
89B GLU 5.4 0.2 + - - -
92B PRO* 3.8 21.5 - - - +
93B LEU* 3.9 23.9 + - + +
96B ALA* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 4.0 26.0 - - + -
35B VAL* 4.1 13.0 - - + -
40B PHE* 3.8 44.4 - + + -
47B LEU* 5.8 2.0 - - + -
54B LEU* 4.4 12.1 - - + -
62B LEU* 3.7 23.1 - - + -
66B ILE* 4.1 10.1 - - + +
67B SER 2.9 19.9 + - - +
68B PRO 4.1 2.9 - - - +
69B SER 3.4 0.2 - - - -
70B THR* 1.3 73.4 - - - +
72B ALA* 1.3 58.1 + - - +
74B LEU* 3.1 24.5 + - + +
75B LEU* 2.9 48.7 + - + +
100B LEU* 4.4 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 3.9 21.1 - - + -
68B PRO 3.0 18.6 + - - +
69B SER* 3.6 8.3 - - - +
71B PHE* 1.3 78.5 - - - +
73B GLN* 1.4 56.1 + - + +
75B LEU* 3.6 4.1 + - - +
76B ASN* 3.1 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B SER* 3.3 17.0 + - - +
70B THR* 3.5 17.2 + - - +
72B ALA* 1.4 73.1 - - + +
74B LEU* 1.3 66.6 + - - +
75B LEU 3.4 0.2 + - - -
76B ASN* 3.4 6.0 + - - +
77B PHE* 3.1 18.2 + - - +
83B VAL* 3.5 27.4 - - + +
84B GLU 4.8 3.6 + - - -
85B LEU* 3.3 26.3 - - - +
89B GLU* 3.5 30.6 + - - +
93B LEU* 3.7 29.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
47B LEU* 6.3 0.7 - - + -
54B LEU* 4.4 14.8 - - + -
70B THR* 3.2 9.8 + - + +
71B PHE* 3.1 31.2 + - + +
73B GLN* 1.3 79.3 - - - +
75B LEU* 1.3 65.3 + - + +
77B PHE* 3.3 4.5 + - - +
78B VAL* 3.2 42.2 + - + +
93B LEU* 4.0 3.7 - - + +
96B ALA* 4.3 5.8 - - + -
97B ALA* 4.1 21.8 - - - +
100B LEU* 4.0 21.8 - - + -
102B VAL* 4.2 10.3 - - + -
105B LEU* 3.8 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 3.7 29.6 - - - +
33B ILE* 6.5 0.2 - - + -
40B PHE* 4.0 26.0 - - + -
41B PRO 4.2 5.4 - - - +
42B ALA* 4.6 6.3 - - + -
47B LEU* 3.9 23.3 - - + -
71B PHE* 2.9 35.4 + - + +
72B ALA* 4.0 5.8 - - - +
74B LEU* 1.3 75.5 - - + +
76B ASN* 1.3 65.0 + - - +
78B VAL* 3.4 6.3 + - + +
79B TYR* 3.1 53.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 6.0 0.2 + - - -
72B ALA* 3.1 27.5 + - - +
73B GLN* 3.7 8.0 - - - +
75B LEU* 1.3 75.7 - - - +
77B PHE* 1.3 58.9 + - - +
79B TYR* 3.2 11.8 + - - +
80B GLY 3.3 0.5 + - - -
81B GLU* 2.9 63.3 + - + +
82B SER 5.6 0.2 - - - +
83B VAL* 4.4 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.4 13.9 - - + -
9B PRO 3.2 23.8 - - - -
10B SER* 2.7 33.9 + - - -
11B PRO* 3.6 23.6 - - + -
12B TYR* 3.6 9.1 - + - -
73B GLN 3.1 13.7 + - - +
74B LEU 3.3 8.9 + - - +
76B ASN* 1.3 74.3 - - - +
78B VAL* 1.3 63.4 + - + +
80B GLY 3.0 8.7 + - - -
81B GLU 3.5 12.3 + - - -
83B VAL* 4.1 8.2 - - + +
93B LEU* 6.4 0.2 - - + -
102B VAL* 5.2 0.9 - - + -
104B SER* 3.5 30.7 - - - -
105B LEU* 3.8 42.4 - - + -
108B ALA* 4.4 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR* 3.9 17.3 - - - +
18B VAL* 3.8 12.0 - - - +
46B VAL* 3.8 24.8 - - + +
47B LEU* 4.6 13.0 - - + -
50B VAL* 4.0 36.5 - - + +
54B LEU* 5.7 0.9 - - + -
74B LEU* 3.2 31.7 + - + +
75B LEU* 3.6 11.9 - - + +
76B ASN 3.3 0.2 - - - -
77B PHE* 1.3 79.1 - - + +
79B TYR* 1.3 60.5 + - + +
80B GLY 3.3 3.0 + - - -
102B VAL* 4.5 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLY* 5.5 0.2 - - - -
18B VAL* 3.5 17.2 - - - +
19B GLN* 5.6 0.3 - - - -
21B ALA* 3.8 27.1 - - + -
22B ALA* 3.9 37.1 - - + +
25B ARG* 4.1 22.9 - - - -
42B ALA* 3.5 7.9 - - + -
43B HIS* 2.8 45.0 + + - +
46B VAL* 4.4 17.0 - - + -
47B LEU* 5.2 2.0 - - + -
75B LEU* 3.1 50.1 + - + +
76B ASN* 3.2 8.0 + - - +
78B VAL* 1.3 79.5 - - + +
80B GLY* 1.3 58.0 - - - +
81B GLU* 3.5 10.0 - - + +
----------------------------------------------------------
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