Contacts of the strand formed by residues 51 - 59 (chain B) in PDB entry 3IML
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 51 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 4.9 2.5 - - + -
55A ALA* 5.9 0.2 - - + -
94A LEU* 3.6 33.9 - - + -
96A ALA* 3.9 23.1 - - + -
46B LEU* 4.9 5.8 - - + +
47B CYS* 3.3 2.6 - - - -
48B ASN* 2.7 48.6 + - + +
49B THR 3.5 3.0 + - - -
50B GLY* 1.3 79.1 - - - +
52B VAL* 1.3 71.3 - - - +
53B VAL* 3.9 16.6 - - + -
91B CYS* 4.1 1.6 - - - +
92B ALA* 3.3 27.8 - - + +
94B LEU* 4.9 0.9 - - + -
51C LEU* 6.5 0.9 - - + -
94D LEU* 4.6 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 4.6 7.9 - - + -
45B THR* 4.3 7.9 - - + -
46B LEU 3.4 6.5 - - - +
47B CYS* 4.2 11.7 - - + -
48B ASN 5.6 0.2 - - - +
51B LEU* 1.3 80.5 - - - +
53B VAL* 1.3 66.8 + - - +
54B LEU* 3.9 27.6 - - + -
70B ALA* 4.7 6.7 - - + -
74B ILE* 4.3 22.0 - - + -
91B CYS* 4.4 16.2 - - + -
92B ALA 3.0 7.2 + - - +
93B VAL* 3.4 16.6 - - + +
94B LEU* 2.8 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.2 20.8 - - + +
51A LEU* 5.2 2.5 - - + -
53A VAL* 4.3 18.2 - - + -
44B GLU 3.8 0.7 - - - +
45B THR* 3.4 7.4 - - - +
46B LEU* 2.7 54.5 + - + +
51B LEU* 3.9 24.0 - - + -
52B VAL* 1.3 78.6 - - - +
54B LEU* 1.3 66.9 + - - +
55B ALA* 4.7 2.7 - - + -
94B LEU* 3.4 34.1 - - + +
96B ALA* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.8 28.5 - - + -
28B ILE* 3.9 7.9 - - + -
44B GLU 3.5 2.9 - - - -
45B THR* 3.9 10.8 - - - +
52B VAL* 3.9 18.6 - - + -
53B VAL* 1.3 74.1 - - - +
55B ALA* 1.3 61.3 + - - +
66B TYR* 3.9 39.9 - - + +
70B ALA* 4.6 3.6 - - + -
93B VAL* 4.2 9.6 - - + -
94B LEU 2.9 11.1 + - - +
95B VAL* 4.0 16.6 - - + +
96B ALA* 2.8 28.8 + - - +
97B TYR* 3.5 21.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.2 22.7 - - + -
48A ASN* 4.3 9.2 - - - +
243A CYS* 3.8 19.7 - - - -
43B ALA 3.7 0.2 - - - -
44B GLU* 2.7 39.0 + - + +
53B VAL* 4.1 3.3 - - + -
54B LEU* 1.3 75.2 - - - +
56B GLY* 1.3 57.3 + - - +
96B ALA* 4.1 11.7 - - + +
97B TYR* 3.4 14.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 4.3 1.9 + - - +
243A CYS* 3.9 11.7 - - - +
42B ALA 3.3 9.9 - - - -
44B GLU* 4.6 1.3 - - - -
55B ALA* 1.3 79.6 - - - +
57B GLU* 1.3 81.6 + - - +
96B ALA 4.2 2.7 + - - +
97B TYR* 3.3 8.5 - - - -
98B ASP 2.9 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 4.1 5.7 - - - +
239A PRO 5.2 0.3 - - - +
241A GLY 4.4 12.0 - - - +
242A ASP* 3.5 14.4 - - + +
243A CYS* 3.1 32.0 + - - +
40B ARG 4.0 1.1 - - - +
41B VAL* 3.6 1.4 - - - -
42B ALA* 2.8 49.5 + - + +
44B GLU* 5.8 0.3 - - - +
56B GLY* 1.3 87.8 - - - +
58B ILE* 1.3 62.4 + - - +
98B ASP* 3.6 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 5.0 1.1 - - + -
32B ILE* 4.1 20.6 - - + -
40B ARG 3.3 8.3 - - - +
41B VAL* 4.4 11.7 - - + -
42B ALA 4.8 0.7 - - - +
43B ALA* 5.4 0.7 - - + -
57B GLU* 1.3 81.1 - - - +
59B THR* 1.3 66.0 + - - +
60B THR* 4.1 24.9 - - + -
66B TYR* 4.0 16.8 - - + +
97B TYR* 3.6 49.6 - - + -
98B ASP 2.8 13.7 + - - +
99B LYS* 3.2 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B SER* 3.2 8.0 - - - -
40B ARG* 2.7 59.0 + - + +
58B ILE* 1.3 73.9 + - - +
60B THR* 1.3 62.7 + - - +
99B LYS 5.5 1.1 - - - -
----------------------------------------------------------
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