Contacts of the strand formed by residues 32 - 39 (chain B) in PDB entry 4PC0
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 TYR 32 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TRP* 3.0 37.8 + + - -
28B THR* 2.8 40.9 + - + +
29B PRO* 4.0 11.6 - - - +
30B PHE 3.7 0.2 - - - -
31B LEU* 1.3 88.0 - - + +
33B ASP* 1.3 64.4 + - - +
34B LEU 3.7 20.2 - - - +
35B VAL* 4.1 9.9 - - + -
368B PHE* 3.5 21.3 - + - -
369B ILE 4.7 0.3 + - - -
370B HIS* 2.8 27.0 + + - -
402B TRP* 3.6 29.2 - + + -
403B GLN 3.3 22.0 - - - +
404B MET* 4.1 2.2 - - - -
405B ALA* 4.2 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 1.3 74.4 - - - +
34B LEU* 1.3 62.1 + - - +
35B VAL* 6.0 0.2 - - - -
108B PHE* 6.0 0.7 - - - +
403B GLN* 3.0 27.2 + - - +
404B MET 3.8 3.9 - - - +
405B ALA* 3.9 15.2 - - - +
406B GLU* 3.3 29.3 + - - +
409B TYR* 5.0 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 3.7 2.5 - - - +
33B ASP* 1.3 83.3 - - - +
35B VAL* 1.3 68.1 + - - +
36B MET* 4.8 5.6 - - + -
86B LEU* 3.8 27.8 - - + -
87B PRO* 4.0 16.2 - - + -
108B PHE* 3.6 42.6 - - + +
389B VAL* 4.7 12.1 - - + -
401B VAL* 4.2 22.4 - - + +
402B TRP* 3.2 4.1 - - - +
403B GLN* 2.7 46.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TRP* 3.7 34.8 - - + -
25B LYS* 6.2 3.1 - - + +
28B THR* 3.8 27.6 - - + +
32B TYR* 4.1 14.4 - - + -
33B ASP 6.0 0.2 - - - -
34B LEU* 1.3 79.9 - - - +
36B MET* 1.3 67.5 + - - +
37B THR* 6.1 1.1 - - + -
107B GLY 6.0 0.2 - - - -
108B PHE 3.9 11.2 + - - +
109B GLY 5.0 2.3 - - - +
110B SER* 5.3 1.4 + - - -
400B GLN* 5.3 3.6 - - - +
401B VAL 3.7 3.1 - - - -
402B TRP* 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.8 8.3 - - + -
35B VAL* 1.3 75.0 - - - +
37B THR* 1.3 60.5 + - - +
38B HIS* 5.7 0.2 - - - -
84B VAL* 4.5 8.7 - - - -
85B GLN 3.8 7.6 - - - +
86B LEU* 5.1 0.4 - - - -
108B PHE* 3.2 45.3 - - + +
109B GLY* 3.5 15.5 - - - +
114B LYS* 3.1 40.2 - - + -
115B ILE* 4.5 15.3 - - + -
399B MET 4.5 0.2 - - - -
400B GLN* 3.1 10.4 - - - +
401B VAL* 2.9 51.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TYR* 4.3 16.6 + - - +
24B TRP* 6.2 0.7 - - + -
25B LYS* 5.0 12.1 - - - -
35B VAL* 6.1 1.3 - - + -
36B MET* 1.3 75.5 - - - +
38B HIS* 1.3 62.9 + - - +
109B GLY 4.9 6.3 + - - +
398B ILE* 3.5 28.6 - - - +
399B MET 3.5 3.1 - - - -
400B GLN* 3.9 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B THR* 1.3 78.2 + - - +
39B ALA* 1.3 73.9 + - - +
40B LEU* 3.6 33.1 + - + +
115B ILE* 3.6 51.9 - - + +
116B GLU* 5.9 0.7 - - - -
117B ILE* 5.4 6.1 - - + +
398B ILE* 3.6 4.6 - - - -
399B MET* 2.8 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B HIS* 1.3 83.4 + - - +
40B LEU* 1.3 67.8 + - - +
41B GLU 3.9 0.2 + - - -
397B ASN* 3.9 9.2 - - + -
398B ILE* 4.7 13.0 - - + -
----------------------------------------------------------
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