Contacts of the helix formed by residues 59 - 72 (chain A) in PDB entry 40ER
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 59 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 4.4 18.4 - - + -
54A ILE* 4.1 15.3 - - - +
57A LEU* 3.2 37.4 - - + -
58A ASP* 1.3 75.1 - - - +
60A VAL* 1.3 61.2 + - - +
61A GLY 3.0 2.7 - - - -
62A LYS* 2.8 45.3 + - + +
63A ILE* 3.0 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 4.0 30.5 - - + +
55A ARG* 5.2 3.8 - - + +
57A LEU 4.5 4.9 - - - +
58A ASP* 3.9 16.8 - - + +
59A VAL* 1.3 77.7 - - - +
61A GLY* 1.3 60.1 + - - +
63A ILE* 3.8 9.3 + - - +
64A ARG* 3.1 26.0 + - - +
165B ALA 5.9 0.2 - - - +
166B LEU* 4.2 35.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASP 3.9 3.4 + - - -
59A VAL 3.0 0.8 - - - -
60A VAL* 1.3 82.6 - - - +
62A LYS* 1.3 64.9 + - - +
63A ILE 3.2 0.4 - - - -
64A ARG* 3.6 11.0 - - - +
65A ARG* 3.0 32.3 + - - +
186B PRO* 5.4 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 4.4 18.1 - - + -
58A ASP 5.0 0.2 + - - -
59A VAL* 2.8 37.8 + - + +
61A GLY* 1.3 77.2 - - - +
63A ILE* 1.3 54.6 - - - +
65A ARG* 3.2 51.8 - - - +
66A GLU* 3.7 10.0 + - - +
140A ARG* 4.5 4.0 - - - +
161A GLY 4.6 12.5 - - - +
163A SER 5.4 0.4 + - - +
174A TPO 2.8 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 4.3 17.3 - - + -
49A LEU* 3.7 30.5 - - + -
54A ILE* 3.6 40.6 - - + -
59A VAL* 3.0 22.3 + - + +
60A VAL* 4.2 6.1 - - - +
62A LYS* 1.3 74.9 - - - +
64A ARG* 1.3 66.7 + - - +
66A GLU* 3.3 10.9 + - - +
67A ILE* 3.2 39.7 + - + +
91A ILE* 5.7 5.8 - - + -
93A MET* 5.3 0.7 - - - -
166B LEU* 6.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL 3.1 19.3 + - - +
61A GLY* 3.3 11.4 + - - +
63A ILE* 1.3 78.9 - - - +
65A ARG* 1.3 64.5 + - - +
66A GLU 3.3 0.3 + - - -
67A ILE* 3.4 4.0 + - - +
68A GLN* 3.0 52.3 + - - +
163B PHE* 4.6 20.9 - - + -
166B LEU* 3.6 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLY 3.0 16.7 + - - +
62A LYS* 3.2 55.8 - - - +
64A ARG* 1.3 77.7 - - - +
66A GLU* 1.3 67.3 + - - +
68A GLN* 3.4 12.8 + - - +
69A ASN* 3.0 38.0 + - - +
140A ARG* 4.0 0.8 - - - +
161A GLY 6.1 0.4 - - - -
163A SER 3.3 22.1 + - - -
164A ASN* 3.2 43.0 + - - +
165A MET* 5.0 11.4 - - + +
174A TPO 3.7 9.5 + - - -
186B PRO* 5.7 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 3.8 9.4 - - - -
47A LYS* 3.2 26.4 + - - +
49A LEU* 5.3 0.2 - - - +
62A LYS 3.8 8.5 - - - +
63A ILE* 3.3 18.4 + - - +
64A ARG 3.2 0.6 - - - -
65A ARG* 1.3 84.9 - - + +
67A ILE* 1.3 59.0 + - - +
69A ASN* 3.3 5.0 + - - +
70A LEU* 3.0 38.7 + - + +
93A MET* 4.3 15.1 - - + +
95A MET* 5.1 1.7 - - - +
160A PHE* 3.7 30.9 + - + +
161A GLY* 3.4 27.6 + - - +
163A SER* 6.1 2.2 - - - -
601A STU 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 3.2 26.3 + - + +
64A ARG* 4.1 4.0 - - - +
66A GLU* 1.3 74.7 - - + +
68A GLN* 1.3 66.5 + - - +
70A LEU* 4.6 0.2 - - - -
71A LYS* 3.0 28.2 + - + +
81A LEU* 4.1 10.0 - - + +
84A VAL* 3.8 35.2 - - + -
91A ILE* 4.8 11.2 - - + -
93A MET* 3.7 42.0 - - + -
163B PHE* 6.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 3.0 51.9 + - + +
65A ARG* 3.5 12.8 - - - +
67A ILE* 1.3 80.0 - - - +
69A ASN* 1.3 66.0 + - - +
71A LYS* 3.8 11.4 - - - +
72A LEU* 4.4 4.9 + - - +
165A MET* 4.2 25.4 - - - +
163B PHE* 6.3 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 3.0 25.0 + - - +
66A GLU* 3.8 4.7 - - - +
68A GLN* 1.3 81.9 + - - +
70A LEU* 1.3 65.0 + - + +
71A LYS 3.1 3.2 + - - -
72A LEU* 3.6 8.0 + - - +
73A PHE* 3.5 22.8 - - + -
137A VAL* 3.5 37.4 - - + +
160A PHE* 6.1 4.7 - - + -
163A SER* 4.5 7.2 + - - +
164A ASN* 4.4 6.9 + - - +
165A MET* 3.8 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU* 3.0 27.4 + - + +
69A ASN* 1.3 76.6 - - + +
71A LYS* 1.3 63.3 + - - +
73A PHE* 3.4 24.3 + - + +
78A ILE* 4.5 6.1 - - + -
79A ILE* 3.5 25.8 - - + +
81A LEU* 3.5 29.1 + - + +
93A MET* 4.5 4.7 - - + -
95A MET* 4.2 24.0 - - + -
158A ALA 5.1 1.8 - - - +
160A PHE* 3.6 53.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 3.0 20.5 + - + +
68A GLN* 3.8 9.2 - - - +
69A ASN 3.1 0.6 - - - -
70A LEU* 1.3 79.1 - - - +
72A LEU* 1.3 62.8 + - + +
73A PHE 3.2 4.4 + - - +
74A ARG* 5.1 5.5 + - - -
80A LYS* 5.4 2.9 - - - -
81A LEU* 3.9 25.3 - - + +
82A TYR 3.5 21.9 + - - -
83A GLN* 3.6 17.0 - - - +
84A VAL* 4.3 14.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN 4.4 3.8 + - - +
69A ASN 3.6 6.3 + - - +
70A LEU 3.4 0.4 - - - -
71A LYS* 1.3 81.9 - - + +
73A PHE* 1.3 66.2 + - + +
74A ARG* 3.7 31.3 + - - +
131A TYR* 4.1 5.4 + - - -
135A HIS* 5.4 3.8 - - - -
306A GLU* 4.7 17.5 - - - +
----------------------------------------------------------
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