Contacts of the strand formed by residues 30 - 39 (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 PHE 30 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 3.3 34.6 + - + -
27A ALA* 2.9 27.8 + - + +
28A PRO 3.6 0.8 + - - -
29A ASN* 1.3 113.0 - - - +
31A ASP* 1.3 71.9 + - - +
50A PHE* 3.6 29.8 - + + -
51A ARG 3.5 2.9 - - - -
52A TYR* 4.0 17.3 - - + -
54A LEU* 3.9 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 2.5 32.0 + - + -
25A ASN* 3.5 8.8 + - - +
26A ILE* 3.8 5.8 - - - +
27A ALA 4.4 0.7 - - - +
28A PRO 5.8 0.8 - - - +
29A ASN 5.9 0.2 - - - -
30A PHE* 1.3 82.7 - - - +
32A ALA* 1.3 61.9 + - - +
50A PHE* 3.1 12.0 - - - -
51A ARG* 2.9 71.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 3.5 6.1 - - - -
24A TRP* 3.0 43.5 + - + -
25A ASN 4.3 3.2 - - - +
26A ILE* 3.5 21.5 - - + +
31A ASP* 1.3 77.5 - - - +
33A THR* 1.3 66.7 + - - +
34A ILE* 4.6 5.6 - - + -
49A GLU 3.2 9.9 - - - +
50A PHE* 4.7 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 5.5 4.8 - - + +
21A PRO* 4.7 5.6 - - + -
22A TYR 3.2 14.9 + - - +
23A TYR* 3.9 14.6 - - - +
32A ALA* 1.3 80.1 + - - +
34A ILE* 1.3 66.2 + - - +
35A THR* 3.4 20.4 - - - +
47A GLN 3.4 1.8 - - - +
48A ASN* 3.3 5.7 - - - +
49A GLU* 2.8 47.2 + - + +
51A ARG* 5.4 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PRO 3.7 0.3 - - - -
22A TYR* 2.9 54.4 + - + +
24A TRP* 4.6 24.0 - - + -
32A ALA* 4.6 4.3 - - + -
33A THR* 1.3 82.3 - - - +
35A THR* 1.3 63.1 + - - +
36A PRO* 3.8 3.7 - - + +
46A TRP* 4.0 26.9 - - + -
47A GLN 3.6 2.7 - - - -
48A ASN* 3.7 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.7 22.9 - - + -
20A LEU 3.7 3.4 - - - +
21A PRO* 3.4 24.2 - - + +
33A THR* 3.4 20.6 - - - +
34A ILE* 1.3 80.7 + - - +
36A PRO* 1.3 75.2 - - - +
37A HIS 3.4 2.1 + - - -
46A TRP* 3.7 2.4 - - - -
47A GLN* 2.9 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 6.3 0.9 - - + -
18A PHE* 3.7 1.9 - - - +
20A LEU* 3.0 62.6 + - + +
22A TYR* 5.8 1.1 - - + -
34A ILE* 3.8 4.9 - - + +
35A THR* 1.3 87.6 - - - +
37A HIS* 1.3 59.2 + - - +
38A TYR 4.0 1.3 - - - -
44A LEU* 4.4 11.4 - - + -
45A GLN 3.5 7.2 - - - +
46A TRP* 3.8 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 3.2 30.9 + - - -
18A PHE 3.4 2.7 - - - -
19A LEU* 3.4 38.7 - - + +
35A THR 4.3 4.3 - - - +
36A PRO* 1.3 73.0 - - - +
38A TYR* 1.3 71.2 + - - +
39A MET* 3.7 21.7 + - - +
44A LEU* 4.0 1.5 - - - +
45A GLN* 2.9 60.8 + - - +
47A GLN* 3.4 13.1 + - - +
117A LEU* 5.7 0.2 - - + -
118A THR* 5.4 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 4.4 14.8 - + - -
17A GLU* 3.2 6.2 - - - -
18A PHE* 2.9 53.1 + - + +
36A PRO 4.0 0.8 - - - -
37A HIS* 1.3 75.0 - - - +
39A MET* 1.3 70.8 + - - +
40A GLU* 3.7 37.8 + - + +
43A GLY* 4.0 11.0 - - - -
44A LEU* 4.0 17.2 - - + +
70A ARG* 5.4 2.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN* 3.9 22.0 - - + -
16A PHE 3.6 3.6 - - - -
17A GLU* 3.8 13.0 - - + +
37A HIS* 3.7 30.5 - - - +
38A TYR* 1.3 84.8 - - - +
40A GLU* 1.3 67.4 + - - +
41A ARG 3.3 1.1 - - - -
42A ARG* 3.1 13.9 + - + -
43A GLY* 2.9 42.4 + - - +
45A GLN* 3.6 31.0 - - + -
66A LEU* 4.0 11.7 - - + -
117A LEU* 3.7 30.7 - - + -
118A THR 6.2 0.2 - - - -
----------------------------------------------------------
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