Contacts of the helix formed by residues 41 - 54 (chain A) in PDB entry 5T8F
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 ASN 41 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASN 3.4 3.8 + - - -
40A ALA* 1.3 74.5 - - - +
42A LEU* 1.3 65.2 + - - +
43A SER* 3.7 8.1 - - - -
44A THR* 2.6 37.9 + - - -
45A ILE* 3.1 10.9 + - - +
85A GLU 3.2 10.7 + - - +
86A GLN* 3.2 38.0 + - - +
87A ARG 3.3 17.5 - - - +
88A ARG* 3.8 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA 4.1 0.2 + - - -
41A ASN* 1.3 72.4 - - - +
43A SER* 1.3 62.9 + - - +
45A ILE* 3.2 15.0 + - + +
46A LYS* 3.0 21.0 + - - +
70A PHE* 3.6 22.0 - - + -
82A LEU* 3.6 45.5 - - + +
84A ASP 4.3 12.3 - - - +
85A GLU* 3.4 15.6 + - + +
87A ARG* 3.1 12.0 + - + +
89A LEU* 4.5 15.3 - - + +
92A VAL* 4.0 14.8 - - + -
99A LEU* 4.1 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASN* 3.1 10.3 + - - -
42A LEU* 1.3 77.2 - - - +
44A THR* 1.3 59.6 + - - +
46A LYS* 3.6 6.5 + - - +
47A GLN* 3.4 24.9 + - - +
85A GLU* 2.9 39.6 + - - +
86A GLN* 4.4 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 4.6 12.3 - - + -
41A ASN* 2.6 30.4 + - - -
43A SER* 1.3 74.8 - - - +
45A ILE* 1.3 66.2 + - - +
47A GLN* 3.2 15.7 + - - +
48A LEU* 3.1 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 5.7 0.2 - - + -
24A PHE* 3.5 35.7 - - + -
34A PHE* 4.6 0.7 - - - -
36A VAL* 4.0 18.8 - - + -
40A ALA* 3.7 32.8 - - + +
41A ASN 3.1 8.8 + - - +
42A LEU* 3.6 19.5 - - + +
44A THR* 1.3 76.2 - - - +
46A LYS* 1.3 57.2 + - - +
48A LEU* 3.4 9.6 + - + +
49A LEU* 2.8 27.0 + - - +
70A PHE* 4.2 3.4 - - + -
89A LEU* 3.9 29.4 - - + -
99A LEU* 4.1 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU 3.0 13.1 + - - +
43A SER* 3.7 7.0 - - - +
44A THR 3.2 0.2 - - - -
45A ILE* 1.3 73.8 - - - +
47A GLN* 1.3 66.6 + - - +
49A LEU* 3.0 3.3 + - - +
50A TRP* 2.8 42.9 + - + +
65A PRO* 3.2 36.9 + - + +
66A GLU* 4.8 3.1 + - - +
68A TYR 2.9 27.9 + - - -
70A PHE* 3.8 28.4 - - + -
85A GLU* 2.8 40.9 + - - +
101A LEU* 5.0 3.1 - - + -
104A ARG* 3.7 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER* 3.4 12.9 + - - +
44A THR* 3.2 18.2 + - - +
46A LYS* 1.3 77.4 - - - +
48A LEU* 1.3 64.2 + - + +
50A TRP* 3.2 5.8 + - - +
51A HIS* 3.1 23.1 + - - +
65A PRO* 6.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 4.1 13.2 - - + -
36A VAL* 4.6 20.9 - - + -
37A SER 6.1 0.2 - - - +
40A ALA* 5.9 2.2 - - + -
44A THR* 3.1 28.5 + - + +
45A ILE* 3.8 9.9 - - + +
47A GLN* 1.3 80.0 - - + +
49A LEU* 1.3 62.9 + - - +
51A HIS* 3.5 8.1 + - + +
52A ARG* 3.2 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.5 45.1 - - + -
26A LEU* 4.1 13.7 - - + -
32A LEU* 4.2 10.3 - - + -
34A PHE* 3.8 17.5 - - + -
45A ILE 2.8 18.5 + - - +
46A LYS* 3.0 6.7 + - - +
48A LEU* 1.3 77.3 - - - +
50A TRP* 1.3 66.7 + - + +
52A ARG* 3.2 2.4 + - - +
53A ALA* 2.8 27.6 + - + +
70A PHE* 3.7 20.0 - - + -
101A LEU* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 5.5 0.4 - - + -
46A LYS* 2.8 40.9 + - + +
47A GLN* 3.8 6.1 - - - +
49A LEU* 1.3 83.0 - - + +
51A HIS* 1.3 65.1 + - - +
53A ALA* 3.4 6.8 + - + +
54A GLN* 3.3 25.8 + - - +
59A PHE* 3.7 31.3 - + - -
62A LEU* 4.4 15.8 - - + +
63A SER 3.5 27.4 + - - -
64A GLY* 4.5 0.4 - - - -
65A PRO* 3.8 32.6 - - + +
68A TYR* 3.5 25.4 - + + -
101A LEU* 3.5 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN 3.1 12.7 + - - +
48A LEU* 3.7 13.9 - - + +
49A LEU 3.3 0.2 - - - -
50A TRP* 1.3 78.2 - - - +
52A ARG* 1.3 64.7 + - + +
54A GLN* 3.5 24.2 + - - +
55A TYR* 3.5 31.7 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.5 20.4 - - + -
34A PHE* 3.6 47.6 - - + +
35A PRO* 4.0 15.4 + - - +
48A LEU* 3.2 15.9 + - + +
49A LEU 3.2 5.7 + - - +
51A HIS* 1.3 80.6 - - + +
53A ALA* 1.3 64.9 + - - +
55A TYR* 3.3 18.1 + - - +
56A GLU* 3.6 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.2 23.5 - - + +
32A LEU* 3.9 8.5 - - + +
49A LEU* 2.8 19.8 + - + +
50A TRP* 3.4 8.7 + - + +
52A ARG* 1.3 75.3 - - - +
54A GLN* 1.3 65.9 + - - +
56A GLU* 2.9 25.8 + - - +
59A PHE* 3.4 24.4 - - + +
62A LEU* 4.6 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TRP 3.3 12.1 + - - +
51A HIS* 3.5 40.0 + - - +
53A ALA* 1.3 78.2 - - - +
55A TYR* 1.3 81.2 + - + +
56A GLU 3.5 6.2 + - - +
59A PHE* 3.4 35.0 - - + +
----------------------------------------------------------
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