Contacts of the strand formed by residues 32 - 39 (chain B) in PDB entry 2EBJ
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 LYS 32 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 5.5 2.9 - - - +
2B ILE* 3.5 24.2 - - + -
28B GLU* 3.1 2.0 - - - -
29B VAL 2.9 37.8 + - - +
30B ASP* 4.2 12.1 + - + +
31B GLY* 1.3 79.5 - - - +
33B PRO* 1.3 70.1 - - + +
34B LEU* 3.0 5.0 - - - +
189B LEU 5.3 1.6 - - - +
192B LEU* 3.2 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.3 26.0 - - + +
2B ILE* 2.8 26.9 + - - -
27B SER 3.7 7.2 - - - +
28B GLU* 3.9 8.3 - - + +
31B GLY 3.4 9.4 - - - +
32B LYS* 1.3 82.2 - - + +
34B LEU* 1.3 62.1 + - - +
35B ARG 3.9 0.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
1B MET* 5.2 0.2 - - - -
2B ILE* 3.4 15.5 - - + +
4B VAL* 4.2 17.3 - - + -
25B LEU* 4.3 14.4 - - + -
26B PRO 3.5 22.2 - - - +
27B SER* 2.9 18.9 + - - +
28B GLU* 3.8 0.9 - - - -
29B VAL* 3.5 37.5 - - + +
32B LYS 3.0 27.8 - - - +
33B PRO* 1.3 72.8 - - - +
35B ARG* 1.3 60.0 + - - +
36B LYS* 3.7 16.5 + - + +
189B LEU* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.6 30.5 - - + -
2B ILE 2.8 8.5 + - - +
3B LEU* 3.4 17.8 - - + +
4B VAL 2.9 24.8 + - - +
33B PRO 3.9 0.8 + - - -
34B LEU* 1.3 70.7 - - - +
36B LYS* 1.3 80.6 + - - +
37B ALA* 3.8 8.3 - - - +
53B LEU* 3.5 16.0 - - - +
56B GLU* 2.8 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 3.2 13.7 - - + +
22B LEU* 3.1 42.5 + - + +
23B ASP* 4.9 2.4 - - - +
25B LEU* 2.7 36.4 + - + -
26B PRO 3.5 19.5 + - - -
27B SER* 5.1 2.8 - - - +
34B LEU* 3.7 17.6 + - + +
35B ARG* 1.3 94.8 + - - +
37B ALA* 1.3 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 4.4 2.5 - - + -
4B VAL 3.1 5.5 + - - -
5B THR* 3.1 15.5 - - + -
6B GLY 2.9 23.2 + - - -
22B LEU* 3.6 3.6 - - - +
35B ARG* 3.8 13.2 - - - +
36B LYS* 1.3 77.5 - - - +
38B VAL* 1.3 66.9 + - - +
39B LEU* 5.1 0.2 - - + -
53B LEU* 4.0 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLY 3.5 3.1 - - - +
7B PHE 3.8 4.7 - - - +
8B GLU* 3.6 30.5 - - + +
19B GLN* 3.8 39.9 - - + +
22B LEU* 4.0 14.4 - - + -
37B ALA* 1.3 76.3 - - - +
39B LEU* 1.3 66.3 + - - +
40B PRO* 4.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B THR* 3.8 26.0 - - + +
6B GLY 2.8 15.7 + - - +
7B PHE* 3.4 35.7 - - + -
8B GLU* 3.2 23.8 + - - +
37B ALA* 5.1 0.7 - - + -
38B VAL* 1.3 75.5 - - - +
40B PRO* 1.3 73.0 - - + +
46B LEU* 4.1 11.4 - - + -
49B ALA* 4.7 5.4 - - + -
50B LEU* 3.9 23.8 - - + -
53B LEU* 3.6 31.0 - - + -
63B HIS* 4.1 1.8 - - - +
142B ALA* 4.1 8.7 - - + -
----------------------------------------------------------
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