Contacts of the strand formed by residues 32 - 38 (chain Q) in PDB entry 5EEY
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 PHE 32 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P GLU* 4.6 1.1 - - - -
22Q ILE* 3.4 48.5 - - + -
23Q GLY 3.7 2.5 - - - -
24Q LEU* 3.9 14.4 - - + -
31Q ARG* 1.3 83.7 + - - +
33Q HIS* 1.3 62.1 + - - +
34Q HIS 4.6 3.4 - - - +
56Q LYS* 4.4 3.4 - - + -
58Q ARG* 4.1 4.7 - - - -
128W G 2.9 84.8 + + + +
129W U 3.7 52.5 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 33 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Q GLY* 2.9 35.3 + - - -
24Q LEU 3.8 7.4 - - - -
25Q THR* 3.8 15.3 - - + -
31Q ARG* 3.7 2.6 + - - +
32Q PHE* 1.3 75.1 - - - +
34Q HIS* 1.3 71.1 + - + +
51Q HIS* 3.5 25.6 + - + +
52Q THR* 2.6 30.0 + - - -
27R GLY 5.4 0.2 + - - -
28R ALA* 4.9 15.8 + - - +
30R THR* 4.8 1.2 + - - -
101R TRP* 4.0 34.2 - + - -
129W U 6.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 34 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Q VAL 3.8 0.7 - - - +
22Q ILE* 3.4 4.8 - - - +
23Q GLY 2.8 27.1 + - - -
32Q PHE* 3.6 2.4 - - - -
33Q HIS* 1.3 100.0 + - + +
35Q SER* 1.3 80.1 + - - +
36Q GLU* 2.6 43.9 + - + -
24R LEU* 5.7 0.4 - - + -
30R THR* 3.6 38.4 + - + +
101R TRP* 3.9 13.2 - + + -
129W U 5.6 2.9 - - - -
132W A 4.0 8.5 - + - -
133W G 3.6 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Q ASN* 3.0 27.2 + - - +
21Q VAL 3.6 4.0 - - - -
22Q ILE* 3.9 11.1 - - - +
34Q HIS* 1.3 83.5 + - - +
36Q GLU* 1.3 59.8 + - - +
37Q LYS* 3.4 14.3 + - - -
129W U 3.0 34.4 + - - -
132W A 3.3 18.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Q VAL 3.5 0.7 - - - +
20Q ASN* 3.4 2.3 - - - -
21Q VAL* 2.8 44.9 + - - +
34Q HIS* 2.6 37.8 + - + +
35Q SER* 1.3 72.3 - - - +
37Q LYS* 1.3 60.9 + - - +
38Q LEU* 3.8 19.6 + - + +
44Q LEU* 4.2 22.9 - - + -
24R LEU* 3.9 13.6 - - + +
56R LYS* 2.7 23.1 + - - +
101R TRP* 5.4 1.6 - - + -
132W A 3.7 4.7 - - - +
133W G 2.6 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Q GLY 5.0 0.2 - - - +
19Q VAL 3.3 2.2 - - - +
20Q ASN* 3.6 27.7 + - - +
35Q SER* 3.4 37.1 + - - -
36Q GLU* 1.3 71.8 - - - +
38Q LEU* 1.3 62.8 + - - +
42Q GLU* 4.3 0.3 - - - +
56R LYS* 3.9 9.0 + - - -
129W U 3.4 17.2 + - - +
131W G 3.0 94.3 + - + +
132W A 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Q ILE* 4.1 19.7 - - + +
14Q ALA* 3.8 16.4 - - + -
16Q GLU 3.9 0.7 - - - +
18Q GLY 3.1 7.2 + - - -
19Q VAL* 2.9 36.0 + - + +
21Q VAL* 4.0 22.7 - - + -
36Q GLU* 4.2 15.5 - - + +
37Q LYS* 1.3 76.6 - - - +
39Q ASP* 1.3 65.6 + - - +
42Q GLU* 3.4 20.9 - - + +
44Q LEU* 4.0 26.5 - - + +
56R LYS* 3.9 26.2 - - + -
----------------------------------------------------------
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