Contacts of the helix formed by residues 45 - 57 (chain D) in PDB entry 5SY1
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 THR 45 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D ASN 3.9 0.4 + - - -
44D PRO* 1.3 75.8 - - - +
46D GLU* 1.3 57.2 + - - +
47D ALA* 3.6 18.6 - - + +
48D GLU* 2.9 26.9 + - - +
49D LEU* 2.7 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D THR* 4.8 15.1 - - + +
44D PRO 3.6 3.0 + - - -
45D THR* 1.3 74.6 - - - +
47D ALA* 1.3 61.4 + - - +
49D LEU* 3.4 12.3 + - + +
50D GLN* 3.0 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D THR* 3.2 12.7 - - + +
46D GLU* 1.3 84.3 + - - +
48D GLU* 1.3 62.2 + - - +
50D GLN* 3.5 8.7 + - - +
51D ASP* 3.1 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B LEU* 5.6 2.3 - - - +
571B SER* 3.3 32.0 + - - +
572B GLY* 4.7 1.9 + - - -
44D PRO* 4.6 6.5 - - + +
45D THR* 2.9 35.2 + - - +
47D ALA* 1.3 77.6 - - - +
49D LEU* 1.3 52.7 + - - +
51D ASP* 3.0 12.7 + - + +
52D MET* 2.7 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D THR* 4.6 16.4 - - + -
33D LEU* 4.7 12.8 - - + -
34D GLY* 4.0 24.0 - - - +
37D MET* 4.4 11.2 - - + -
38D ARG* 6.0 2.5 - - - +
44D PRO* 3.8 29.8 - - + +
45D THR 2.7 21.4 + - - +
46D GLU* 3.8 12.1 - - + +
47D ALA 3.4 0.2 - - - -
48D GLU* 1.3 72.9 - - - +
50D GLN* 1.3 61.4 + - - +
52D MET* 3.7 29.5 - - + +
53D ILE* 3.1 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D THR* 5.1 8.7 - - + +
46D GLU* 3.0 25.5 + - - +
47D ALA* 3.8 7.8 - - - +
48D GLU 3.2 0.2 - - - -
49D LEU* 1.3 76.9 - - - +
51D ASP* 1.3 67.7 + - - +
53D ILE* 4.0 8.8 + - - +
54D ASN* 2.4 58.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ALA* 3.1 18.2 + - - +
48D GLU* 3.0 13.0 + - + +
50D GLN* 1.3 91.5 - - - +
52D MET* 1.3 59.5 + - + +
53D ILE 3.3 0.2 - - - -
54D ASN* 3.1 28.2 + - - +
55D GLU* 3.5 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B LEU* 3.3 58.8 - - + +
568B LEU* 4.7 5.4 - - + +
571B SER* 4.3 8.7 - - - -
33D LEU* 5.3 1.6 - - + -
37D MET* 3.7 20.9 - - + -
44D PRO* 4.8 5.6 - - + -
48D GLU* 2.7 40.9 + - + +
49D LEU* 3.2 31.8 + - + +
51D ASP* 1.3 72.4 - - - +
53D ILE* 1.3 65.8 + - + +
55D GLU* 3.8 11.8 + - - +
56D VAL* 4.1 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B LEU* 5.8 0.2 - - - -
28D ILE 5.3 0.9 - - - +
29D THR 4.0 8.7 - - - +
30D THR* 3.3 41.3 - - + +
33D LEU* 3.8 19.7 - - + -
49D LEU 3.1 17.1 + - - +
50D GLN* 4.4 7.0 - - - +
51D ASP 3.3 0.2 - - - -
52D MET* 1.3 76.3 - - - +
54D ASN* 1.3 59.6 + - - +
56D VAL* 2.8 6.9 + - - +
57D ASP* 2.8 31.5 + - + +
62D GLY* 3.8 27.6 - - - +
63D THR* 4.9 0.2 - - - -
64D ILE* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D GLN* 2.4 48.3 + - - +
51D ASP* 3.1 17.5 + - - +
53D ILE* 1.3 79.1 - - - +
55D GLU* 1.3 59.6 + - - +
57D ASP* 3.5 19.9 - - - +
62D GLY* 5.6 5.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B LEU 5.0 1.7 - - - +
567B LEU* 5.7 4.7 - - - +
570B SER* 3.9 18.8 + - - -
574B ASP* 5.3 5.0 - - - +
604B LYS* 5.7 7.0 - - - -
608B ALA* 6.0 1.9 - - - +
51D ASP 3.5 7.5 + - - +
52D MET* 4.2 9.4 - - - +
53D ILE 3.2 0.8 - - - -
54D ASN* 1.3 79.1 - - - +
56D VAL* 1.3 65.8 + - + +
57D ASP 4.6 1.0 - - - +
72D MET* 4.2 23.4 - - + +
75D ARG* 5.0 5.6 + - - -
76D LYS* 3.8 20.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B PHE* 4.8 5.4 - - + -
567B LEU* 4.4 16.8 - - + -
52D MET 4.1 12.6 - - - +
53D ILE 2.8 8.3 + - - +
55D GLU* 1.3 79.5 - - + +
57D ASP* 1.3 63.4 + - - +
58D ALA* 3.2 7.1 + - - +
64D ILE* 3.7 36.8 - - + -
68D GLU* 3.6 31.7 - - + +
69D PHE* 4.8 1.3 - - - -
71D THR* 5.5 1.0 + - - -
72D MET* 3.7 35.2 - - + +
75D ARG* 5.6 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B ARG* 6.1 1.2 - - - +
53D ILE* 2.8 28.4 + - + +
54D ASN* 3.5 18.6 - - - +
55D GLU 4.6 1.0 - - - +
56D VAL* 1.3 71.8 - - - +
58D ALA* 1.3 59.3 + - - +
59D ASP* 1.5 33.0 - - - +
60D GLY* 3.7 8.9 + - - -
61D ASN* 2.8 6.2 + - - +
62D GLY* 2.8 32.7 + - - -
63D THR 2.9 17.8 + - - +
64D ILE* 4.7 0.7 - - + -
68D GLU* 2.9 7.2 - - - +
204D CA 2.5 6.4 - - - -
----------------------------------------------------------
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