Contacts of the strand formed by residues 41 - 50 (chain D) in PDB entry 6B0B
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 THR 41 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PHE* 4.4 17.7 - - + -
142A ALA* 5.3 2.5 - - + -
163A LEU* 5.2 4.6 - - - +
35D GLY* 3.4 1.0 - - - -
36D ARG* 2.9 53.1 + - - +
39D GLU* 3.9 10.0 - - + +
40D GLY* 1.3 78.4 - - - +
42D GLN* 1.3 63.1 + - - +
72D TYR* 4.4 1.7 + - - -
214D TYR* 3.7 20.9 - - + +
215D GLU 3.2 3.8 - - - -
216D ARG* 3.4 32.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D PHE* 4.0 17.8 - - - -
34D GLU 3.7 9.6 - - - +
35D GLY* 4.0 1.1 - - - -
41D THR* 1.3 77.6 - - - +
43D THR* 1.3 67.3 + - - +
44D ALA* 5.6 2.2 - - + +
65D PHE* 4.6 14.0 - - - +
70D LYS 4.9 1.6 + - - -
72D TYR* 3.2 53.1 + - + +
214D TYR* 3.2 6.0 - - - -
215D GLU* 2.9 76.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TYR* 3.9 35.9 - - + -
163A LEU* 4.9 10.4 - - + +
14D PHE* 4.3 3.0 - - - -
33D GLY* 3.2 1.9 - - - -
34D GLU* 2.9 54.4 + - - +
36D ARG* 5.9 0.2 + - - -
42D GLN* 1.3 81.4 - - - +
44D ALA* 1.3 61.5 + - - +
45D LYS* 5.8 4.4 - - - -
212D GLU* 6.1 1.8 - - - -
213D GLN 3.0 11.2 - - - +
214D TYR* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D PHE* 3.8 24.0 - - + -
32D GLU 3.8 5.2 - - - +
33D GLY* 3.9 0.7 - - - -
42D GLN* 5.6 2.2 - - - +
43D THR* 1.3 77.6 - - - +
45D LYS* 1.3 63.3 + - - +
46D LEU* 4.0 17.9 - - + +
65D PHE* 5.5 7.6 - - + -
211D VAL 3.7 1.0 - - - +
212D GLU* 3.1 6.8 - - - +
213D GLN* 2.9 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TYR* 5.1 4.0 - - - -
31D GLY* 3.2 3.1 - - - -
32D GLU* 2.9 45.1 + - + +
33D GLY* 5.9 0.2 - - - -
34D GLU* 5.2 9.0 + - - -
43D THR* 5.8 3.8 - - - -
44D ALA* 1.3 77.2 - - - +
46D LEU* 1.3 63.1 + - - +
47D LYS* 5.2 13.1 + - - +
210D ILE* 6.5 1.1 - - + -
211D VAL 3.6 4.7 - - - -
212D GLU* 3.4 36.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
16D VAL* 4.1 10.8 - - + -
29D ILE* 4.0 9.0 - - + -
30D GLU 3.7 2.0 - - - -
31D GLY* 3.7 16.8 - - - +
44D ALA* 4.0 20.0 - - + +
45D LYS* 1.3 83.0 - - - +
47D LYS* 1.3 70.1 + - - +
58D TRP* 3.7 40.6 - - + -
65D PHE* 4.1 22.2 - - + -
209D THR 4.6 1.1 - - - -
210D ILE* 3.8 8.5 - - - +
211D VAL 2.9 35.0 + - - +
213D GLN* 4.2 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ILE* 3.5 4.7 - - - -
30D GLU* 2.9 39.5 + - + +
32D GLU* 4.4 15.2 + - - +
45D LYS* 5.2 13.5 + - - +
46D LEU* 1.3 80.6 + - - +
48D VAL* 1.3 66.7 + - - +
49D THR* 3.6 7.0 + - + +
209D THR 3.8 4.9 - - - -
210D ILE* 3.7 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D GLU 3.8 7.2 - - - +
29D ILE* 4.4 8.7 - - + -
47D LYS* 1.3 74.4 - - - +
49D THR* 1.3 60.9 + - - +
50D LYS 3.3 27.6 - - - +
52D GLY* 4.2 15.3 - - - +
54D LEU* 4.2 36.3 - - + -
58D TRP* 4.5 6.3 - - + -
208D TYR 4.4 2.7 - - - +
209D THR* 3.4 36.3 + - + +
210D ILE* 5.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D GLU* 3.0 33.8 + - - +
29D ILE 4.0 0.5 + - - -
30D GLU* 3.7 28.9 - - + +
47D LYS* 4.0 11.0 - - + +
48D VAL* 1.3 77.3 - - - +
50D LYS* 1.3 75.9 + - - +
52D GLY 5.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D GLU 5.0 1.3 - - - +
27D PHE* 3.3 26.5 - - - +
28D GLU* 3.6 32.1 + - + +
48D VAL* 3.3 9.4 - - - +
49D THR* 1.3 94.3 + - - +
51D GLY* 1.3 63.7 + - - +
52D GLY 3.3 2.7 - - - +
54D LEU* 4.7 0.2 - - - +
----------------------------------------------------------
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