Contacts of the helix formed by residues 9 - 32 (chain j) in PDB entry 4IL6
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 9 (chain j).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6j GLY* 3.7 11.2 - - - +
7j ARG 3.5 10.3 - - - +
8j ILE* 1.3 83.8 - - - +
10j LEU* 1.3 66.5 + - - +
11j TRP* 3.1 28.0 - - + +
12j ILE* 2.9 33.5 + - + +
13j VAL 3.2 8.3 + - - -
102y UNL 3.8 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 10 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11e SER* 4.5 19.5 - - - +
14e ILE* 3.8 29.8 - - + -
15e THR* 3.8 21.7 - - + +
6j GLY* 6.1 0.2 - - - -
8j ILE 3.3 1.8 + - - -
9j PRO* 1.3 72.0 - - - +
11j TRP* 1.3 57.0 + - - +
13j VAL* 3.2 7.7 + - + +
14j ALA* 2.8 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 11 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9j PRO* 3.1 30.6 - - + +
10j LEU* 1.3 78.6 - - - +
12j ILE* 1.3 75.7 + - + +
14j ALA* 3.9 4.3 - - - +
15j THR* 2.7 40.4 + - - -
38k VAL* 3.7 35.2 - - + -
41k ALA* 3.4 38.1 + - + +
42k ALA* 3.6 24.8 + - + +
33y PRO* 4.4 6.3 - - + -
36y ILE* 3.9 9.4 - - + -
37y PHE* 3.8 33.0 - + + -
40y ALA* 4.1 24.9 - - + +
101y BCR 4.5 1.2 - - - +
102y UNL 5.6 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 12 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8j ILE* 4.5 6.7 - - + -
9j PRO* 2.9 35.2 + - + +
11j TRP* 1.3 104.7 - - + +
13j VAL* 1.3 66.0 + - - +
15j THR* 3.2 3.5 + - - -
16j VAL* 2.9 37.5 + - + +
37y PHE* 3.9 23.1 - - + -
102y UNL 3.8 42.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 13 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14e ILE* 3.5 43.5 - - + +
15e THR* 4.6 1.8 - - + -
20e TRP* 3.8 31.8 - - + +
8j ILE* 3.8 24.5 - - + +
9j PRO 3.2 5.6 + - - +
10j LEU* 3.2 11.3 + - + +
12j ILE* 1.3 76.7 - - - +
14j ALA* 1.3 58.4 + - - +
16j VAL* 4.0 3.8 - - - +
17j ALA* 2.9 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10j LEU* 2.8 24.6 + - + +
11j TRP* 3.9 7.9 - - - +
13j VAL* 1.3 74.7 - - - +
15j THR* 1.3 56.2 + - - +
17j ALA* 4.0 3.5 - - - +
18j GLY* 2.8 28.2 + - - -
41k ALA* 5.5 0.7 - - + -
101y BCR 3.7 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 15 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11j TRP* 2.7 27.2 + - + -
12j ILE* 3.2 5.8 + - - -
14j ALA* 1.3 74.1 - - - +
16j VAL* 1.3 63.0 + - + +
19j MET* 2.9 47.2 + - - +
38k VAL* 3.8 31.1 - - + +
33y PRO* 4.2 16.2 - - + -
101y BCR 3.5 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 16 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12j ILE* 2.9 34.3 + - + +
13j VAL* 4.1 3.6 - - - +
15j THR* 1.3 75.8 - - + +
17j ALA* 1.3 66.5 + - - +
19j MET* 3.2 12.6 + - - +
20j GLY* 2.9 19.6 + - - -
102y UNL 4.5 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20e TRP* 6.1 4.0 - - + -
13j VAL* 2.9 26.0 + - + +
14j ALA* 4.0 3.8 - - - +
16j VAL* 1.3 76.5 - - - +
18j GLY* 1.3 63.0 + - - +
20j GLY* 3.1 5.1 + - - +
21j VAL* 3.0 27.9 + - + +
101y BCR 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 18 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518c SQD 4.9 4.2 - - - +
14j ALA 2.8 21.5 + - - -
15j THR 3.8 1.1 - - - -
17j ALA* 1.3 73.3 - - - +
19j MET* 1.3 55.8 + - - +
21j VAL* 3.2 11.0 + - - +
22j ILE* 3.0 30.8 + - - +
101y BCR 3.7 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 19 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15j THR* 2.9 34.0 + - - +
16j VAL* 3.6 9.6 - - - +
18j GLY* 1.3 71.3 - - - +
20j GLY* 1.3 60.5 + - - +
22j ILE* 3.5 10.3 + - + +
23j VAL* 3.0 36.2 + - + +
26y ALA* 5.8 2.0 - - - +
29y GLY* 4.6 12.8 - - - +
30y ILE* 5.0 10.5 - - + +
33y PRO* 4.7 4.9 - - + -
101y BCR 3.6 40.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 20 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103f LMT 4.2 17.3 - - - +
16j VAL 2.9 12.4 + - - -
17j ALA* 3.1 6.7 + - - -
19j MET* 1.3 74.0 - - - +
21j VAL* 1.3 63.2 + - - +
23j VAL* 3.3 5.4 + - - +
24j ILE* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518c SQD 6.4 1.3 - - + -
404d BCR 3.7 42.6 - - + -
17j ALA* 3.0 16.0 + - + +
18j GLY* 3.2 11.2 + - - +
20j GLY* 1.3 75.1 - - - +
22j ILE* 1.3 60.5 + - + +
24j ILE* 3.2 11.6 - - + +
25j VAL* 2.9 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518c SQD 3.8 35.2 - - + -
519c LMG 3.8 54.5 - - + -
18j GLY 3.0 19.6 + - - +
19j MET* 3.8 9.9 - - + +
20j GLY 3.4 0.2 - - - -
21j VAL* 1.3 77.0 - - + +
23j VAL* 1.3 61.3 + - + +
25j VAL* 3.9 3.3 - - - +
26j GLY* 2.8 27.2 + - - -
101j UNL 4.1 12.5 - - + +
101y BCR 4.3 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 23 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103f LMT 3.8 29.4 - - + -
19j MET* 3.0 23.2 + - + +
20j GLY* 3.8 5.4 - - - +
22j ILE* 1.3 79.1 - - + +
24j ILE* 1.3 58.9 + - - +
26j GLY* 3.3 2.0 + - - -
27j LEU* 2.8 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404d BCR 6.1 1.1 - - + -
31e PHE* 3.8 34.5 - - + -
34f LEU* 4.3 17.5 - - + +
38f ALA* 4.0 14.8 - - + -
103f LMT 4.8 13.5 - - + -
20j GLY 3.0 16.0 + - - +
21j VAL* 3.2 17.9 - - + +
23j VAL* 1.3 77.1 - - - +
25j VAL* 1.3 68.1 + - + +
27j LEU* 3.3 11.7 + - + +
28j PHE* 3.1 56.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516c DGD 4.8 11.2 - - + -
404d BCR 3.5 37.7 - - + -
409d LMG 4.7 10.8 - - + -
21j VAL* 2.9 21.0 + - + +
22j ILE* 4.2 3.4 - - - +
24j ILE* 1.3 78.4 - - + +
26j GLY* 1.3 65.3 + - - +
28j PHE* 3.2 14.3 + - + +
29j PHE* 3.0 46.7 + - + -
101j UNL 4.7 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 26 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22j ILE 2.8 20.2 + - - -
23j VAL* 3.6 2.2 - - - -
25j VAL* 1.3 77.1 - - - +
27j LEU* 1.3 54.8 + - - +
29j PHE 3.4 1.3 + - - -
30j TYR* 3.0 26.9 + - - +
101j UNL 3.7 36.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38f ALA* 3.8 38.1 - - + +
41f GLN* 3.9 14.5 - - + +
42f PHE* 3.9 27.1 - - + -
103f LMT 4.5 21.1 - - + -
23j VAL* 2.8 14.7 + - + +
24j ILE* 3.4 17.7 - - + +
25j VAL 3.2 0.2 - - - -
26j GLY* 1.3 74.6 - - - +
28j PHE* 1.3 65.6 + - + +
30j TYR* 3.2 17.9 + - + +
31j GLY 3.0 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 28 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517c DGD 5.5 0.2 - - - +
404d BCR 4.2 11.4 - - + -
409d LMG 3.4 56.5 + - + +
34f LEU* 4.1 22.4 - - + -
37f ILE* 3.6 29.4 - - + -
38f ALA* 3.9 17.5 - - - -
41f GLN* 3.6 21.1 - - + +
24j ILE* 3.1 40.0 + - + -
25j VAL* 3.2 14.1 + - + +
27j LEU* 1.3 80.5 - - + +
29j PHE* 1.3 60.8 + - - +
31j GLY* 3.2 10.0 + - - -
32j ALA* 3.3 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516c DGD 3.7 66.6 - - + -
517c DGD 3.6 72.2 - - + -
409d LMG 4.3 9.0 - - + -
25j VAL* 3.0 44.5 + - + -
26j GLY* 3.7 8.3 - - - +
28j PHE* 1.3 74.9 - - - +
30j TYR* 1.3 63.0 + - - +
32j ALA* 3.1 13.9 + - - +
33j TYR* 3.2 21.1 - + + -
101j UNL 4.6 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 30 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41f GLN* 4.2 13.5 - - + -
42f PHE* 4.7 17.6 - + - -
26j GLY 3.0 15.0 + - - +
27j LEU* 3.2 25.8 + - + +
29j PHE* 1.3 75.0 - - - +
31j GLY* 1.3 61.4 + - - +
33j TYR* 3.0 22.0 + - - +
34j ALA* 3.4 30.9 + - + +
101j UNL 4.0 49.3 - - + +
18y VAL* 5.9 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 31 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409d LMG 3.0 7.7 + - - -
41f GLN* 3.1 25.8 - - - -
27j LEU 3.0 11.1 + - - -
28j PHE 3.2 0.6 + - - -
30j TYR* 1.3 82.4 - - - +
32j ALA* 1.3 59.6 + - - +
33j TYR 3.1 0.2 - - - -
34j ALA 2.8 11.3 - - - +
36j LEU 3.6 0.9 - - - +
102j MG 2.3 29.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain j).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517c DGD 2.7 71.5 + - - +
72d ASN* 6.4 0.2 - - - +
409d LMG 3.3 21.5 + - - +
28j PHE 3.3 6.7 + - - +
29j PHE* 3.1 14.3 + - - +
30j TYR 3.1 1.4 - - - -
31j GLY* 1.3 77.5 - - - +
33j TYR* 1.3 57.5 + - - +
34j ALA 3.6 0.2 - - - -
38j SER* 3.5 7.5 - - - -
----------------------------------------------------------
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