Contacts of the helix formed by residues 58 - 70 (chain B) in PDB entry 2BAM
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 VAL 58 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B VAL* 1.3 79.2 - - + +
59B PRO* 1.3 67.7 - - + +
60B ILE 3.2 0.9 + - - -
61B LYS* 3.2 22.5 + - + +
62B GLU* 3.9 10.9 + - + +
194B GLY 5.7 3.1 - - - +
197B GLY 3.5 20.6 - - - +
198B MET* 4.3 18.6 - - + -
199B SER 4.9 3.1 - - - +
6C A 3.6 50.9 - - - +
7C T 4.9 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TRP* 4.2 21.1 - - + -
56B GLY 4.6 0.2 - - - +
58B VAL* 1.3 87.9 - - + +
60B ILE* 1.3 60.7 + - - +
61B LYS 3.1 1.0 + - - -
62B GLU* 3.3 26.4 + - + +
63B LEU* 4.8 2.4 + - - +
191B ILE* 3.6 30.1 - - + -
192B PRO* 4.2 11.9 - - + +
197B GLY* 3.1 33.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 4.0 24.5 - - + -
36B PRO* 3.5 27.1 - - + +
38B TRP* 6.2 0.2 - - - -
45B PHE* 3.8 15.7 - - + -
47B ILE* 4.9 0.7 - - + -
56B GLY 3.8 10.1 - - - +
57B VAL* 3.5 14.6 - - + +
58B VAL 3.2 0.8 - - - -
59B PRO* 1.3 77.2 - - - +
61B LYS* 1.3 59.3 + - + +
63B LEU 4.9 0.7 + - - -
112B PHE* 4.7 2.1 - - + -
114B THR* 5.7 2.5 - - + -
148B LEU* 5.7 0.4 - - + -
152B LEU* 3.3 43.1 - - + -
179B PHE* 4.0 20.2 - - + -
191B ILE* 3.6 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B VAL 3.9 8.3 - - - +
58B VAL* 3.2 11.4 + - + +
59B PRO 3.1 1.0 - - - -
60B ILE* 1.3 80.9 - - + +
62B GLU* 1.3 63.7 + - - +
63B LEU 3.5 1.8 - - - -
64B CYS* 3.3 4.4 + - - +
65B TYR* 2.9 70.1 + - + -
112B PHE* 3.3 44.8 + - + -
114B THR* 3.0 41.1 + - + +
5C G 4.8 6.3 + - - -
6C A 4.0 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B VAL* 3.9 8.8 + - + +
59B PRO* 3.3 23.7 + - + +
61B LYS* 1.3 77.5 - - - +
63B LEU* 1.3 64.4 + - + +
65B TYR* 3.8 8.0 - - - +
66B THR* 2.7 40.1 + - - +
199B SER* 2.9 40.4 + - - +
201B ARG* 3.2 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER* 3.4 24.7 + - - +
36B PRO* 4.0 10.5 - - + -
37B ILE* 3.6 44.4 - - + +
59B PRO 4.8 2.2 + - - +
60B ILE 4.9 1.0 + - - -
61B LYS 3.5 0.6 - - - -
62B GLU* 1.3 80.6 - - + +
64B CYS* 1.3 65.2 + - - +
66B THR* 3.9 9.9 - - + +
67B LEU* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B SER* 3.2 42.4 - - - +
33B ILE* 3.8 7.9 - - - -
35B SER* 3.6 0.8 + - - -
36B PRO* 4.1 11.6 - - + +
61B LYS 3.3 4.7 + - - +
63B LEU* 1.3 79.9 - - - +
65B TYR* 1.3 62.0 + - - +
68B LEU* 3.2 39.4 + - - +
112B PHE* 3.6 37.5 - - + -
142B LEU* 4.1 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LYS* 2.9 68.6 + - + +
62B GLU* 3.8 10.8 - - - +
64B CYS* 1.3 75.4 - - - +
66B THR* 1.3 54.4 + - - +
68B LEU* 3.2 8.9 + - + +
69B GLU* 2.8 50.3 + - - +
76B ARG* 3.4 38.2 + - - +
94B ASP* 2.5 33.0 + - - -
95B VAL* 3.8 15.0 - - + -
112B PHE* 3.3 15.7 - + + +
201B ARG* 4.2 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLU* 2.7 25.2 + - - -
63B LEU* 3.9 13.1 - - + +
65B TYR* 1.3 78.1 - - - +
67B LEU* 1.3 56.1 + - - +
69B GLU* 4.6 1.3 - - - +
70B ASP* 3.0 45.3 + - + +
71B THR* 4.9 0.3 + - - -
201B ARG* 3.4 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B THR* 3.9 18.6 - - + +
32B SER* 3.6 31.2 - - - +
35B SER* 4.2 10.8 - - - +
63B LEU 3.1 18.0 + - - +
64B CYS 4.0 0.7 - - - +
66B THR* 1.3 75.2 - - - +
68B LEU* 1.3 61.3 + - - +
71B THR* 3.0 49.0 + - + +
72B TYR* 3.0 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLU 4.0 8.7 - - - +
29B VAL* 4.2 9.2 - - - -
32B SER* 3.2 26.9 - - - +
64B CYS* 3.2 32.0 + - - +
65B TYR* 3.2 9.6 + - + +
67B LEU* 1.3 80.4 - - - +
69B GLU* 1.3 52.6 + - + +
72B TYR* 3.3 3.3 - - + -
73B ASN 3.1 8.7 + - - -
74B TRP* 2.6 71.1 + - + +
95B VAL* 4.3 12.8 - - + -
110B MET* 3.4 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TYR* 2.8 19.3 + - - +
66B THR 4.3 0.9 - - - +
68B LEU* 1.3 78.9 - - + +
70B ASP* 1.3 69.1 + - - +
73B ASN* 3.2 12.3 + - - -
74B TRP* 3.5 17.9 - - + +
76B ARG* 2.8 46.4 + - + +
95B VAL* 5.8 0.2 - - + -
201B ARG* 2.7 34.4 + - - +
202B SER 4.6 0.3 - - - +
203B ILE* 3.4 0.5 - - - -
204B LYS* 2.8 54.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B THR* 3.0 33.0 + - + +
69B GLU* 1.3 88.1 - - - +
71B THR* 1.3 62.2 + - - +
73B ASN* 4.3 6.3 - - - +
201B ARG* 5.1 6.1 + - - -
204B LYS* 3.9 12.9 - - - +
----------------------------------------------------------
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