Contacts of the helix formed by residues 21 - 34 (chain B) in PDB entry 2JB3
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 GLY 21 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLY 3.4 4.0 + - - -
20B GLY* 1.3 79.4 - - - +
22B PRO* 1.3 76.7 - - - +
23B ALA 3.3 3.1 - - - -
24B GLY 3.4 1.2 + - - +
25B LEU* 2.9 26.7 + - - +
48B GLY* 3.7 11.2 - - - -
1489B FAD 3.5 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY* 1.3 82.4 - - - +
23B ALA* 1.3 56.5 + - - +
25B LEU* 4.3 0.3 - - - +
26B CYS* 2.9 33.8 + - - +
48B GLY* 3.1 16.8 - - - +
51B VAL* 3.8 8.1 - - + -
243B TYR* 3.5 41.8 - - + +
468B GLN* 4.8 2.9 - - + -
471B ALA* 3.9 10.8 - - + -
472B LEU* 3.6 9.4 - - + +
1489B FAD 3.3 40.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PRO* 1.3 73.5 - - - +
24B GLY* 1.3 58.4 + - - +
27B SER* 2.8 33.8 + - - -
292B THR* 3.8 16.6 - - + -
457B ALA* 4.4 1.8 - - + -
458B GLY* 3.9 12.8 - - - +
471B ALA* 3.7 25.5 - - + +
475B ALA* 3.2 7.6 - - + +
1489B FAD 2.8 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 3.4 32.6 - - - +
19B GLY 3.5 13.5 - - - -
21B GLY 3.4 3.4 + - - -
22B PRO 3.3 0.4 - - - -
23B ALA* 1.3 81.3 - - - +
25B LEU* 1.3 56.7 + - - +
27B SER* 3.4 0.8 + - - -
28B ALA* 2.9 27.0 + - - +
40B VAL* 4.2 1.9 - - - +
292B THR* 3.7 10.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLY 4.5 0.2 + - - -
20B GLY* 3.3 31.4 - - - +
21B GLY 2.9 17.1 + - - +
22B PRO 4.3 1.3 - - - +
24B GLY* 1.3 74.0 - - - +
26B CYS* 1.3 57.7 + - - +
28B ALA* 3.3 0.9 + - - -
29B PHE* 2.8 31.9 + - - +
40B VAL* 4.5 8.3 - - + -
47B PRO* 3.8 22.9 - - + -
48B GLY 4.1 0.2 - - - +
243B TYR* 3.9 29.4 - - + +
246B PHE* 4.0 17.5 - - + -
247B GLN 4.9 3.6 - - - +
250B ILE* 3.5 23.7 - - + +
255B ILE* 4.2 19.1 - - + -
257B PHE* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PRO 2.9 20.3 + - - +
23B ALA 3.8 3.4 - - - +
25B LEU* 1.3 76.5 - - - +
27B SER* 1.3 62.1 + - - +
29B PHE* 3.3 1.2 + - - +
30B GLU* 3.0 31.9 + - - +
94B TYR* 3.3 36.3 - - - -
246B PHE* 4.1 12.0 - - + -
472B LEU* 3.5 36.8 - - + -
475B ALA* 3.9 7.4 - - + -
476B ARG* 4.2 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 4.4 4.9 - - - -
23B ALA 2.8 23.3 + - - -
24B GLY* 3.5 8.1 - - - -
26B CYS* 1.3 75.6 - - - +
28B ALA* 1.3 58.6 + - - +
30B GLU 3.3 0.2 + - - -
31B LEU* 2.9 37.0 + - - +
290B ILE* 4.0 35.0 - - - +
457B ALA* 5.0 0.2 - - - +
475B ALA* 3.2 19.9 + - - +
478B VAL* 5.3 0.2 - - - +
479B VAL* 3.7 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 4.5 7.3 - - + +
24B GLY 2.9 11.5 + - - +
25B LEU 3.9 3.6 - - - +
27B SER* 1.3 75.6 - - - +
29B PHE* 1.3 57.4 + - - +
31B LEU* 3.8 3.1 - - - -
32B GLN* 2.9 33.5 + - - +
38B VAL* 3.9 21.0 - - + +
40B VAL* 3.4 33.2 - - + -
250B ILE* 3.9 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU 2.8 17.3 + - - +
26B CYS 3.5 3.6 - - - +
28B ALA* 1.3 76.7 - - - +
30B GLU* 1.3 82.5 + - + +
32B GLN* 3.4 7.2 + - - +
33B LYS* 3.0 54.7 + - + +
94B TYR* 4.1 10.3 - + - -
97B GLU* 4.0 12.1 - - + -
98B LEU* 4.3 5.2 - - + -
246B PHE* 3.7 29.2 - + + -
249B ARG* 3.6 56.1 - - + -
250B ILE* 4.0 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 3.7 44.5 + - + +
6B ILE* 4.4 4.8 - - + +
26B CYS* 3.0 23.2 + - - +
27B SER 3.9 2.0 - - - +
29B PHE* 1.3 89.9 - - + +
31B LEU* 1.3 63.9 + - - +
33B LYS* 3.3 22.9 + - - +
34B ALA* 3.3 20.6 + - - +
94B TYR* 2.5 39.6 + - - +
476B ARG* 3.8 4.9 + - + -
479B VAL* 4.3 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 3.9 24.9 - - + -
17B VAL* 4.7 1.8 - - + -
27B SER* 2.9 24.7 + - - +
28B ALA* 4.0 1.1 - - - +
30B GLU* 1.3 76.3 - - - +
32B GLN* 1.3 61.2 + - - +
34B ALA* 3.2 3.8 + - - -
35B GLY 3.1 5.9 + - - -
36B TYR* 3.1 59.9 + - + -
38B VAL* 3.5 17.5 - - + -
290B ILE* 3.8 27.6 - - + -
479B VAL* 3.8 26.7 - - + +
482B ILE* 4.7 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA 2.9 21.7 + - - +
29B PHE* 3.6 6.9 - - - +
31B LEU* 1.3 72.7 - - - +
33B LYS* 1.3 59.1 + - - +
35B GLY* 3.0 19.9 + - - -
36B TYR 3.9 13.4 - - - +
38B VAL* 4.1 10.4 - - + +
249B ARG 3.3 20.2 - - - +
250B ILE* 2.8 41.8 + - - +
254B ASN* 3.3 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ASP* 5.2 15.9 - - + +
5B LEU 5.9 0.4 - - - +
8B LYS* 3.8 18.9 + - - -
29B PHE* 3.0 48.0 + - + +
30B GLU* 3.5 22.0 + - - +
31B LEU 3.2 0.2 - - - -
32B GLN* 1.3 78.7 - - - +
34B ALA* 1.3 58.2 + - - +
35B GLY 3.6 0.3 + - - -
97B GLU* 3.5 25.6 + - - +
249B ARG* 4.9 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 3.5 32.8 - - + +
7B GLY 3.3 23.1 - - - +
8B LYS* 3.6 13.7 - - - +
9B VAL* 2.8 33.8 + - - +
30B GLU 3.3 2.5 + - - +
31B LEU 3.2 8.5 + - - +
33B LYS* 1.3 78.9 - - - +
35B GLY* 1.3 55.3 + - - +
36B TYR* 3.6 7.6 - - + -
----------------------------------------------------------
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