Contacts of the strand formed by residues 37 - 45 (chain A) in PDB entry 1L4W
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 GLY 37 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP 2.2 38.5 + - - +
31A ALA* 3.3 0.2 - - - +
32A PHE* 3.0 24.0 - - - +
36A ARG* 1.3 82.2 - - - +
38A LYS* 1.3 62.4 + - - -
190B TYR* 3.7 11.2 - - - -
191B THR 3.9 6.5 - - - -
192B CYS* 4.3 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 5.6 2.2 - - + -
28A TRP 2.7 23.6 - - - +
29A CYS* 3.9 17.5 - - - -
30A ASP 3.9 1.8 - - - +
32A PHE* 3.2 33.4 - - + +
37A GLY* 1.3 72.6 - - - -
39A VAL* 1.3 53.8 + - - +
190B TYR* 2.6 14.9 - - - -
191B THR* 2.5 57.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 3.0 29.1 - - - +
28A TRP* 2.8 64.3 + - + +
30A ASP* 2.9 40.3 - - + +
37A GLY 3.8 0.8 + - - -
38A LYS* 1.3 68.6 - - - +
40A VAL* 1.3 75.1 + - - +
41A GLU* 4.4 0.4 - - + -
188B VAL* 4.0 24.7 - - + -
189B TYR 3.7 2.2 - - - -
190B TYR* 4.3 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 3.8 6.1 + - - +
25A ARG* 2.8 44.2 - - - +
26A LYS 3.4 9.2 - - - +
27A MET* 3.9 0.9 - - + -
39A VAL* 1.3 78.7 - - - +
41A GLU* 1.3 64.9 + - - +
42A LEU* 4.2 3.6 - - + -
68A HIS* 3.2 16.6 - - + +
188B VAL* 4.6 1.9 - - - -
189B TYR* 2.5 50.0 + - - +
191B THR* 2.9 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 3.4 8.5 - - - +
24A TYR* 3.8 14.6 + - + +
26A LYS* 3.0 58.8 + - + +
28A TRP* 3.1 40.5 - - + -
39A VAL* 4.4 0.4 - - + -
40A VAL* 1.3 74.5 - - - +
42A LEU* 1.3 66.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A HIS* 3.7 14.4 - - + -
5A THR* 3.1 39.2 + - - -
6A THR* 3.3 25.2 + - + +
11A ILE* 4.1 11.2 - - + -
24A TYR* 3.9 6.2 + - - +
25A ARG* 3.3 36.8 - - - +
40A VAL* 4.2 1.6 - - + -
41A GLU* 1.3 79.0 - - - +
43A GLY* 1.3 57.0 + - - +
66A ASN* 2.7 38.6 - - + +
67A PRO* 4.5 4.3 - - + -
68A HIS* 4.1 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A CYS* 3.5 6.8 - - - -
4A HIS 3.9 5.2 - - - -
5A THR* 4.6 2.2 - - - -
23A CYS* 3.3 6.6 - - - -
24A TYR* 2.9 55.2 + - - +
42A LEU* 1.3 75.6 - - - +
44A CYS* 1.3 58.9 + - - -
66A ASN* 3.5 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A CYS* 3.7 10.1 - - + -
4A HIS 5.5 0.4 - - - +
14A VAL* 6.4 1.6 - - + -
16A CYS* 2.0 45.3 - - - -
20A GLU* 2.9 28.2 - - - +
21A ASN* 3.4 13.9 - - - -
22A LEU 3.1 3.6 - - - -
24A TYR* 3.3 4.5 - - - -
43A GLY* 1.3 72.3 - - - -
45A ALA* 1.3 60.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 3.4 13.3 - - - -
22A LEU* 2.7 40.3 + - + +
24A TYR* 3.9 21.2 - - + -
44A CYS* 1.3 73.7 - - - +
46A ALA* 1.3 60.3 + - - +
47A THR* 4.3 8.1 - - + +
48A CYS* 4.5 14.6 - - + +
49A PRO* 5.6 2.7 - - + -
----------------------------------------------------------
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