Contacts of the strand formed by residues 40 - 47 (chain D) 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 ARG 40 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D TYR 3.6 8.2 + - - +
39D SER* 1.3 73.8 + - - +
41D VAL* 1.3 61.7 + - - +
57D GLU 4.5 1.5 - - - -
58D ILE* 3.4 4.2 - - - -
59D THR* 2.8 52.8 + - + +
270D ASP* 3.4 5.6 + - - -
272D SER* 3.2 39.2 + - - -
273D LYS* 4.5 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LEU* 3.6 33.7 - - + -
32D ILE* 3.9 39.9 - - + -
39D SER* 4.1 8.3 - - - +
40D ARG* 1.3 80.0 - - - +
42D ALA* 1.3 61.6 + - - +
43D ALA* 3.8 18.4 - - + -
57D GLU 3.6 2.9 - - - -
58D ILE* 4.5 6.7 - - + +
268D GLY 3.0 21.2 - - - +
269D LYS* 3.3 2.6 - - - -
270D ASP* 2.9 26.0 + - + +
273D LYS* 3.4 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C ASP* 5.8 0.2 - - - +
41D VAL* 1.3 73.4 - - - +
43D ALA* 1.3 60.7 + - - +
44D GLU* 3.6 11.1 + - - +
56D GLY* 3.3 8.7 - - - -
57D GLU* 2.8 51.1 + - + +
268D GLY 3.3 4.3 - - - -
269D LYS* 4.7 8.3 - - + +
273D LYS* 4.0 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D SER* 2.6 41.8 + - - +
28D ILE* 4.5 7.2 - - + -
41D VAL* 3.8 18.2 - - + -
42D ALA* 1.3 70.0 - - - +
44D GLU* 1.3 62.6 + - - +
45D THR* 5.6 0.2 - - - +
55D ALA 3.9 4.0 - - - -
58D ILE* 5.0 1.6 - - + -
97D TYR* 4.1 22.9 - - + +
267D SER 4.2 0.5 - - - +
268D GLY* 2.8 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ASP* 5.7 0.2 - - - +
46C LEU* 5.0 3.8 - - + -
243C CYS* 4.1 22.2 - - + +
245C LEU* 3.6 30.8 - - + +
248C ARG* 3.0 40.3 + - - -
25D SER* 3.9 0.2 - - - -
42D ALA* 4.1 14.7 - - - +
43D ALA* 1.3 77.9 - - - +
45D THR* 1.3 64.8 + - - +
54D LEU* 3.5 4.9 - - - +
55D ALA* 2.8 42.4 + - - +
57D GLU* 5.6 1.1 - - - +
97D TYR* 4.5 1.4 + - - -
246D THR* 3.7 7.8 - - - +
267D SER 4.7 1.6 - - - +
269D LYS* 5.6 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LEU* 5.1 0.4 - - - -
245C LEU* 4.5 4.0 - - - +
21D ALA* 3.6 16.4 - - + +
24D ILE* 3.7 38.4 - - + +
25D SER* 3.0 23.6 + - - -
43D ALA 4.8 0.2 - - - -
44D GLU* 1.3 76.3 + - - +
46D LEU* 1.3 65.9 + - - +
47D CYS* 4.8 1.1 - - + +
52D VAL* 4.1 5.8 - - + -
53D VAL 3.2 9.4 - - - +
54D LEU* 3.7 9.2 - - + +
97D TYR* 5.1 1.4 + - - -
245D LEU* 3.5 4.9 - - - +
246D THR* 3.0 37.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU* 5.0 5.2 - - + +
46C LEU* 4.1 39.7 - - + +
53C VAL* 4.2 15.5 - - + +
55C ALA* 4.3 14.6 - - + -
45D THR* 1.3 73.7 - - - +
47D CYS* 1.3 68.0 + - - +
48D ASN* 4.7 3.8 - - + +
51D LEU* 5.2 5.6 - - + +
52D VAL* 3.4 2.1 - - - +
53D VAL* 2.6 55.6 + - + +
243D CYS* 3.9 25.4 - - - -
244D GLY 3.4 6.1 - - - +
245D LEU* 4.3 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D PRO 3.7 23.1 - - - -
20D VAL* 4.2 6.5 - - + -
21D ALA* 4.1 17.5 - - - -
24D ILE* 5.0 2.7 - - + -
45D THR* 4.9 2.5 - - + -
46D LEU* 1.3 77.2 - - - +
48D ASN* 1.3 62.1 + - - +
51D LEU 3.2 9.4 - - - +
52D VAL* 4.3 16.4 - - + -
239D PRO* 3.9 24.5 - - + +
243D CYS* 3.5 1.4 - - - -
244D GLY* 2.9 39.1 + - - +
----------------------------------------------------------
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