Contacts of the strand formed by residues 43 - 54 (chain A) in PDB entry 5IXM
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 GLY 43 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 3.8 6.6 - - - -
39A MET* 2.9 41.8 + - - +
42A ARG* 1.3 77.6 - - - +
44A LEU* 1.3 60.8 + - - -
45A GLN 3.9 0.9 + - - -
66A LEU* 3.7 8.7 - - - -
68A ASN 4.5 3.4 - - - -
70A ARG* 3.8 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO* 4.4 9.4 - - + -
37A HIS 3.9 17.9 - - - +
38A TYR* 4.0 18.4 - - + +
43A GLY* 1.3 70.9 - - - -
45A GLN* 1.3 69.6 + - - +
46A TRP* 3.7 34.4 - - + +
65A TRP 4.1 0.2 - - - +
66A LEU* 3.4 5.3 - - - +
67A PRO* 3.2 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO* 3.5 4.3 - - - +
37A HIS* 2.9 45.8 + - + +
39A MET* 3.6 16.6 - - + -
43A GLY 3.9 0.2 + - - -
44A LEU* 1.3 75.9 - - - +
46A TRP* 1.3 72.1 + - - +
47A GLN* 2.6 35.5 + - - +
64A ASP* 4.0 6.8 + - - +
65A TRP 3.6 13.6 - - - +
66A LEU* 3.7 13.3 - - + +
84A ARG 5.7 0.2 + - - -
113A TYR* 3.5 23.6 + - - -
117A LEU* 3.5 30.8 - - - +
118A THR 5.0 1.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ILE* 4.0 23.8 - - + -
35A THR 3.7 1.8 - - - -
36A PRO* 3.8 36.1 - - + -
44A LEU* 3.7 35.7 + - + +
45A GLN* 1.3 79.6 - - - +
47A GLN* 1.3 63.0 + - - +
48A ASN* 3.9 11.7 + - - +
63A LEU 3.5 2.9 - - - +
64A ASP* 3.3 4.3 - - - +
65A TRP* 2.9 67.2 + + + +
67A PRO* 5.1 1.7 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
19A LEU* 4.4 10.0 - - - +
33A THR* 3.4 5.4 - - - +
34A ILE* 3.6 0.2 - - - -
35A THR* 2.9 53.0 + - - +
37A HIS* 3.4 23.7 + - + -
45A GLN* 2.6 31.5 + - - +
46A TRP* 1.3 73.4 - - - +
48A ASN* 1.3 62.2 + - - +
49A GLU* 5.8 0.2 - - - -
64A ASP* 3.6 25.0 + - - +
118A THR 3.8 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR 3.3 4.7 - - - +
34A ILE* 3.7 29.8 - - + +
46A TRP* 3.9 16.4 + - - +
47A GLN* 1.3 77.2 + - - +
49A GLU* 1.3 60.6 + - - +
62A ALA* 3.2 7.5 - - - +
63A LEU* 2.9 65.5 + - + +
64A ASP* 4.0 1.8 + - - +
65A TRP* 5.3 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP 4.5 0.2 - - - -
32A ALA* 3.2 5.9 - - - +
33A THR* 2.8 50.8 + - + +
47A GLN 4.2 0.2 + - - -
48A ASN* 1.3 74.7 - - - +
50A PHE* 1.3 62.5 + - - +
51A ARG* 3.7 30.2 + - + +
60A THR* 3.9 19.6 - - + +
61A MET 3.5 4.0 - - - +
62A ALA* 5.0 0.9 - - + -
120A GLN* 4.4 10.7 - - - +
121A TYR* 3.2 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 5.0 5.6 - - + -
30A PHE* 3.6 40.2 - + + -
31A ASP 3.1 24.0 - - - -
32A ALA* 4.4 8.3 - - + +
49A GLU* 1.3 74.5 - - - +
51A ARG* 1.3 63.8 + - - +
52A TYR* 4.1 18.8 + + + -
60A THR* 3.5 1.4 - - - -
61A MET* 2.9 65.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 4.4 10.7 + - - -
29A ASN 4.1 0.4 - - - +
30A PHE* 3.5 4.2 - - - -
31A ASP* 2.9 69.2 + - + +
33A THR* 5.4 5.8 + - - -
49A GLU* 3.7 24.8 + - + +
50A PHE* 1.3 77.8 - - - +
52A TYR* 1.3 62.1 + - - +
59A GLY 3.5 5.6 - - - +
60A THR* 3.5 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASN 3.5 5.8 - - - -
30A PHE* 4.0 23.8 - - + -
50A PHE* 4.1 21.3 - + + -
51A ARG* 1.3 77.0 - - - +
53A LEU* 1.3 62.6 + - - +
54A LEU* 4.1 22.2 - - + -
57A GLY 4.1 3.1 - - - -
58A SER* 3.5 3.6 - - - -
59A GLY* 2.9 53.5 + - - +
60A THR 3.9 1.3 - - - -
61A MET* 4.2 11.9 - - + -
89A TRP* 2.8 35.9 + + - -
91A HIS* 2.7 42.7 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASN* 3.2 36.5 + - + +
52A TYR* 1.3 75.9 - - - +
54A LEU* 1.3 82.4 + - - +
57A GLY 4.0 1.8 - - - -
58A SER* 3.8 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASN* 3.8 16.6 - - - +
30A PHE* 3.9 21.3 - - + -
52A TYR* 4.1 22.2 - - + -
53A LEU* 1.3 90.8 - - - +
55A ALA* 1.3 61.7 + - - +
56A PRO* 3.3 19.7 - - + -
57A GLY* 2.9 30.6 + - - +
----------------------------------------------------------
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