Contacts of the strand formed by residues 35 - 40 (chain H) in PDB entry 5T0J
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 SER 35 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H ALA 3.4 1.8 + - - -
34H PRO* 1.3 75.0 - - - +
36H VAL* 1.3 65.1 + - - +
47H ALA 3.8 3.4 - - - -
48H THR* 3.5 16.3 + - - +
75H VAL* 3.3 28.9 - - - +
76H TYR 3.4 18.4 - - - -
77H SER* 3.3 22.1 + - - -
135H LEU* 3.3 13.4 - - - +
162H ALA* 4.0 1.3 - - - -
163H MET 3.8 15.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H PRO 4.2 0.4 - - - -
35H SER* 1.3 81.5 + - - +
37H GLY* 1.3 60.4 + - - +
38H ILE* 5.7 3.4 - - + -
46H LEU* 3.8 2.4 - - - -
47H ALA* 2.6 45.0 + - + +
135H LEU* 3.8 3.9 - - - +
161H THR 3.5 8.7 - - - +
162H ALA* 4.4 9.0 - - + +
191H ALA* 4.9 8.3 - - + +
195H LEU* 4.5 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 37 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H VAL* 1.3 76.5 - - - +
38H ILE* 1.3 67.2 + - - +
45H VAL 3.4 8.5 - - - -
46H LEU* 3.7 13.5 - - - -
135H LEU* 4.1 1.1 - - - +
146H LEU* 3.8 7.2 - - - -
160H ALA* 3.4 3.8 - - - +
161H THR* 2.8 38.9 + - - +
174H LEU* 5.5 0.2 - - - +
191H ALA* 5.2 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 38 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H VAL* 5.5 2.0 - - + -
37H GLY* 1.3 77.6 - - - +
39H LYS* 1.3 60.8 + - - +
40H ALA* 3.9 22.7 - - + -
44H VAL* 3.2 5.9 - - - +
45H VAL* 2.4 70.4 + - + +
47H ALA* 5.4 8.3 - - + +
146H LEU* 3.5 6.7 - - - +
159H LYS 3.5 5.2 - - - +
160H ALA* 4.4 4.0 - - + +
187H ALA* 4.5 13.5 - - + +
188H ILE* 3.7 35.7 - - + +
191H ALA* 3.6 28.7 - - + -
192H ILE* 5.1 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 39 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H ILE* 1.3 69.1 - - - +
40H ALA* 1.3 61.7 + - - +
41H ALA* 2.9 29.8 + - - +
43H GLY 3.9 8.5 - - - +
44H VAL* 3.9 14.4 - - + +
143H ARG* 6.3 0.2 - - - -
144H PRO* 3.5 37.2 - - - +
145H TYR* 4.6 1.6 - - - +
146H LEU* 3.5 20.6 - - + +
158H TRP 4.6 0.4 - - - +
159H LYS* 2.3 63.4 + - + +
181H ASP* 4.6 12.5 + - - +
187H ALA* 5.3 2.9 - - - +
57I ASP* 5.0 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H ILE* 3.9 16.5 + - + -
39H LYS* 1.3 73.4 - - - +
41H ALA* 1.3 69.1 + - - +
42H ASN* 3.2 1.6 + - - +
43H GLY* 2.8 30.1 + - - +
45H VAL* 5.1 4.3 - - + -
181H ASP* 5.0 1.6 - - - -
182H LEU 5.6 1.1 - - - -
184H LEU* 3.5 36.2 - - + +
187H ALA* 4.4 5.2 - - + -
188H ILE* 4.7 6.5 - - + -
----------------------------------------------------------
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