Contacts of the helix formed by residues 54 - 68 (chain C) in PDB entry 4UQJ
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 54 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C GLU* 3.0 21.7 + - + +
53C ALA* 1.3 75.8 - - - +
55C SER* 1.3 62.3 + - - +
56C PHE* 3.0 8.9 + - - +
57C ALA* 3.8 19.6 - - + +
58C VAL* 3.1 26.0 + - - +
87D SER* 2.6 29.2 + - - -
91D THR* 4.3 12.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ALA 3.1 5.2 + - - -
54C ASN* 1.3 70.7 + - - +
56C PHE* 1.3 65.1 + - - +
58C VAL* 3.3 3.7 + - - +
59C THR* 2.8 28.3 + - - -
80C LYS* 3.4 27.2 + - - +
81C SER* 3.8 9.6 - - - -
84C THR* 4.1 14.9 + - - -
83D ASN* 3.6 18.7 + - - +
84D THR* 4.4 4.0 - - - -
87D SER* 3.3 19.1 + - - -
88D PHE* 4.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ASN* 3.4 7.0 - - - +
55C SER* 1.3 72.6 - - - +
57C ALA* 1.3 70.5 + - + +
59C THR* 3.0 14.9 + - - -
60C ASN* 3.1 38.9 + - - +
87D SER* 2.7 27.2 + - - +
88D PHE* 3.3 46.2 - + + -
91D THR* 3.4 42.4 - - + +
92D LEU* 4.3 5.6 - - + -
315D CYS 3.8 15.7 - - - -
320D ALA* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 3.3 30.7 - - + +
51C GLU* 4.5 9.0 - - + +
54C ASN* 3.5 26.9 + - + +
55C SER 3.4 0.4 - - - -
56C PHE* 1.3 86.0 - - + +
58C VAL* 1.3 57.5 + - - +
60C ASN* 3.2 6.3 + - - +
61C ALA 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 4.6 10.8 - - + +
50C LEU* 5.1 2.9 - - + -
51C GLU 4.3 2.0 - - - +
52C VAL* 3.4 32.3 - - + +
54C ASN 3.1 15.8 + - - +
55C SER 3.6 7.9 - - - +
56C PHE 3.2 0.2 - - - -
57C ALA* 1.3 76.3 - - + +
59C THR* 1.3 63.0 + - - +
61C ALA* 3.5 6.9 + - - +
62C PHE* 3.1 22.3 + - - +
76C PHE 5.7 2.7 - - - +
77C TYR* 6.2 0.2 - - + -
81C SER* 3.9 12.8 - - - +
84C THR* 4.6 8.3 - - + -
85C ILE* 3.5 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C SER 2.8 19.5 + - - -
56C PHE 3.0 8.8 + - - -
58C VAL* 1.3 78.7 - - - +
60C ASN* 1.3 57.9 + - - +
62C PHE* 3.4 4.8 + - - +
63C CYS* 3.0 38.4 + - - -
84C THR* 3.5 17.2 + - - +
88C PHE* 3.8 29.2 - - + -
316C LEU* 5.8 0.4 - - + -
59D THR* 4.3 2.9 - - + +
84D THR* 5.9 0.2 - - - +
88D PHE* 3.6 30.3 - - + -
316D LEU* 4.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 5.4 2.7 - - + -
56C PHE* 3.1 38.5 + - - +
57C ALA* 3.6 9.2 - - - +
59C THR* 1.3 75.3 - - - +
61C ALA* 1.3 55.9 + - - +
63C CYS* 3.2 4.6 + - - +
64C SER* 2.7 38.3 + - - -
316D LEU* 3.4 44.9 + - - +
317D ALA 4.3 2.0 + - - -
318D ASN* 3.9 26.0 - - - +
320D ALA* 5.4 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 4.2 24.3 - - + +
48C ASP* 4.0 12.5 - - + +
50C LEU* 3.7 27.5 - - + +
57C ALA 2.9 16.1 + - - +
58C VAL* 3.9 6.5 - - - +
60C ASN* 1.3 75.8 - - - +
62C PHE* 1.3 59.7 + - - +
64C SER* 3.9 6.1 - - - -
65C GLN* 3.2 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 4.8 4.9 - - + +
58C VAL 3.1 18.2 + - - +
59C THR* 3.6 5.6 - - - +
60C ASN 3.1 0.4 - - - -
61C ALA* 1.3 76.7 - - - +
63C CYS* 1.3 66.3 + - - +
64C SER 3.2 0.4 - - - -
65C GLN* 3.4 5.1 + - - +
66C PHE* 2.9 32.4 + - + +
73C ILE* 3.6 30.3 - - + +
84C THR* 6.2 1.1 - - + -
85C ILE* 4.6 16.4 - - + -
88C PHE* 3.4 44.6 - + + -
89C CYS* 3.5 27.6 - - - -
92C LEU* 3.4 32.1 - - + -
94C VAL* 4.2 13.9 - - + -
96C PHE* 5.5 0.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C THR* 3.0 25.3 + - - +
60C ASN* 3.9 3.6 - - - +
62C PHE* 1.3 76.5 - - - +
64C SER* 1.3 60.4 + - - +
66C PHE* 3.6 7.4 - - - +
67C SER* 2.9 35.2 + - - +
88C PHE* 4.2 13.9 - - - -
314C ASP* 5.0 1.6 - - - +
315C CYS* 2.0 45.9 + - - +
316D LEU* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C HIS* 5.2 7.8 - - - -
48C ASP* 4.7 7.6 + - - -
60C ASN* 2.7 23.9 + - - -
61C ALA* 3.9 7.2 - - - -
63C CYS* 1.3 73.8 - - - +
65C GLN* 1.3 61.7 + - - +
67C SER* 3.4 5.6 + - - -
68C ARG* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLY* 4.6 13.7 - - - -
17C LEU* 5.1 4.9 - - + -
46C HIS* 5.5 7.6 - - + +
48C ASP* 4.8 8.5 + - - +
61C ALA 3.2 16.4 + - - +
62C PHE 3.9 3.4 - - - +
64C SER* 1.3 79.0 - - - +
66C PHE* 1.3 60.8 + - - +
68C ARG* 3.7 7.1 + - - +
69C GLY 3.6 2.9 + - - -
70C VAL* 3.1 45.9 + - + +
73C ILE* 4.6 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PHE* 2.9 23.3 + - + +
63C CYS* 3.6 7.0 - - - +
64C SER 3.1 0.2 - - - -
65C GLN* 1.3 77.9 - - - +
67C SER* 1.3 60.3 + - - +
68C ARG 3.2 0.2 - - - -
69C GLY* 3.1 17.7 + - - -
70C VAL* 4.6 11.0 - - + -
73C ILE* 5.8 1.6 - - + -
92C LEU* 4.1 28.3 - - + -
94C VAL* 3.9 31.4 - - + -
312C ALA* 3.5 39.5 - - + +
313C GLY 3.6 22.7 - - - -
314C ASP 4.7 0.7 - - - -
315C CYS* 4.0 21.1 - - + -
323C TRP* 4.6 16.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C CYS* 2.9 20.0 + - - +
64C SER* 3.9 5.8 - - - -
66C PHE* 1.3 72.1 - - - +
68C ARG* 1.3 58.2 + - - +
69C GLY* 2.9 10.0 + - - -
311C ASN* 5.0 10.7 - - - +
312C ALA* 4.8 7.9 + - - -
313C GLY 3.7 23.3 + - - +
314C ASP* 4.7 5.7 + - - -
315C CYS 5.3 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLN* 5.4 3.3 - - - +
46C HIS* 5.7 14.1 - - + +
64C SER 3.1 16.7 + - - +
65C GLN* 3.9 10.8 - - - +
66C PHE 3.2 0.2 - - - -
67C SER* 1.3 75.5 - - - +
69C GLY* 1.3 64.5 + - - +
70C VAL* 4.9 6.0 - - + +
----------------------------------------------------------
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