Contacts of the helix formed by residues 0 - 22 (chain B) in PDB entry 5JHC
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 PRO 0 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1B GLY* 1.3 81.5 - - - +
1B MET* 1.3 64.0 + - + +
2B GLU 2.8 11.6 + - - -
3B GLU* 3.9 11.9 - - + -
4B GLN* 2.9 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 1 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1B GLY* 3.5 28.3 - - - -
0B PRO* 1.3 79.3 - - + +
2B GLU* 1.3 64.6 + - + +
4B GLN* 5.1 3.3 + - - +
5B ARG* 3.9 14.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 2 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1B GLY* 3.4 9.3 + - - +
0B PRO 2.8 0.4 - - - -
1B MET* 1.3 90.1 - - + +
3B GLU* 1.3 60.8 + - - +
4B GLN 3.4 1.1 - - - -
5B ARG* 3.3 9.0 - - - +
6B GLU* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 3 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1B GLY 3.2 14.8 + - - +
0B PRO* 3.1 10.5 + - + +
2B GLU* 1.3 73.9 - - - +
4B GLN* 1.3 68.9 + - - +
6B GLU* 3.1 33.3 + - - +
7B ILE* 3.0 31.8 + - + +
6G GLU* 4.8 19.7 - - - +
10G GLN* 4.4 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 4 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 3.5 36.7 + - + +
22A LEU* 5.5 3.0 + - - +
0B PRO* 2.9 17.3 + - + +
1B MET* 5.1 3.5 + - - +
3B GLU* 1.3 79.5 - - - +
5B ARG* 1.3 60.2 + - - +
7B ILE* 3.1 11.0 - - - +
8B LEU* 2.9 38.4 + - + +
10G GLN* 4.7 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 3.9 15.8 + - - +
2B GLU* 3.2 12.8 + - - +
3B GLU 3.1 0.8 - - - -
4B GLN* 1.3 80.9 - - - +
6B GLU* 1.3 58.3 + - - +
8B LEU* 3.3 12.2 + - - +
9B GLU* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLU 2.9 13.8 + - - +
3B GLU* 3.1 32.7 + - - +
5B ARG* 1.3 75.8 - - - +
7B ILE* 1.3 63.3 + - + +
9B GLU* 3.3 7.5 + - - +
10B GLN* 2.9 27.2 + - - +
6G GLU* 5.1 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 4.0 15.5 - - + +
3B GLU* 3.0 22.9 + - + +
4B GLN* 3.1 23.6 - - - +
6B GLU* 1.3 77.5 - - + +
8B LEU* 1.3 59.1 + - - +
10B GLN* 3.1 12.2 + - + +
11B LEU* 2.9 30.1 + - + +
3G GLU* 4.1 9.2 - - + +
6G GLU* 3.1 40.2 - - + +
7G ILE* 3.4 35.0 - - + +
10G GLN* 4.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.0 15.7 - - + -
21A GLU* 3.7 24.9 - - + -
22A LEU* 3.6 33.0 - - + +
4B GLN* 2.9 27.7 + - + +
5B ARG* 3.4 9.9 - - - +
7B ILE* 1.3 80.1 - - + +
9B GLU* 1.3 56.5 + - - +
11B LEU* 3.5 8.7 + - - +
12B LYS* 3.0 25.1 + - - +
22a LEU* 4.8 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ARG 3.0 16.3 + - - +
6B GLU* 3.7 7.4 - - - +
8B LEU* 1.3 75.1 - - - +
10B GLN* 1.3 60.4 + - - +
12B LYS* 3.8 10.9 - - + +
13B LYS* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU* 2.9 15.0 + - - +
7B ILE* 3.1 13.1 + - - +
9B GLU* 1.3 75.7 - - - +
11B LEU* 1.3 65.2 + - - +
13B LYS* 3.1 10.0 + - + +
14B THR* 3.1 18.6 + - - +
-1G GLY 4.1 18.1 + - - +
2G GLU* 4.1 7.1 - - - +
3G GLU* 3.1 36.9 - - - +
6G GLU* 2.9 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A THR* 3.9 19.2 - - + +
17A MET* 3.7 29.4 - - + +
18A LEU* 3.5 45.1 - - + +
21A GLU* 4.1 16.2 - - + -
7B ILE* 2.9 16.8 + - + +
8B LEU* 3.7 8.1 - - - +
10B GLN* 1.3 75.7 - - - +
12B LYS* 1.3 64.2 + - - +
14B THR* 3.0 5.7 + - - -
15B LEU* 2.9 25.1 + - - +
3G GLU* 2.9 33.8 + - + +
7G ILE* 4.8 2.0 - - + -
22a LEU* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU 3.0 14.9 + - - +
9B GLU* 3.8 10.5 - - + +
10B GLN 3.3 0.2 - - - -
11B LEU* 1.3 77.4 - - - +
13B LYS* 1.3 66.2 + - - +
15B LEU* 3.9 4.8 - - - +
16B GLN* 2.9 20.3 + - + +
19a THR* 3.1 34.9 + - + +
20a VAL* 4.6 4.6 + - - +
22a LEU* 3.1 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLU 3.0 14.7 + - - +
10B GLN* 3.1 13.5 - - + +
11B LEU 3.1 0.2 - - - -
12B LYS* 1.3 74.6 - - - +
14B THR* 1.3 56.9 + - - +
16B GLN* 2.7 30.5 + - - +
17B MET* 3.0 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A THR* 3.7 27.4 - - + +
10B GLN* 3.1 4.8 + - - +
11B LEU 3.0 9.7 + - - -
13B LYS* 1.3 77.4 - - - +
15B LEU* 1.3 57.5 + - - +
17B MET* 3.3 7.8 + - + +
18B LEU* 2.9 42.9 + - + +
-1G GLY* 4.8 13.3 + - - -
0G PRO* 4.8 11.2 - - + +
3G GLU* 3.6 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 5.7 6.9 - - + +
14A THR* 4.5 12.5 - - + +
15A LEU* 6.3 3.4 - - + -
18A LEU* 6.2 2.9 - - + -
11B LEU 2.9 15.7 + - - +
12B LYS* 3.9 6.5 - - - +
14B THR* 1.3 74.9 - - - +
16B GLN* 1.3 67.1 + - - +
18B LEU* 3.3 6.3 + - - +
19B THR* 2.9 28.3 + - - +
15a LEU* 5.4 1.9 - - + +
18a LEU* 6.3 3.1 - - + -
19a THR* 3.9 15.9 - - - +
22a LEU* 5.7 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 2.9 13.9 + - + +
13B LYS* 2.7 19.3 + - - +
15B LEU* 1.3 73.8 - - - +
17B MET* 1.3 55.3 + - - +
19B THR* 3.4 5.3 + - - -
20B VAL* 3.0 33.0 + - + +
19a THR* 4.1 20.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LYS 3.0 10.1 + - - +
14B THR* 3.6 13.7 - - - +
16B GLN* 1.3 76.8 - - - +
18B LEU* 1.3 62.8 + - + +
20B VAL* 3.2 10.2 + - - +
21B GLU* 2.9 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.2 18.7 - - + +
10A GLN* 3.8 18.8 - - + +
11A LEU* 3.6 48.4 - - + +
14A THR* 4.6 7.9 - - - +
14B THR* 2.9 30.5 + - + +
15B LEU* 3.3 5.8 + - - +
17B MET* 1.3 80.6 - - + +
19B THR* 1.3 64.2 + - - +
21B GLU* 3.8 19.8 - - - +
22B LEU* 3.4 21.0 + - - +
15a LEU* 5.5 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 2.9 18.1 + - - +
16B GLN* 3.8 6.5 - - - -
18B LEU* 1.3 74.5 - - - +
20B VAL* 1.3 68.1 + - + +
22B LEU* 3.4 19.0 + - - +
12a LYS* 3.8 30.9 - - + +
15a LEU* 3.3 34.9 + - + +
16a GLN* 4.4 11.2 - - + +
19a THR* 4.7 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLN* 3.0 22.7 + - + +
17B MET* 3.2 12.3 + - - +
19B THR* 1.3 77.1 - - + +
21B GLU* 1.3 62.6 + - + +
22B LEU 2.8 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 3.3 39.8 - - + +
17B MET* 2.9 23.5 + - + +
18B LEU* 4.0 20.9 - - - +
19B THR 3.3 0.4 - - - -
20B VAL* 1.3 79.7 - - + +
22B LEU* 1.3 58.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 6.1 1.1 - - - +
7A ILE* 4.7 13.0 - - + +
18B LEU 3.4 14.3 + - - +
19B THR* 3.4 12.1 + - - +
20B VAL 2.8 15.7 - - - +
21B GLU* 1.3 79.7 - - - +
8a LEU* 5.4 9.0 - - + +
12a LYS* 4.3 21.1 - - + +
----------------------------------------------------------
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