Contacts of the strand formed by residues 33 - 38 (chain A) in PDB entry 1PR9
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 ARG 33 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLY* 4.4 22.7 + - - -
8A ARG 2.8 10.6 + - - +
9A ARG* 3.2 40.5 - - + +
10A VAL* 2.6 34.3 + - - +
31A GLY 5.1 1.6 - - - +
32A ALA* 1.3 75.3 - - - +
34A VAL* 1.3 55.3 + - - +
53A GLY 6.0 2.9 - - - +
55A GLU* 5.1 5.2 - - - +
76A PRO* 5.9 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.4 7.0 - - + +
12A VAL* 4.4 6.7 - - + -
24A VAL* 3.8 35.0 - - + +
27A LEU* 3.9 31.0 - - + -
28A HIS* 4.2 10.5 - - + +
32A ALA* 3.7 10.1 + - + +
33A ARG* 1.3 77.6 - - - +
35A VAL* 1.3 76.7 + - - +
36A ALA* 4.2 1.6 - - + +
53A GLY 4.7 1.6 + - - +
54A ILE* 3.4 20.0 - - + +
55A GLU* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 3.4 43.1 - - + +
10A VAL 2.8 13.0 + - - +
11A LEU* 3.5 17.2 - - + +
12A VAL 2.9 28.2 + - - +
34A VAL* 1.3 77.4 - - - +
36A ALA* 1.3 60.6 + - - +
37A VAL* 4.0 4.7 + - + -
55A GLU* 3.4 18.6 - - + +
57A VAL* 3.9 22.2 - - + -
71A LEU* 5.4 0.2 - - + -
74A VAL* 3.9 15.7 - - + -
77A VAL* 4.8 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL 3.8 3.8 - - - -
15A ALA* 3.6 19.3 - - + -
24A VAL* 4.4 7.0 - - + -
34A VAL* 3.9 3.7 - - + -
35A VAL* 1.3 71.6 - - - +
37A VAL* 1.3 56.8 + - - +
44A LEU* 3.7 11.1 - - + +
47A LEU* 4.2 4.0 - - + -
54A ILE* 3.9 28.3 - - + -
55A GLU 2.8 10.0 + - - +
56A PRO* 3.3 2.8 - - + +
57A VAL 2.7 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.0 22.7 - - + -
12A VAL 3.0 10.3 + - - +
13A THR* 4.2 6.5 - - + -
14A GLY 2.9 25.9 + - - -
15A ALA* 3.0 7.7 + - - +
35A VAL* 4.3 8.1 - - + -
36A ALA* 1.3 75.3 - - - +
38A SER* 1.3 65.2 + - - +
57A VAL* 3.2 21.1 - - + +
59A VAL* 3.7 28.3 - - + -
61A LEU* 4.1 23.1 - - + -
71A LEU* 4.2 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY 4.0 1.0 - - - -
15A ALA 3.7 2.6 + - - -
16A GLY* 3.0 31.6 + - - -
36A ALA 4.1 0.6 + - - -
37A VAL* 1.3 76.6 - - - +
39A ARG* 1.3 67.0 + - - +
40A THR 3.4 5.3 + - - -
43A ASP* 4.8 0.7 + - - -
44A LEU* 3.9 19.6 - - - +
57A VAL 3.1 5.3 + - - -
58A CYS* 3.3 8.8 - - - -
59A VAL 3.1 24.5 + - - -
245A NAP 3.2 25.1 + - - -
----------------------------------------------------------
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