Contacts of the helix formed by residues 40 - 62 (chain B) in PDB entry 4HYJ
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 TYR 40 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.5 11.9 - - + +
37B ALA* 2.8 20.4 + - + +
39B GLU* 1.3 112.5 + - + +
41B ARG* 1.3 64.4 + - - +
42B SER* 3.3 3.1 - - - -
43B THR* 3.2 25.7 + - - -
100B LEU* 5.2 5.2 - - + -
173B PRO* 5.3 2.1 - - - +
176B ILE* 4.1 14.7 - - + +
236B VAL* 3.4 38.8 - - + -
239B MET* 3.5 40.1 - - + +
240B SER* 3.6 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG* 3.3 47.7 + - + +
34B ASN* 3.0 20.8 + - - +
36B LEU* 2.6 31.2 + - + +
37B ALA 3.3 13.0 - - - +
38B PRO* 3.2 39.8 + - - +
40B TYR* 1.3 76.4 - - - +
42B SER* 1.3 64.7 + - - +
44B ALA* 3.0 7.3 + - - +
45B THR* 3.0 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 5.5 13.9 - - - -
38B PRO 4.8 1.4 + - - -
39B GLU 4.4 10.9 + - - -
41B ARG* 1.3 75.1 - - - +
43B THR* 1.3 66.0 + - - +
45B THR* 3.5 10.0 - - - -
46B VAL* 2.9 29.9 + - - +
99B LEU* 3.8 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 3.3 16.8 + - - -
41B ARG 3.1 0.4 - - - -
42B SER* 1.3 81.7 + - - +
44B ALA* 1.3 61.9 + - - +
46B VAL* 3.6 0.5 + - - +
47B ALA* 3.2 21.5 + - - +
96B LYS* 3.9 13.0 - - + +
99B LEU* 4.4 14.9 - - + +
100B LEU* 3.9 21.2 - - + +
229B GLY 5.8 0.2 - - - +
232B ALA* 4.0 29.4 - - + -
233B PHE* 4.6 2.7 - - - +
236B VAL* 3.9 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PHE* 3.7 29.2 - - + +
30B LEU* 6.2 0.2 - - - -
33B ARG* 3.9 15.5 - - + +
36B LEU* 4.0 18.1 - - + +
40B TYR 4.0 0.6 + - - -
41B ARG 3.0 9.3 + - - +
43B THR* 1.3 77.3 - - - +
45B THR* 1.3 60.6 + - - +
47B ALA* 3.4 6.8 + - - +
48B ALA* 2.8 31.4 + - - +
233B PHE* 5.0 9.9 - - + -
236B VAL* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LFA 4.0 26.7 - - + -
30B LEU* 5.5 0.9 - - - -
33B ARG* 2.7 34.0 + - - +
41B ARG 3.0 9.3 + - - -
42B SER* 3.2 13.2 + - - -
44B ALA* 1.3 77.3 - - - +
46B VAL* 1.3 57.5 + - + +
48B ALA* 3.1 7.5 + - - +
49B LEU* 2.9 29.5 + - + +
303B LFA 3.5 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LFA 5.5 7.9 - - + -
42B SER* 2.9 20.3 + - - +
43B THR 4.0 3.1 - - - +
45B THR* 1.3 78.7 - - + +
47B ALA* 1.3 59.0 + - - +
49B LEU* 3.1 10.2 + - + +
50B VAL* 2.9 30.0 + - + +
92B LEU* 3.3 46.9 - - + +
95B VAL* 4.7 7.0 - - + -
96B LYS* 4.1 15.7 - - + +
99B LEU* 3.7 20.4 - - + -
309B LFA 5.5 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PHE* 3.8 32.1 - - + -
43B THR* 3.2 15.7 + - + +
44B ALA* 3.6 5.4 - - - +
45B THR 3.3 0.2 - - - -
46B VAL* 1.3 79.5 - - - +
48B ALA* 1.3 61.6 + - - +
50B VAL* 3.5 3.5 + - - +
51B THR* 3.2 29.3 + - - +
96B LYS* 3.5 23.1 - - - +
225B LYS 5.6 0.9 - - - +
229B GLY* 4.4 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B THR* 3.4 7.6 + - + +
29B PHE* 3.9 13.9 - - + +
30B LEU* 3.7 35.7 - - + +
44B ALA 2.8 20.4 + - - +
45B THR 3.1 4.7 + - - +
47B ALA* 1.3 73.3 - - - +
49B LEU* 1.3 58.2 + - - +
51B THR* 3.0 9.6 + - - -
52B PHE* 2.8 30.3 + - - +
303B LFA 4.1 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 4.0 15.5 - - + -
305A LFA 3.7 64.6 - - + -
45B THR* 2.9 13.7 + - + +
46B VAL* 3.1 12.1 + - + +
48B ALA* 1.3 76.5 - - - +
50B VAL* 1.3 62.5 + - - +
52B PHE* 3.1 3.4 + - + +
53B VAL* 3.0 28.0 + - + +
92B LEU* 3.5 31.0 - - + -
303B LFA 4.0 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 2.9 18.0 + - + +
47B ALA* 3.9 6.5 - - - +
48B ALA 3.3 0.2 - - - -
49B LEU* 1.3 76.9 - - - +
51B THR* 1.3 63.7 + - + +
53B VAL 3.5 0.3 + - - -
54B ALA* 3.2 20.4 + - - +
89B THR* 3.6 27.3 - - - +
92B LEU* 3.5 34.5 - - + -
93B LEU* 4.0 19.1 - - + +
96B LYS* 5.6 0.2 - - - +
225B LYS* 3.6 41.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B MET* 3.4 31.7 - - - +
25B GLY* 3.5 1.3 - - - -
26B THR* 2.9 30.8 + - - -
29B PHE* 4.4 13.0 - - + -
47B ALA 3.2 14.4 + - - +
48B ALA 3.0 7.6 + - - -
50B VAL* 1.3 76.3 - - + +
52B PHE* 1.3 58.8 + - - +
54B ALA 3.5 0.2 + - - -
55B ALA* 2.9 25.6 + - - +
225B LYS* 4.2 23.6 - - + +
226B VAL* 4.3 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 3.8 21.5 - + - -
56A ILE* 3.6 24.2 - - + -
305A LFA 4.1 18.8 - - + -
26B THR* 3.1 19.0 + - + +
48B ALA 2.8 18.2 + - - +
49B LEU 3.4 5.8 - - - +
51B THR* 1.3 74.7 - - - +
53B VAL* 1.3 66.7 + - - +
55B ALA* 3.1 7.9 + - + +
56B ILE* 3.1 46.4 + - + +
303B LFA 3.9 37.5 - - + -
306B LFA 6.1 0.7 - - + -
314B LFA 3.5 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LFA 3.6 22.4 - - + +
305A LFA 3.9 25.6 - - + -
49B LEU* 3.0 26.1 + - + +
52B PHE* 1.3 75.6 - - - +
54B ALA* 1.3 63.2 + - - +
56B ILE* 3.2 11.9 + - - +
57B HIS* 3.1 19.6 + - - +
85B ASP* 3.9 7.2 - - - -
88B VAL* 3.5 37.5 - - + -
89B THR* 3.6 19.5 - - + -
92B LEU* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B MET* 3.7 32.5 - - + -
50B VAL 3.2 13.8 + - - +
51B THR 3.8 0.2 - - - +
53B VAL* 1.3 78.1 - - - +
55B ALA* 1.3 57.6 + - - +
57B HIS* 3.1 2.8 + - - +
58B TYR* 2.9 40.2 + - + -
85B ASP* 3.6 15.3 - - - +
89B THR* 4.6 0.4 - - - +
221B ASP* 5.8 0.4 - - + +
225B LYS* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PHE* 3.2 21.8 - - + -
22B MET* 3.7 16.5 - - + +
23B ALA* 4.0 22.7 - - + +
51B THR 2.9 15.3 + - - +
52B PHE* 3.2 13.9 - - + +
54B ALA* 1.3 75.4 - - - +
56B ILE* 1.3 55.6 + - - +
58B TYR* 3.3 2.9 + - - -
59B TYR* 2.9 25.1 + - - +
314B LFA 4.9 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 4.2 13.5 - - + -
52A PHE* 4.2 11.2 - - + -
304A LFA 4.1 13.7 - - + -
305A LFA 3.8 21.3 - - + -
52B PHE* 3.1 45.1 + - + +
53B VAL* 3.2 5.8 + - - +
55B ALA* 1.3 75.0 - - - +
57B HIS* 1.3 63.4 + - - +
59B TYR* 3.3 6.3 + - - +
60B PHE* 3.1 55.0 + - + -
314B LFA 4.1 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LFA 3.9 17.4 - - + +
15B PHE* 5.3 0.6 - - - -
53B VAL 3.1 12.5 + - - +
54B ALA 3.2 8.6 + - - +
56B ILE* 1.3 78.6 - - - +
58B TYR* 1.3 79.3 + + - +
60B PHE* 3.2 3.1 + - - +
61B MET* 3.2 40.8 + - + +
81B ILE* 3.6 15.9 - - + +
82B ARG* 3.7 35.4 - - + +
85B ASP* 2.7 31.5 + - + +
86B TRP* 5.2 1.1 - - - -
214B GLU* 5.3 5.3 + - - -
221B ASP* 4.6 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.3 47.2 - + - +
18B GLY* 4.0 12.8 - - - -
19B PHE* 3.7 15.9 - - - +
22B MET* 4.1 22.9 - - + -
54B ALA* 2.9 34.3 + - + +
55B ALA 3.9 0.7 - - - +
57B HIS* 1.3 88.8 - + - +
59B TYR* 1.3 66.7 + - - +
61B MET* 3.0 13.4 + - - +
62B LYS* 3.1 13.3 + - - +
214B GLU* 5.8 1.3 - - - -
217B TYR 4.3 0.2 - - - -
218B ASN* 3.1 38.1 + - - -
221B ASP* 2.4 36.7 + - - +
222B LEU* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 5.7 0.4 - + - -
19B PHE* 3.8 28.4 - + + -
55B ALA 2.9 17.6 + - - +
56B ILE 3.3 4.5 + - - +
58B TYR* 1.3 76.3 - - - +
60B PHE* 1.3 86.8 + + - +
62B LYS* 3.2 65.7 + - + +
304B LFA 4.3 26.8 - - + +
314B LFA 3.5 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 5.4 2.0 - - - -
45A THR* 3.5 32.5 - - + -
49A LEU* 4.6 7.4 - - + -
304A LFA 3.5 54.3 - - + +
56B ILE* 3.1 46.4 + - + +
57B HIS 3.9 3.4 - - - +
58B TYR 3.2 0.2 - - - -
59B TYR* 1.3 101.1 - + - +
61B MET* 1.3 65.2 + - - +
62B LYS* 3.2 1.2 + - - +
63B ASP* 3.9 15.4 - - - +
81B ILE* 4.8 5.6 - - + -
314B LFA 4.0 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.4 47.7 - - + -
57B HIS* 3.2 39.5 + - + +
58B TYR* 3.0 9.1 + - - +
60B PHE* 1.3 77.7 - - - +
62B LYS* 1.3 57.8 + - - +
63B ASP* 2.9 20.2 + - + +
77B PHE 4.9 0.2 - - - -
78B PRO* 3.6 45.8 - - + +
81B ILE* 4.4 11.7 - - + -
82B ARG* 5.8 0.4 - - - -
214B GLU* 5.4 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLN* 5.2 8.1 - - - +
15B PHE* 4.4 11.2 - - + -
16B TRP* 3.4 51.6 + - + +
19B PHE* 6.4 0.7 - - + -
58B TYR 3.1 10.0 + - - +
59B TYR* 3.2 59.3 + - + +
60B PHE* 3.2 2.0 + - - +
61B MET* 1.3 76.6 - - - +
63B ASP* 1.3 70.2 + - - +
304B LFA 3.6 31.9 - - + +
----------------------------------------------------------
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