Contacts of the strand formed by residues 34 - 39 (chain J) in PDB entry 5A15
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 GLN 34 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I PHE* 5.3 12.3 - - + -
30J ASN* 3.7 0.6 - - - -
31J VAL 2.8 38.6 + - - +
32J GLY 3.3 1.7 - - - +
33J GLY* 1.3 84.0 - - - +
35J VAL* 1.3 66.2 + - - +
36J TYR* 3.4 35.3 + - + +
79J GLY* 3.7 12.8 - - - +
80J PHE* 3.5 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 35 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I GLY 4.8 2.9 - - - +
33I GLY* 5.7 1.7 - - - +
28J GLU* 4.3 7.0 - - + +
29J LEU 3.3 11.7 - - - +
30J ASN* 4.6 5.2 - - - +
33J GLY 3.9 7.2 + - - +
34J GLN* 1.3 76.4 - - - +
36J TYR* 1.3 74.2 + - - +
37J PHE* 3.9 27.4 - - + -
72J ARG* 3.4 37.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 36 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I GLY 4.3 8.3 - - - -
78I ASP* 5.7 1.1 - - - -
80I PHE* 5.5 10.7 - + - -
27J VAL 3.7 0.5 - - - +
28J GLU* 3.6 1.7 - - - -
29J LEU* 2.7 49.9 + - + +
31J VAL* 4.3 4.7 - - + -
34J GLN* 3.4 38.1 - - + +
35J VAL* 1.3 76.1 - - - +
37J PHE* 1.3 64.0 + - - +
38J THR* 6.2 0.2 - - + -
79J GLY 2.7 29.5 + - - -
80J PHE* 4.2 2.9 - - - -
82J PHE* 3.8 22.2 - + + -
83J ARG* 3.5 39.5 - - + +
86J LEU* 4.0 26.5 - - + -
90J ARG* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 37 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ASN* 3.8 21.5 - - - -
32I GLY* 3.5 8.5 + - - -
33I GLY* 3.2 31.0 - - - +
68I ASP* 4.8 8.5 - - + -
69I SER* 5.4 6.1 - - - -
72I ARG* 5.5 4.7 - - - -
74I PHE* 3.3 22.7 - - + -
26J VAL* 4.0 18.2 - - + -
27J VAL 3.4 3.8 - - - -
28J GLU* 3.2 49.6 - - + -
35J VAL* 3.9 13.0 - - + -
36J TYR* 1.3 80.0 - - - +
38J THR* 1.3 61.5 + - - +
86J LEU* 4.3 1.2 - - - +
90J ARG* 3.0 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74I PHE* 3.6 14.1 - - - -
76I ASP* 3.0 19.7 + - - -
26J VAL* 3.4 1.7 - - - -
27J VAL 2.6 42.4 + - - +
29J LEU* 4.3 9.9 - - + -
37J PHE* 1.3 77.9 - - - +
39J ARG* 1.3 69.8 + - - +
42J THR* 3.3 16.6 - - - +
43J LEU* 3.8 29.4 - - + -
86J LEU* 4.0 17.9 - - + +
90J ARG* 4.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 39 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I LEU 4.6 2.6 + - - -
66I ALA* 3.4 27.4 - - - +
74I PHE* 4.2 12.4 + - + -
76I ASP* 3.2 31.2 + - + +
25J GLU* 3.1 38.4 + - + +
26J VAL* 4.3 2.6 - - + +
27J VAL* 4.5 0.2 - - - -
38J THR* 1.3 84.0 + - - +
40J HIS* 1.3 65.2 + - - +
41J SER* 3.5 23.4 + - - +
42J THR* 3.1 18.9 + - - +
43J LEU* 3.7 4.2 + - - +
----------------------------------------------------------
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