Contacts of the strand formed by residues 33 - 39 (chain B) in PDB entry 1PRX
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 TRP 33 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 4.4 1.5 - - - +
32B SER* 1.3 79.1 - - - +
34B GLY* 1.3 59.1 + - - +
64B ARG 4.6 0.2 - - - -
65B ASN* 2.8 25.9 + - + +
66B VAL* 3.8 15.0 - - + -
67B LYS* 2.8 23.4 + - - +
136B VAL* 4.3 11.7 - - + -
137B PHE 3.5 20.0 - - - -
138B GLY* 3.6 7.0 - - - -
139B PRO* 3.7 26.5 - - + +
144B LYS* 3.8 31.4 - - + -
164B VAL* 6.0 3.1 - - + -
167B LEU* 3.9 37.9 - - + -
168B GLN* 3.6 36.7 - - + +
171B ALA* 4.2 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PHE* 6.3 0.2 - - - -
28B PHE* 5.8 0.2 - - - -
29B LEU* 3.7 22.3 - - - +
32B SER 3.9 0.2 + - - -
33B TRP* 1.3 76.6 - - - +
35B ILE* 1.3 65.2 + - - +
36B LEU 4.1 0.4 - - - -
67B LYS 3.2 7.6 - - - -
69B ILE* 6.0 0.2 - - - -
135B PHE 3.7 0.7 - - - +
136B VAL* 3.4 4.5 - - - +
137B PHE* 2.9 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLY* 1.3 76.9 - - - +
36B LEU* 1.3 60.3 + - - +
37B PHE* 3.5 26.7 - - + -
61B PHE* 4.0 13.7 - - + -
66B VAL* 3.8 19.7 - - + -
67B LYS 2.8 9.1 + - - -
68B LEU* 3.5 14.2 - - + -
69B ILE* 2.9 32.7 + - - +
134B VAL* 3.9 20.6 - - + -
135B PHE 3.3 4.0 - - - +
136B VAL* 4.3 15.3 - - + -
160B ILE* 4.1 11.2 - - + -
164B VAL* 3.9 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PHE* 5.1 3.6 - - + -
25B PHE* 4.7 11.2 - - + -
34B GLY 4.1 0.8 - - - -
35B ILE* 1.3 72.1 - - - +
37B PHE* 1.3 59.0 + - - +
38B SER* 4.6 6.1 - - - +
69B ILE* 3.2 29.8 - - + +
71B LEU* 4.1 23.8 - - + -
103B ILE* 4.1 13.9 - - + -
114B LEU* 3.4 34.3 - - + -
133B VAL 3.6 1.6 - - - +
134B VAL* 3.3 5.2 - - - +
135B PHE* 2.9 59.3 + - + +
137B PHE* 4.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 3.5 30.5 - - + -
36B LEU* 1.3 73.6 - - - +
38B SER* 1.3 61.5 + - - +
39B HIS* 3.8 18.1 - - - +
51B LEU* 4.8 7.2 - - + -
54B ALA* 4.6 4.5 - - + -
61B PHE* 5.8 0.9 - + - -
68B LEU* 3.6 28.9 - - + -
69B ILE 2.9 20.6 + - - +
70B ALA* 3.4 6.5 - - + -
71B LEU* 2.9 27.9 + - - +
100B PHE* 6.0 2.5 - + - -
133B VAL 4.2 0.9 - - - -
134B VAL* 4.0 11.9 - - + -
155B ARG* 3.6 19.3 - - - +
157B PHE* 3.4 39.0 - + - -
160B ILE* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 4.6 4.2 + - - +
37B PHE* 1.3 71.7 - - - +
39B HIS* 1.3 66.7 + - - +
71B LEU* 3.6 7.9 - - - +
116B MET* 3.1 34.8 - - - +
131B ALA 3.5 10.1 - - - +
132B ARG* 3.8 3.5 - - - -
133B VAL 2.8 36.2 + - - -
135B PHE* 3.9 7.1 - - - -
155B ARG* 2.8 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.8 11.5 - - - +
38B SER* 1.3 78.1 + - - +
40B PRO* 1.4 70.7 - - - +
41B ARG 4.5 2.9 - - - +
47B CSO 3.0 45.2 - - + +
50B GLU* 3.3 24.4 + - + -
51B LEU* 3.4 32.8 - - + +
70B ALA* 4.5 3.4 - - + -
71B LEU* 3.0 18.6 + - - +
72B SER* 3.4 27.6 - - - +
73B ILE* 3.6 3.6 + - - +
82B TRP* 4.6 3.8 - + + -
131B ALA* 3.4 10.5 - - - +
132B ARG* 3.8 0.2 + - - -
155B ARG* 3.4 18.6 + - - -
----------------------------------------------------------
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