Contacts of the helix formed by residues 44 - 68 (chain L) in PDB entry 2B4X
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 THR 44 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L PRO* 4.1 23.0 - - + +
43L ALA* 1.3 70.6 - - - +
45L ASN* 1.3 68.3 + - - +
46L ARG 2.9 0.9 - - - -
47L ARG* 2.5 31.2 + - - +
48L VAL* 2.6 28.5 + - + +
121L PHE* 5.2 12.3 - - + -
122L PHE* 4.2 9.3 - - + -
125L LYS* 5.7 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 45 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L ALA 2.6 6.9 + - - +
44L THR* 1.3 90.9 - - - +
46L ARG* 1.3 57.0 + - - +
48L VAL* 3.9 11.8 - - - +
49L TRP* 3.4 21.5 + - - +
129L ARG* 4.7 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 46 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L ALA* 2.7 33.7 + - + +
45L ASN* 1.3 77.7 - - - +
47L ARG* 1.3 62.5 + - - +
49L TRP* 3.7 10.8 - - - +
50L GLU* 3.3 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 47 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L ALA 4.0 6.4 - - - +
44L THR 2.5 23.6 + - - +
46L ARG* 1.3 71.7 - - - +
48L VAL* 1.3 57.1 + - - +
49L TRP 3.0 1.6 - - - -
50L GLU* 2.8 24.2 + - - +
51L LEU* 2.8 14.7 + - - +
111L ILE* 5.7 2.8 - - + +
112L SER* 5.1 12.6 - - - +
122L PHE* 3.3 41.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44L THR* 2.6 31.4 + - + +
45L ASN* 4.1 13.2 - - - +
47L ARG* 1.3 70.7 - - - +
49L TRP* 1.3 59.9 + - - +
51L LEU* 3.4 8.8 + - - +
52L SER* 3.2 20.3 + - - -
122L PHE* 4.3 15.0 - - + +
125L LYS* 3.9 23.6 - - + -
126L LEU* 3.7 42.4 - - + +
129L ARG* 5.1 5.4 - - + +
417L LEU* 4.9 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 49 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L ASN 3.4 16.1 + - - +
46L ARG* 3.7 11.2 - - - +
47L ARG 3.0 0.4 - - - -
48L VAL* 1.3 81.5 - - - +
50L GLU* 1.3 68.8 + - + +
52L SER* 2.5 28.3 + - - -
53L LYS* 3.1 22.1 + - + +
416L PRO 5.8 3.1 - - - -
417L LEU 5.4 3.4 - - - -
418L ASN* 4.5 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46L ARG 3.3 12.1 + - - +
47L ARG* 2.8 12.4 + - - +
49L TRP* 1.3 88.4 - - + +
51L LEU* 1.3 60.4 + - - +
53L LYS* 3.5 6.0 + - - +
54L ALA* 3.0 25.3 + - - +
110L THR* 4.6 8.7 + - - +
111L ILE* 4.7 18.9 - - + -
112L SER* 5.0 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L ARG 2.8 10.6 + - - +
48L VAL* 3.5 9.6 - - - +
50L GLU* 1.3 75.2 - - - +
52L SER* 1.3 54.0 + - - +
54L ALA* 3.0 7.8 + - + +
55L ASN* 2.7 39.5 + - - +
108L PHE* 3.7 37.0 - - + -
111L ILE* 5.5 7.4 - - + +
119L ILE* 4.8 12.3 - - + -
122L PHE* 3.8 12.3 - - + +
123L PHE* 3.2 46.7 - - + +
126L LEU* 3.9 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 52 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48L VAL 3.2 9.6 + - - -
49L TRP* 2.5 27.1 + - - -
51L LEU* 1.3 81.8 - - - +
53L LYS* 1.3 55.7 + - - +
55L ASN* 3.5 5.9 - - - +
56L SER* 2.8 35.3 + - - -
126L LEU* 4.8 4.7 - - - -
417L LEU 3.5 11.1 + - - -
418L ASN* 3.6 15.9 + - - +
419L THR* 3.4 32.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 53 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L TRP* 3.1 27.7 + - + +
50L GLU* 3.8 7.9 - - - +
51L LEU 3.2 0.2 - - - -
52L SER* 1.3 79.0 + - - +
54L ALA* 1.3 60.7 + - - +
56L SER* 3.7 6.6 - - - -
57L ARG* 2.8 43.3 + - - +
301L PRO* 4.7 5.6 - - + +
418L ASN* 4.5 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L GLU 3.0 14.9 + - - +
51L LEU* 3.0 16.1 + - + +
53L LYS* 1.3 77.5 - - - +
55L ASN* 1.3 59.3 + - - +
57L ARG* 3.3 6.1 + - - +
58L PHE* 3.0 23.9 + - - +
106L PHE 4.5 2.9 - - - +
107L LYS* 2.9 40.2 - - - +
108L PHE* 4.7 4.3 - - - -
110L THR* 3.5 12.1 + - - +
111L ILE* 5.5 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 55 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51L LEU* 2.7 27.5 + - - +
52L SER* 3.5 7.2 - - - +
54L ALA* 1.3 71.6 - - - +
56L SER* 1.3 60.4 + - - +
58L PHE* 3.0 7.7 + - - +
59L ALA* 2.8 28.9 + - - +
80L PRO* 5.5 0.2 - - - +
81L LEU* 4.1 16.7 - - + +
84L SER* 3.2 28.5 + - - +
106L PHE 4.6 2.0 + - - -
108L PHE* 3.9 22.4 - - - -
123L PHE* 4.0 19.2 - - - -
126L LEU* 4.3 7.4 - - - +
419L THR* 5.7 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 56 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L SER 2.8 25.6 + - - -
53L LYS* 3.7 7.4 - - - -
55L ASN* 1.3 73.4 - - - +
57L ARG* 1.3 64.6 + - - +
59L ALA* 3.2 8.8 + - - +
60L THR* 3.1 21.7 + - - +
301L PRO* 3.6 21.7 - - - +
418L ASN* 3.5 20.7 + - - -
419L THR* 4.4 0.5 - - - -
420L ILE* 4.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L LYS* 2.8 31.0 + - - +
54L ALA* 3.5 6.9 - - - +
55L ASN 3.1 0.2 - - - -
56L SER* 1.3 76.8 - - - +
58L PHE* 1.3 62.9 + - - +
60L THR* 3.2 3.7 + - - +
61L THR* 2.9 34.7 + - - +
107L LYS* 4.7 11.7 - - + -
110L THR* 3.8 29.9 + - - +
301L PRO* 3.4 19.1 - - + +
302L GLU* 3.6 24.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54L ALA 3.0 12.5 + - - +
55L ASN* 3.0 9.5 + - - +
57L ARG* 1.3 75.6 - - - +
59L ALA* 1.3 61.9 + - - +
61L THR* 4.5 4.0 - - - -
62L PHE* 2.8 72.6 + + + +
80L PRO* 4.3 11.2 - - + -
83L ILE* 3.9 22.0 - - + -
84L SER* 3.6 19.3 - - - +
105L VAL 3.1 28.0 - - - +
106L PHE* 3.5 44.4 - + - -
107L LYS* 5.0 1.9 - - - +
335L LEU* 4.2 7.4 - - + -
338L MET* 4.3 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55L ASN 2.8 12.6 + - - +
56L SER* 3.4 13.9 - - - +
57L ARG 3.2 0.2 - - - -
58L PHE* 1.3 78.0 - - - +
60L THR* 1.3 58.6 + - - +
62L PHE* 3.9 3.0 - - - +
63L TYR* 2.9 29.3 + - - +
78L LEU* 5.6 0.2 - - - +
80L PRO* 3.4 26.1 - - + +
420L ILE* 4.2 6.7 - - + -
423L MET* 3.2 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56L SER 3.1 9.9 + - - +
57L ARG* 3.2 9.4 + - - +
59L ALA* 1.3 73.5 - - - +
61L THR* 1.3 72.7 + - - +
63L TYR* 3.1 7.3 + - - +
64L GLN* 2.9 26.3 + - - +
299L LEU* 3.8 43.5 + - + -
300L THR* 4.0 4.6 - - - -
301L PRO* 3.4 27.9 - - + +
304L LEU* 5.8 1.6 - - + -
411L PHE* 5.3 2.0 - - + -
420L ILE* 4.7 13.9 - - + -
423L MET* 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57L ARG* 2.9 25.5 + - - +
58L PHE* 3.8 5.4 - - - -
60L THR* 1.3 82.6 + - - +
62L PHE* 1.3 65.4 + - - +
64L GLN* 2.9 21.8 + - - +
65L HIS* 3.0 39.5 + - + +
338L MET* 3.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 62 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58L PHE* 2.8 50.8 + + + +
59L ALA* 3.9 3.1 - - - +
61L THR* 1.3 74.0 - - - +
63L TYR* 1.3 65.4 + - - +
65L HIS* 3.2 4.9 + - - +
66L LEU* 2.9 41.5 + - + +
78L LEU* 4.0 23.6 - - + -
80L PRO* 5.8 0.4 - - + -
83L ILE* 4.0 3.8 - - + -
329L PHE* 3.9 9.6 - + - -
331L LEU* 3.4 34.3 - - + -
334L GLN* 4.3 15.3 - - + -
335L LEU* 4.4 9.4 - - + -
338L MET* 3.1 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 63 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L ALA 2.9 20.9 + - - +
60L THR* 3.1 6.7 + - - +
62L PHE* 1.3 82.6 - - + +
64L GLN* 1.3 65.5 + - + +
66L LEU* 3.0 7.3 + - + +
67L ALA* 2.8 31.2 + - + +
76L ILE* 4.1 23.3 - - + -
78L LEU* 4.5 10.3 - - + -
296L GLU* 2.7 45.4 + - + -
299L LEU* 4.3 20.0 - - + -
409L LEU* 3.7 9.4 - - + +
423L MET* 3.7 26.7 - - + -
424L GLY* 4.4 13.0 - - - -
425L ARG* 3.5 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60L THR 3.1 15.3 - - - +
61L THR* 2.9 17.6 + - - +
63L TYR* 1.3 78.8 - - + +
65L HIS* 1.3 61.7 + - + +
66L LEU 3.0 1.6 - - - -
67L ALA* 2.9 6.0 + - - +
68L ASP* 2.7 37.9 + - - +
296L GLU* 3.1 29.1 + - - +
297L LYS* 3.8 16.8 + - - -
298L GLU 4.5 0.2 - - - -
299L LEU* 3.1 24.1 + - + +
300L THR* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 65 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61L THR* 3.0 39.3 + - + +
62L PHE 3.2 5.8 + - - +
64L GLN* 1.3 81.2 - - + +
66L LEU* 1.3 60.2 + - - +
68L ASP* 3.6 23.8 + - - +
69L SER* 3.9 3.8 + - - -
334L GLN* 3.7 19.6 - - + +
337L ASP* 4.4 22.6 - - + +
338L MET* 3.3 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62L PHE* 2.9 25.0 + - + +
63L TYR* 3.3 11.9 - - + +
64L GLN 3.0 0.2 - - - -
65L HIS* 1.3 76.7 - - - +
67L ALA* 1.3 60.0 + - - +
69L SER* 2.7 20.6 + - - +
70L LYS* 4.2 7.6 + - - +
76L ILE* 4.0 28.5 - - + +
78L LEU* 4.6 7.9 - - + -
327L ASP* 5.2 0.7 - - - +
329L PHE* 3.6 50.5 - - + -
334L GLN* 4.2 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63L TYR* 2.8 22.8 + - + +
64L GLN* 2.9 10.3 + - - +
66L LEU* 1.3 75.5 - - - +
68L ASP* 1.3 52.3 + - - +
69L SER 2.4 20.7 + - - -
70L LYS* 2.8 21.4 + - - +
72L ASP* 5.4 0.7 - - - +
76L ILE* 4.3 7.0 - - + -
296L GLU* 4.1 10.1 - - + +
425L ARG* 3.7 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64L GLN* 2.7 21.7 + - + +
65L HIS* 3.6 11.7 + - - +
67L ALA* 1.3 68.2 - - - +
69L SER* 1.3 62.4 + - - +
----------------------------------------------------------
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