Contacts of the strand formed by residues 32 - 38 (chain V) in PDB entry 5EEV
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 V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36U GLU* 4.7 1.3 - - - -
22V ILE* 3.4 46.7 - - + -
23V GLY 3.5 4.0 - - - -
24V LEU* 4.2 12.8 - - + -
25V THR* 4.4 0.7 - - - -
31V ARG* 1.3 81.0 + - - +
33V HIS* 1.3 60.5 + - - +
34V HIS 4.5 2.9 - - - +
56V LYS* 4.6 2.9 - - + -
58V ARG* 3.9 10.5 - - - -
153W G 3.0 87.2 + + + +
154W U 3.5 46.0 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 33 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L GLY 5.2 0.4 + - - -
28L ALA* 4.9 14.5 + - - +
30L THR* 4.6 1.8 + - - -
101L TRP* 3.9 33.6 - + - -
23V GLY* 2.9 30.3 + - - -
24V LEU 3.9 6.7 - - - -
25V THR* 3.8 13.9 - - + -
31V ARG* 3.7 3.1 + - - +
32V PHE* 1.3 75.1 - - - +
34V HIS* 1.3 70.5 + - + +
51V HIS* 3.5 27.0 + - + +
52V THR* 2.5 33.3 + - - -
154W U 5.6 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 34 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L LEU* 5.6 0.2 - - + -
30L THR* 3.4 38.7 + - + +
101L TRP* 4.0 12.3 - + + -
21V VAL 3.8 1.0 - - - +
22V ILE* 3.5 4.9 - - - +
23V GLY 2.8 27.3 + - - -
32V PHE* 3.6 2.9 - - - +
33V HIS* 1.3 100.2 + - + +
35V SER* 1.3 82.2 + - - +
36V GLU* 2.7 35.6 + - + -
102W A 3.9 9.4 - + - -
103W G 3.5 16.6 - - - -
154W U 5.8 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20V ASN* 3.2 19.6 + - - +
21V VAL 3.7 3.1 - - - -
22V ILE* 3.7 18.0 - - - +
34V HIS* 1.3 82.7 + - - +
36V GLU* 1.3 58.7 + - - +
37V LYS* 3.7 12.3 + - - -
101W G 5.3 0.7 + - - -
102W A 3.3 17.7 - - - -
154W U 3.2 40.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L LEU* 3.9 12.2 - - + +
32L PHE* 4.6 0.2 - - - -
56L LYS* 2.6 32.9 + - + +
101L TRP* 5.6 1.1 - - + -
19V VAL 3.6 0.7 - - - +
20V ASN* 3.4 3.1 - - - -
21V VAL* 2.8 44.1 + - - +
34V HIS* 2.7 36.3 + - + +
35V SER* 1.3 71.1 - - - +
37V LYS* 1.3 63.3 - - - +
38V LEU* 3.8 20.4 + - + -
44V LEU* 4.2 23.6 - - + -
102W A 3.6 4.0 - - - -
103W G 2.7 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56L LYS* 3.8 5.7 + - - -
18V GLY 5.6 1.8 - - - +
19V VAL 3.3 4.7 - - - +
20V ASN* 3.2 27.0 + - - +
35V SER* 3.7 22.7 + - - -
36V GLU* 1.3 73.1 - - - +
38V LEU* 1.3 66.3 + - - +
39V ASP 4.3 0.5 + - - -
42V GLU* 4.1 1.7 - - - +
101W G 3.4 84.5 + - + +
102W A 2.9 42.0 + - + +
154W U 4.2 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56L LYS* 4.3 11.9 - - + -
12V ILE* 4.1 20.2 - - + +
14V ALA* 3.8 15.7 - - + +
16V GLU 3.9 1.7 - - - +
17V ASP 3.9 0.3 - - - -
18V GLY* 3.1 20.9 + - - -
19V VAL* 2.7 25.5 + - + +
21V VAL* 3.9 28.0 - - + -
36V GLU* 3.9 18.6 - - + +
37V LYS* 1.3 80.8 - - - +
39V ASP* 1.3 63.7 + - - +
42V GLU* 3.4 23.8 - - + +
44V LEU* 4.0 24.9 - - + +
----------------------------------------------------------
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