Contacts of the strand formed by residues 21 - 32 (chain A) in PDB entry 5EXU
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 HIS 21 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA* 3.2 3.3 - - - -
18A VAL 2.9 34.0 + - - +
19A ASN 3.4 3.0 + - - +
20A GLY* 1.4 68.8 + - - -
22A LYS* 1.3 67.1 + - - +
23A PHE* 3.4 7.5 - - + -
47A GLY* 4.5 11.0 - - - -
49A PRO 4.7 2.6 + - - -
51A PRO* 3.3 45.1 - - + +
52A PHE* 4.7 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU* 5.7 5.2 - - + +
16A GLY 3.2 13.2 - - - +
17A ALA* 4.1 7.4 - - + +
20A GLY 3.2 10.0 + - - +
21A HIS* 1.3 78.5 - - - +
23A PHE* 1.3 62.3 + - - +
46A GLU* 5.9 0.4 - - - -
47A GLY* 3.5 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A MET* 3.7 27.1 - - + -
15A GLU* 4.0 1.2 - - - +
16A GLY* 2.9 44.5 + - - +
17A ALA* 3.5 12.1 - - - -
18A VAL* 3.5 32.8 - - + -
21A HIS 3.4 12.8 - - - -
22A LYS* 1.3 76.5 - - - +
24A VAL* 1.3 72.9 + - - +
25A ILE* 4.1 19.1 - - + -
46A GLU* 3.3 16.8 - - - +
47A GLY* 4.5 0.2 - - - -
50A LEU* 3.6 19.7 - - + -
52A PHE* 3.7 11.4 - + - -
57A LEU* 3.9 17.5 - - + -
120A PHE* 4.2 6.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 2.9 53.8 - - + +
14A MET 3.1 12.1 - - - +
15A GLU* 4.3 9.6 - - + -
23A PHE* 1.3 79.4 - - - +
25A ILE* 1.3 75.5 + - - +
26A GLU* 4.5 6.5 - - + -
44A VAL* 3.6 0.7 - - - -
45A GLU* 3.0 26.7 + - + -
46A GLU* 3.1 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.1 2.1 - - - +
13A ARG* 3.5 4.0 - - - -
14A MET* 3.0 34.7 + - + +
23A PHE* 4.1 16.4 - - + -
24A VAL* 1.3 80.5 - - - +
26A GLU* 1.3 73.4 + - - +
42A LEU* 4.1 3.6 - - + -
43A THR 3.1 15.9 - - - +
44A VAL* 3.9 17.0 - - + -
45A GLU 4.5 0.2 - - - +
50A LEU* 4.2 3.1 - - + -
54A TYR* 3.8 23.1 - - + +
57A LEU* 3.6 30.5 - - + -
61A PHE* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.5 10.5 - - - +
13A ARG* 4.3 23.0 + - + +
24A VAL* 4.5 9.6 - - + -
25A ILE* 1.3 81.3 - - - +
27A GLY* 1.3 58.9 + - - +
28A GLU* 6.4 0.7 - - + -
41A ASP 3.8 0.7 - - - +
42A LEU* 3.4 1.0 - - - -
43A THR* 2.7 50.3 + - + +
45A GLU* 3.5 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 3.3 4.4 - - - +
12A LEU* 3.1 37.9 + - - +
26A GLU* 1.3 76.5 - - - +
28A GLU* 1.3 71.9 + - - +
40A LEU* 4.6 3.1 - - - -
41A ASP 3.2 9.9 - - - -
42A LEU* 3.7 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE 3.2 11.5 - - - +
11A LYS* 4.9 8.5 - - + +
26A GLU* 6.4 0.4 - - + -
27A GLY* 1.3 81.9 - - - +
29A GLY* 1.3 57.8 + - - +
40A LEU* 3.8 4.0 - - - +
41A ASP* 3.0 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS* 3.5 6.8 - - - +
10A ILE* 3.0 29.8 + - - +
28A GLU* 1.3 74.8 - - - +
30A ILE* 1.3 65.1 + - - +
39A THR 3.1 15.3 - - - -
40A LEU* 3.5 9.2 - - - +
41A ASP* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU* 3.3 35.2 - - + +
8A MET 3.6 14.8 - - - +
9A LYS* 4.5 17.0 - - + +
10A ILE* 4.1 5.2 - - - +
29A GLY* 1.3 77.1 - - - +
31A GLY* 1.3 62.2 + - - +
32A LYS* 4.5 3.5 + - + +
38A GLN* 3.6 0.8 - - - -
39A THR* 3.0 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU* 2.7 20.1 - - - +
8A MET 3.1 28.0 + - - -
30A ILE* 1.3 76.7 - - - +
32A LYS* 1.3 62.7 + - - -
33A PRO* 3.6 0.2 - - - +
37A THR 3.3 13.2 - - - -
38A GLN* 3.7 3.6 - - - -
68A PHE* 3.5 14.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO 3.3 11.2 - - - +
7A GLU* 2.9 26.5 - - - +
30A ILE* 4.5 4.1 + - + +
31A GLY* 1.3 77.6 - - - -
33A PRO* 1.3 69.2 - - - +
34A TYR 3.3 2.2 - - - +
35A GLU* 3.0 21.7 + - + -
36A GLY 3.0 17.3 + - - -
37A THR* 2.6 55.9 + - - -
38A GLN* 3.8 5.7 - - - +
39A THR* 4.9 4.9 + - - -
68A PHE* 4.1 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