Contacts of the helix formed by residues 68 - 80 (chain A) in PDB entry 2X1B
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 ASP 68 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 4.1 10.7 - - - +
43A PRO* 5.2 5.5 - - - +
66A PHE* 3.2 4.8 - - - +
67A ARG* 1.3 89.9 - - + +
69A LEU* 1.3 63.5 + - - +
70A GLU* 4.2 8.6 - - + +
71A SER* 2.7 40.9 + - - -
72A SER* 3.3 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PRO* 3.9 25.4 - - + -
17A SER* 3.6 39.5 - - - +
18A ARG* 3.9 14.1 - - + +
68A ASP* 1.3 72.1 - - - +
70A GLU* 1.3 64.9 + - + +
72A SER* 3.2 5.6 + - - -
73A ALA* 3.2 24.4 + - - +
93A TYR* 5.6 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 3.3 10.1 + - + +
69A LEU* 1.3 77.3 - - + +
71A SER* 1.3 58.5 + - - +
73A ALA* 3.4 6.1 + - - +
74A SER* 2.9 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 3.4 12.4 + - - +
42A GLY* 3.7 20.4 - - - -
43A PRO* 3.8 8.0 - - - +
66A PHE* 3.7 25.2 - - - -
68A ASP* 2.7 28.3 + - - -
70A GLU* 1.3 75.9 - - - +
72A SER* 1.3 61.2 + - - +
74A SER* 3.3 5.5 + - - -
75A ALA* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER 2.7 28.5 + - - -
18A ARG* 3.5 25.5 - - - -
20A VAL* 3.6 13.8 - - - +
66A PHE* 3.7 12.0 - - - -
68A ASP 3.3 6.1 + - - -
69A LEU* 3.2 10.4 + - - -
71A SER* 1.3 77.2 - - - +
73A ALA* 1.3 62.9 + - - +
75A ALA* 3.2 3.8 + - - +
76A VAL* 3.0 27.0 + - - +
93A TYR* 4.1 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU 3.2 18.0 + - - +
70A GLU* 3.6 6.5 - - - +
72A SER* 1.3 77.7 + - - +
74A SER* 1.3 61.7 + - - +
76A VAL* 3.3 4.3 + - - +
77A ARG* 3.0 24.5 + - - +
93A TYR* 3.2 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 3.6 18.6 + - - +
70A GLU 2.9 17.2 + - - -
71A SER* 3.5 7.9 - - - -
73A ALA* 1.3 77.3 - - - +
75A ALA* 1.3 57.3 + - - +
77A ARG* 3.6 19.0 + - - +
78A ASN* 2.8 53.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.4 1.3 - - + -
41A VAL* 3.4 8.9 - - + +
66A PHE* 3.6 29.4 - - + -
71A SER 2.9 13.4 + - - +
72A SER 3.2 8.9 + - - +
74A SER* 1.3 73.4 - - - +
76A VAL* 1.3 60.1 + - - +
79A LEU* 2.8 50.8 + - + +
91A CYS* 3.5 11.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 3.8 18.4 - - + -
72A SER 3.0 14.9 + - - +
73A ALA 3.3 7.6 + - - +
75A ALA* 1.3 76.1 - - - +
77A ARG* 1.3 63.0 + - - +
80A ASN* 3.1 28.0 + - + +
91A CYS* 3.8 18.4 - - - +
92A GLY* 3.8 23.1 - - - -
93A TYR* 3.9 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA 3.0 15.5 + - - +
74A SER* 3.6 28.9 + - - +
76A VAL* 1.3 80.7 - - - +
78A ASN* 1.3 80.5 + - - +
80A ASN* 4.3 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 4.7 9.9 - - + -
74A SER* 2.8 41.7 + - - +
77A ARG* 1.3 101.4 + - - +
79A LEU* 1.3 69.9 + - + +
80A ASN 3.6 2.8 - - - +
82A TYR* 3.7 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 6.1 0.7 - - + -
22A LEU* 4.0 26.2 - - + -
37A LEU* 3.9 34.5 - - + -
38A CYS* 4.3 21.3 - - - -
41A VAL* 4.1 24.0 - - + -
75A ALA* 2.8 37.5 + - + +
78A ASN* 1.3 79.6 - - + +
80A ASN* 1.3 62.3 + - - +
81A GLY 3.2 1.0 + - - -
82A TYR* 3.1 28.0 + - + +
89A LEU* 3.5 13.2 - - + +
91A CYS* 4.0 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 3.1 23.5 + - + +
77A ARG 4.3 8.7 - - - +
78A ASN 4.4 1.9 - - - +
79A LEU* 1.3 75.8 - - - +
81A GLY* 1.3 59.9 + - - +
82A TYR 3.5 0.3 + - - -
89A LEU 4.0 0.3 - - - +
90A LYS* 3.3 12.3 - - - +
91A CYS* 2.9 41.9 + - - +
----------------------------------------------------------
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