Contacts of the helix formed by residues 54 - 68 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C SER* 3.0 21.8 + - - -
91C THR* 5.2 3.9 + - - -
51D GLU* 3.0 22.6 + - + +
53D ALA* 1.3 76.0 - - - +
55D SER* 1.3 62.4 + - - +
56D PHE* 3.0 12.4 + - - +
57D ALA* 3.8 21.8 - - + +
58D VAL* 3.1 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ASN* 3.5 31.3 - - - +
84C THR* 4.6 3.6 - - - -
87C SER* 3.9 5.6 + - - -
88C PHE* 5.3 0.9 - - - -
53D ALA 3.1 4.5 + - - -
54D ASN* 1.3 71.6 + - - +
56D PHE* 1.3 63.4 + - - +
58D VAL* 3.3 3.5 + - - +
59D THR* 2.8 28.0 + - - -
80D LYS* 3.4 27.4 + - - +
81D SER* 3.8 9.4 - - - -
84D THR* 4.1 14.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C SER* 2.9 24.5 + - - +
88C PHE* 3.7 43.5 - + + -
91C THR* 3.8 42.2 - - + +
92C LEU* 4.8 2.7 - - + -
315C CYS 3.9 18.2 - - - -
320C ALA* 4.1 13.0 - - + -
54D ASN* 3.0 8.5 + - - +
55D SER* 1.3 77.0 - - - +
57D ALA* 1.3 70.0 + - + +
59D THR* 3.0 18.9 + - - -
60D ASN* 3.1 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D LEU* 3.3 31.0 - - + +
51D GLU* 4.5 8.1 - - + +
54D ASN* 3.5 28.1 + - + +
55D SER 3.4 0.2 - - - -
56D PHE* 1.3 86.1 - - + +
58D VAL* 1.3 58.7 + - - +
60D ASN* 3.2 6.8 + - - +
61D ALA 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU* 4.6 9.7 - - + +
50D LEU* 5.1 2.7 - - + -
51D GLU 4.3 2.0 - - - +
52D VAL* 3.4 32.1 - - + +
54D ASN 3.1 16.5 + - - +
55D SER 3.6 7.4 - - - +
56D PHE 3.2 0.2 - - - -
57D ALA* 1.3 76.8 - - + +
59D THR* 1.3 62.1 - - - +
61D ALA* 3.9 7.0 - - - +
62D PHE* 3.1 22.5 + - - +
76D PHE 5.7 3.1 - - - +
81D SER* 3.9 13.2 - - - +
84D THR* 4.6 7.4 - - + -
85D ILE* 3.5 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C THR* 4.3 4.8 + - + -
84C THR* 5.7 0.7 - - - +
88C PHE* 3.9 29.5 - - + -
316C LEU* 4.4 6.5 - - + -
55D SER 2.8 20.6 + - - -
56D PHE 3.0 9.0 + - - -
58D VAL* 1.3 77.4 - - - +
60D ASN* 1.3 57.8 + - - +
62D PHE* 3.4 4.8 + - - +
63D CYS* 3.0 41.9 + - - -
84D THR* 3.5 17.6 + - - +
88D PHE* 3.8 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C LEU* 3.1 46.3 + - - +
317C ALA 4.7 1.4 + - - -
318C ASN* 4.2 20.8 - - - +
320C ALA* 5.8 0.2 - - - +
50D LEU* 5.4 2.9 - - + -
56D PHE* 3.1 38.3 + - - +
57D ALA* 3.6 8.7 - - - +
59D THR* 1.3 74.7 - - - +
61D ALA* 1.3 56.2 + - - +
63D CYS* 3.2 5.1 + - - +
64D SER* 2.7 38.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU* 4.2 25.1 - - + +
48D ASP* 4.0 11.7 - - + +
50D LEU* 3.7 28.2 - - + +
57D ALA 2.9 15.7 + - - +
58D VAL* 3.9 6.7 - - - +
60D ASN* 1.3 77.1 - - - +
62D PHE* 1.3 60.8 + - - +
64D SER* 3.9 5.8 - - - -
65D GLN* 3.2 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU* 4.8 4.9 - - + +
58D VAL 3.1 18.4 + - - +
59D THR* 3.6 5.4 - - - +
60D ASN 3.1 0.2 - - - -
61D ALA* 1.3 76.7 - - - +
63D CYS* 1.3 66.4 + - - +
64D SER 3.2 0.2 - - - -
65D GLN* 3.4 4.6 + - - +
66D PHE* 2.9 32.9 + - + +
73D ILE* 3.6 28.9 - - + +
84D THR* 6.2 1.3 - - + -
85D ILE* 4.7 16.6 - - + -
88D PHE* 3.4 42.4 - + + -
89D CYS* 3.5 27.6 - - - -
92D LEU* 3.4 32.8 - - + -
94D VAL* 4.2 13.9 - - + -
96D PHE* 5.5 0.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C LEU* 3.8 21.3 - - + -
59D THR* 3.0 29.4 + - - +
60D ASN* 3.9 2.5 - - - +
62D PHE* 1.3 77.7 - - - +
64D SER* 1.3 59.8 + - - +
66D PHE* 3.6 5.0 - - - +
67D SER* 2.9 34.3 + - - -
88D PHE* 4.2 17.7 - - - -
314D ASP* 4.9 1.3 - - - +
315D CYS* 2.0 44.5 - - - -
316D LEU* 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D HIS* 5.2 7.8 - - - -
48D ASP* 4.7 7.1 + - - -
60D ASN 2.7 23.3 + - - -
61D ALA* 3.9 7.0 - - - -
63D CYS* 1.3 73.8 - - - +
65D GLN* 1.3 61.7 + - - +
67D SER* 3.4 6.2 + - - -
68D ARG* 3.1 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D GLY* 4.6 13.7 - - - -
17D LEU* 5.1 4.5 - - + -
46D HIS* 5.5 8.5 - - + +
48D ASP* 4.8 8.5 + - - +
61D ALA 3.2 16.9 + - - +
62D PHE 3.9 3.4 - - - +
64D SER* 1.3 78.8 + - - +
66D PHE* 1.3 60.0 - - - +
68D ARG* 3.7 7.0 + - - +
69D GLY 3.6 2.8 + - - -
70D VAL* 3.1 45.7 + - + +
73D ILE* 4.6 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D PHE* 2.9 22.7 + + + +
63D CYS* 3.6 6.7 - - - +
64D SER 3.1 0.2 - - - -
65D GLN* 1.3 77.9 - - - +
67D SER* 1.3 60.2 + - - +
68D ARG 3.2 0.2 - - - -
69D GLY* 3.1 14.2 + - - -
70D VAL* 4.6 10.5 - - + -
73D ILE* 5.8 1.6 - - + -
92D LEU* 4.1 24.0 - - + -
94D VAL* 3.9 30.3 - - + -
312D ALA* 3.4 39.7 - - + +
313D GLY 3.8 14.6 - - - -
314D ASP 4.5 1.6 - - - -
315D CYS* 3.6 33.9 - - + -
321D VAL 5.8 4.0 - - - -
323D TRP* 4.7 16.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D CYS* 2.9 19.8 + - - +
64D SER* 3.4 6.3 + - - -
66D PHE* 1.3 72.4 - - - +
68D ARG* 1.3 59.5 + - - +
69D GLY 2.9 10.2 + - - -
310D GLY 3.3 21.3 - - - +
311D ASN* 4.2 0.7 + - - -
312D ALA 4.5 2.3 + - - -
313D GLY 3.4 26.9 + - - +
314D ASP* 4.2 9.0 + - - -
315D CYS 4.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D GLN* 5.4 2.9 - - - +
46D HIS* 5.7 13.7 - - + +
64D SER 3.1 17.3 + - - +
65D GLN* 3.9 10.8 - - - +
66D PHE 3.2 0.2 - - - -
67D SER* 1.3 75.5 - - - +
69D GLY* 1.3 64.0 + - - +
70D VAL* 4.9 5.9 - - + +
310D GLY* 3.7 13.3 - - - -
----------------------------------------------------------
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