Contacts of the strand formed by residues 38 - 45 (chain A) in PDB entry 2I32
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 LEU 38 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 3.9 21.8 - - + -
28A PHE* 3.8 31.2 - - + -
34A LEU* 3.9 16.2 - - + -
36A GLU 4.2 0.2 + - - -
37A ASP* 1.3 74.1 - - - +
39A GLU* 1.3 59.7 + - - +
40A TRP* 3.6 31.0 - - + +
61A LEU* 3.2 5.6 - - - +
62A VAL* 2.8 36.8 + - + +
65A VAL* 4.1 8.5 - - + +
99A CYS* 3.8 3.4 - - - -
100A THR 4.0 1.6 - - - -
101A TYR* 4.0 11.2 - - + -
106A PHE* 3.8 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP 5.3 0.9 - - - +
38A LEU* 1.3 75.1 - - - +
40A TRP* 1.3 63.4 + - - +
41A LYS* 2.8 29.6 + - - +
59A SER* 3.6 11.9 + - - +
60A VAL 3.4 9.2 - - - +
61A LEU* 4.0 13.2 - - + -
99A CYS* 3.3 3.4 - - - -
100A THR* 2.9 57.1 + - + +
103A GLY* 6.0 0.7 - - - -
458E ARG* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 5.4 0.9 - - + -
6A VAL* 4.0 26.0 - - + -
9A VAL* 6.4 0.2 - - + -
26A ILE* 4.0 33.7 - - + -
28A PHE* 3.9 24.2 - + + -
38A LEU* 3.6 24.0 - - + +
39A GLU* 1.3 78.6 - - - +
41A LYS* 1.3 62.0 + - - +
59A SER* 3.3 4.3 + - - -
60A VAL* 2.8 44.7 + - + +
62A VAL* 3.3 36.3 - - + +
72A PHE* 3.9 10.3 - + + -
74A PHE* 3.6 20.4 - - + -
97A ILE* 3.9 21.8 - - + -
98A THR 3.3 3.8 - - - -
99A CYS* 3.4 32.5 - - + -
107A ILE* 5.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLU* 2.8 32.3 + - + +
40A TRP* 1.3 80.5 - - - +
42A ILE* 1.3 61.7 + - - +
43A ILE* 4.0 15.9 + - + -
56A VAL* 4.5 16.8 - - + -
58A ASP 3.3 9.0 - - - +
59A SER* 3.5 20.4 - - - +
74A PHE* 3.6 6.0 - - - -
96A LEU 3.7 0.2 - - - +
97A ILE* 3.2 5.2 - - - -
98A THR* 2.9 47.4 + - - +
100A THR* 3.9 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 4.6 4.5 - - + -
24A PHE* 3.4 38.1 - - + -
41A LYS* 1.3 73.2 - - - +
43A ILE* 1.3 60.8 + - - +
56A VAL* 3.6 3.5 - - - -
57A LEU* 2.8 55.2 + - + -
58A ASP 3.2 7.5 + - - +
74A PHE* 3.3 42.1 - - + +
76A ALA* 3.9 20.9 - - + -
95A VAL* 4.1 13.9 - - + -
96A LEU 3.2 5.8 - - - +
97A ILE* 4.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 4.4 18.2 - - + -
42A ILE* 1.3 77.7 - - - +
44A TYR* 1.3 64.5 + - - +
45A VAL* 4.0 2.3 + - + +
54A ASP* 4.1 29.4 - - + +
55A GLN 3.4 9.6 - - - +
56A VAL* 4.4 14.8 - - + +
95A VAL* 3.2 4.9 - - - -
96A LEU* 2.6 59.3 + - + +
98A THR* 4.2 27.8 - - + +
108A ARG* 4.9 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 3.8 11.6 - + - -
22A PHE* 3.6 33.7 - + - -
42A ILE 4.2 0.6 - - - -
43A ILE* 1.3 74.5 - - - +
45A VAL* 1.3 79.3 + - - +
46A GLY* 3.4 5.9 + - - -
53A TYR 3.8 0.2 - - - +
54A ASP* 3.4 3.1 - - - -
55A GLN* 2.8 39.5 + - + +
57A LEU* 4.1 18.6 - - + -
79A PRO* 3.9 30.3 - - + -
84A ILE* 4.1 15.6 - - + +
93A THR* 3.9 10.8 + - - -
94A VAL 4.0 3.6 - - - -
95A VAL* 4.2 9.2 - - + -
113A VAL* 4.7 15.3 - - + -
115A ASN* 3.1 27.0 + - - -
137A ARG* 5.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 4.9 4.0 - - + +
44A TYR* 1.3 77.7 - - - +
46A GLY* 1.3 58.3 + - - +
47A SER 3.2 29.8 - - - +
48A ALA* 4.0 8.1 - - + +
54A ASP* 4.2 20.9 - - - +
93A THR* 2.9 36.6 - - + +
94A VAL* 3.0 43.0 + - + +
96A LEU* 5.0 10.1 - - + -
----------------------------------------------------------
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