Contacts of the strand formed by residues 17 - 25 (chain A) in PDB entry 1PU5
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 ALA 17 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASN* 4.6 1.2 - - - +
15A ASP* 3.9 2.3 - - - +
16A PRO* 1.3 78.3 - - + +
18A VAL* 1.3 66.3 + - - +
42A SER 3.3 5.8 - - - +
43A THR* 3.9 17.5 - - - +
47A LEU* 4.6 6.5 - - + -
145A LEU* 4.3 19.7 - - + -
152A LEU* 2.9 24.1 + - + +
153A GLY* 3.5 12.9 - - - -
154A CYS 4.6 0.7 + - - -
155A ILE* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASN* 3.4 22.0 - - + +
11A ASP 5.5 0.2 - - - -
12A GLU* 4.0 22.7 - - + +
15A ASP* 3.4 22.2 - - + +
16A PRO 5.1 2.0 - - - +
17A ALA* 1.3 80.0 - - - +
19A ILE* 1.3 66.2 + - - +
20A ARG* 3.7 17.0 + - - +
41A GLY* 3.3 1.6 - - - -
42A SER* 2.9 50.4 + - - +
155A ILE* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TRP* 3.4 33.4 - - + -
9A ASN* 2.8 27.6 + - - +
18A VAL* 1.3 78.1 - - - +
20A ARG* 1.3 64.4 + - - +
21A SER 3.4 23.1 - - - +
22A LEU* 4.1 9.4 - - + -
39A VAL* 4.0 19.3 - - + -
40A VAL 3.7 1.3 - - - +
41A GLY* 4.4 8.3 - - - -
155A ILE* 3.6 32.8 - - + -
900A EPE 5.4 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TRP* 3.8 11.0 - - - -
18A VAL* 3.7 18.2 - - - +
19A ILE* 1.3 74.4 - - - +
21A SER* 1.3 60.4 + - - +
40A VAL* 2.7 36.4 + - + +
41A GLY* 4.3 4.9 - - - -
42A SER* 2.6 35.8 + - - +
115A THR* 4.8 6.1 + - + -
900A EPE 5.0 6.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TRP* 3.7 7.0 - - - -
19A ILE* 3.4 7.6 - - - +
20A ARG* 1.3 82.4 - - - +
22A LEU* 1.3 63.8 + - - +
23A THR* 5.9 3.4 - - - -
38A SER* 4.7 1.8 + - - -
39A VAL* 3.3 3.7 - - - -
40A VAL* 3.0 48.3 + - - +
88B MET* 4.7 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 3.8 27.0 - - + -
7A TRP* 3.4 45.3 + - + +
19A ILE* 4.1 8.7 - - + -
21A SER* 1.3 76.5 - - - +
23A THR* 1.3 68.7 + - - +
24A LEU* 5.7 0.7 - - + -
37A LEU* 3.3 33.9 - - + -
38A SER* 3.4 6.7 - - - +
39A VAL* 3.9 13.5 - - + -
155A ILE* 5.5 4.5 - - + -
157A ILE* 3.9 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 4.2 4.9 - - - -
21A SER* 5.9 2.2 - - - -
22A LEU* 1.3 83.5 - - - +
24A LEU* 1.3 62.4 + - - +
25A GLU* 4.4 9.4 + - - -
36A THR 4.1 1.1 - - - -
37A LEU* 3.3 10.0 - - - +
38A SER* 2.7 52.0 + - - +
120A LYS* 3.9 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 3.6 53.0 - - + +
22A LEU* 5.5 0.9 - - + -
23A THR* 1.3 76.4 - - - +
25A GLU* 1.3 66.9 + - - +
26A PRO 3.9 6.3 - - - +
27A ASP* 4.7 3.5 - - - +
29A ILE* 3.6 28.5 - - + -
35A VAL* 3.9 29.2 - - + -
36A THR 3.3 5.6 - - - +
37A LEU* 4.6 13.0 - - + -
157A ILE* 5.1 4.0 - - + -
159A ALA* 4.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A THR* 4.4 7.5 + - - -
24A LEU* 1.3 83.4 - - - +
26A PRO* 1.3 71.9 - - + +
27A ASP* 5.6 0.7 - - + +
29A ILE* 5.1 0.4 - - - -
35A VAL* 3.1 8.4 - - - +
36A THR* 2.7 51.2 + - - +
120A LYS* 2.9 42.2 + - - +
----------------------------------------------------------
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