Contacts of the strand formed by residues 44 - 52 (chain J) in PDB entry 6AVO
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 44 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J CYS* 2.8 34.0 + - - -
43J ASP* 1.3 81.5 + - - +
45J VAL* 1.3 68.6 + - - +
140J TYR* 3.9 2.9 - - - -
146J ALA* 3.3 15.3 - - - +
186J CYS* 4.2 5.2 - - - -
216J VAL 3.3 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J ILE 3.6 13.7 - - - +
40J ARG* 4.0 11.0 - - + -
44J GLY* 1.3 80.1 - - - +
46J VAL* 1.3 71.1 + - - +
47J PHE* 3.6 29.6 - - + -
138J GLY* 4.3 7.4 - - - -
139J SER 4.2 5.8 - - - +
146J ALA* 3.9 13.2 - - + -
147J GLN 3.7 23.1 - - - +
148J LEU* 3.9 14.4 - - + -
186J CYS* 4.7 0.8 - - - -
215J TRP* 3.0 28.4 - - - +
216J VAL* 3.2 11.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J GLY* 3.0 25.1 - - - -
39J ILE 3.1 9.6 + - - +
41J CYS* 5.2 0.7 - - - -
45J VAL* 1.3 80.9 - - - +
47J PHE* 1.3 74.9 + - - +
186J CYS* 4.4 10.5 - - + +
189J ILE* 3.6 31.9 - - + -
190J VAL* 4.2 27.8 - - + -
193J VAL* 3.9 22.0 - - + +
213J LEU* 5.0 4.3 - - + -
214J SER 3.3 10.3 - - - +
215J TRP* 3.8 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 47 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J ILE 3.4 2.7 - - - +
38J GLY* 4.1 0.7 - - - -
45J VAL* 3.6 23.6 - - + -
46J VAL* 1.3 81.2 - - - +
48J GLY* 1.3 57.8 + - - +
66J LEU* 3.8 16.4 - - + -
74J GLY 4.6 5.4 - - - -
75J MET 4.8 0.7 - - - -
76J ALA* 3.6 18.6 - - + -
136J MET* 3.8 26.7 - - + -
137J LEU 4.0 0.7 - - - -
138J GLY* 3.5 31.2 - - - -
148J LEU* 3.7 19.3 - - + -
193J VAL* 4.3 0.9 - - - -
212J GLU 4.5 0.2 - - - -
213J LEU* 3.0 32.7 - - - +
214J SER* 2.7 39.6 + - - +
216J VAL* 5.5 1.1 - - + -
224J HIS* 4.2 17.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 48 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J ALA* 3.6 2.8 - - - +
37J ILE* 3.0 30.8 + - - +
47J PHE* 1.3 75.5 - - - +
49J VAL* 1.3 69.9 + - - +
50J GLU 4.3 0.7 - - - -
136J MET* 5.4 0.3 - - - +
193J VAL* 3.8 13.1 - - - +
197J ILE* 4.6 8.3 - - - -
212J GLU 3.9 0.9 - - - -
213J LEU* 3.3 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J ALA* 4.4 12.3 - - + -
48J GLY* 1.3 79.1 - - - +
50J GLU* 1.3 55.1 + - - +
51J LYS* 2.7 38.1 + - + +
65J ARG* 3.9 35.0 - - + +
66J LEU* 3.5 37.5 - - + -
76J ALA* 5.0 0.4 - - + -
197J ILE* 4.6 4.0 - - - +
210J GLU 2.9 12.8 - - - +
211J LEU* 3.9 6.3 - - - +
212J GLU* 3.4 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J SER* 3.0 20.5 + - - -
35J THR* 3.1 45.2 + - - +
48J GLY 4.3 0.2 - - - -
49J VAL* 1.3 68.9 - - - +
51J LYS* 1.3 57.2 + - - +
52J LEU* 2.9 11.3 + - + +
167J LYS* 4.1 18.3 + - - -
168J ALA* 5.3 0.9 - - - +
197J ILE* 3.9 21.8 - - + +
200J VAL* 4.5 5.2 - - - +
201J HIS* 2.3 57.4 + - + +
209J PHE* 4.2 13.9 - - + -
210J GLU 4.0 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J VAL* 2.7 25.0 + - + +
50J GLU* 1.3 67.4 - - - +
52J LEU* 1.3 71.5 + - - +
53J VAL* 3.2 2.5 + - + -
61J GLY* 4.1 5.9 - - - -
62J SER 3.2 22.6 + - - +
63J ASN* 2.9 26.9 - - + +
64J LYS* 3.6 11.3 - - - +
65J ARG* 4.2 16.2 - - - +
209J PHE* 3.7 2.0 - - - -
210J GLU* 2.8 59.8 + - + +
212J GLU* 2.4 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J SER 6.3 0.2 - - - -
34J SER* 4.4 15.9 + - - -
50J GLU* 2.9 16.4 + - + +
51J LYS* 1.3 76.6 - - - +
53J VAL* 1.3 63.6 + - - +
54J LEU* 3.7 19.8 + - + +
65J ARG* 4.8 1.0 - - - +
167J LYS* 4.1 14.1 - - - +
201J HIS* 3.5 19.1 - - + +
206J ASP* 3.2 48.7 - - + +
207J LYS 4.1 6.7 - - - +
208J ALA 4.7 0.2 - - - +
209J PHE* 3.5 11.9 - - + -
----------------------------------------------------------
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