Contacts of the strand formed by residues 80 - 85 (chain B) in PDB entry 3Q3G
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 80 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B SER* 3.7 11.0 - - - -
24B CYS 3.4 7.2 - - - +
25B THR* 2.7 26.9 + - - +
31B ILE* 3.5 5.5 - - - +
74B ALA* 3.5 1.4 - - - -
75B ASP 2.7 35.4 + - - +
78B SER* 3.0 28.8 + - - -
79B ASN* 1.3 74.3 - - - +
81B ALA* 1.3 66.8 + - - +
82B TYR* 3.5 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B SER* 3.5 2.6 - - - -
24B CYS* 2.8 34.2 + - + +
31B ILE* 4.8 3.3 - - + +
36B MET* 3.6 43.7 - - + -
38B TRP* 3.8 8.0 - - - +
53B ILE* 4.7 5.8 - - + -
55B PRO* 5.6 0.2 - - + -
73B THR 3.4 8.5 - - - +
74B ALA* 4.2 4.9 - - + +
80B THR* 1.3 74.3 - - - +
82B TYR* 1.3 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LYS* 3.7 26.7 - - + -
22B LEU 3.2 7.9 - - - +
23B SER* 3.7 20.2 - - - -
38B TRP* 3.5 5.1 + - - -
71B THR 4.4 0.4 - - - +
72B ILE* 3.3 13.3 - - - +
73B THR* 2.7 55.9 + - - +
75B ASP* 3.6 13.4 + - + -
78B SER* 3.5 18.4 + - - -
80B THR* 3.5 34.5 - - + +
81B ALA* 1.3 73.6 - - - +
83B LEU* 1.3 58.6 + - - +
84B GLN 4.3 0.2 - - - -
201K SER* 3.3 27.4 + - - -
202K GLU* 3.5 17.7 - - + +
203K THR* 5.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL 3.7 1.2 - - - +
21B LYS* 3.4 3.1 - - - -
22B LEU* 2.8 49.2 + - + +
38B TRP* 3.5 39.9 - - + -
50B ILE* 3.9 14.8 - - + -
70B ALA* 3.7 29.8 - - + -
71B THR 3.6 1.6 - - - +
72B ILE* 3.8 18.4 - - + -
82B TYR* 1.3 73.8 - - - +
84B GLN* 1.3 61.4 + - - +
85B LEU* 4.0 15.8 + - + -
96B TYR* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B SER* 3.7 20.6 + - - +
20B VAL 3.2 15.9 - - - +
21B LYS* 3.9 25.4 - - + +
69B LYS 3.3 2.3 - - - +
70B ALA* 3.3 6.6 - - - +
71B THR* 2.8 57.9 + - + +
83B LEU* 1.3 73.8 - - - +
85B LEU* 1.3 61.0 + - - +
86B SER* 4.8 9.5 - - - -
197K SER* 4.6 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B SER* 3.0 6.5 + - - -
20B VAL* 2.9 48.8 + - + -
22B LEU* 4.5 5.2 - - + -
50B ILE* 4.8 2.7 - - + -
66B PHE* 5.5 2.9 - - + -
69B LYS* 3.4 18.2 - - + +
70B ALA* 4.2 11.9 - - + -
83B LEU* 4.0 31.6 - - + +
84B GLN* 1.3 76.5 - - - +
86B SER* 1.3 58.9 + - - +
88B LEU* 3.7 22.2 - - + +
92B ASP* 5.6 0.9 - - - +
96B TYR* 3.6 44.6 - - + +
120B VAL* 4.8 1.6 - - + -
----------------------------------------------------------
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