Contacts of the strand formed by residues 77 - 82 (chain H) in PDB entry 2FD6
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 77 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H SER* 3.8 13.5 - - - -
22H CYS 3.4 11.7 - - - +
23H LYS* 3.5 4.9 - - - +
29H PHE* 3.9 4.6 - - - -
71H ALA* 3.3 4.0 - - - +
72H ASP 2.8 32.1 + - - -
75H SER* 3.0 21.7 + - - -
76H SER* 1.3 77.2 - - - +
78H ALA* 1.3 70.9 + - - +
79H TYR* 3.4 30.7 - - + +
403H ETX 2.9 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H SER* 3.4 2.4 - - - -
22H CYS* 2.8 36.8 + - + +
29H PHE* 4.3 3.9 - - + -
34H ILE* 3.9 31.9 - - + -
36H TRP* 3.8 16.4 - - + +
51H ILE* 4.4 11.7 - - + -
70H THR 3.5 9.6 - - - +
71H ALA* 4.2 1.3 - - - +
77H THR* 1.3 74.7 - - - +
79H TYR* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 79 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H LYS* 3.6 28.3 - - + -
20H ILE 3.2 9.2 - - - +
21H SER* 3.5 24.9 - - - -
36H TRP* 4.0 5.2 + - - -
69H LEU* 3.5 6.2 - - - +
70H THR* 2.9 46.4 + - - +
72H ASP* 3.8 24.3 + - + +
75H SER* 4.5 0.2 + - - -
77H THR* 3.4 34.9 - - + +
78H ALA* 1.3 76.3 - - - +
80H MET* 1.3 62.2 + - - +
403H ETX 4.3 16.1 - - - -
404H EDO 3.9 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 80 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H VAL* 3.9 1.0 - - - +
19H LYS* 3.3 3.2 - - - -
20H ILE* 2.9 54.1 + - + +
36H TRP* 3.7 34.5 - - + -
48H ILE* 3.6 29.8 - - + -
67H ALA* 4.3 2.0 - - + -
68H THR 3.4 3.4 - - - -
69H LEU* 3.7 15.5 - - + -
79H TYR* 1.3 77.4 - - - +
81H GLN* 1.3 72.4 + - - +
82H LEU* 4.2 15.8 - - + +
90H TYR* 3.4 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H SER* 4.3 18.4 + - - -
18H VAL 3.2 15.0 - - - +
19H LYS* 4.0 23.5 + - + +
66H LYS 3.4 0.9 - - - +
67H ALA* 3.1 9.0 - - - +
68H THR* 2.9 50.6 + - - +
79H TYR 4.3 0.2 - - - -
80H MET* 1.3 75.4 - - - +
82H LEU* 1.3 78.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H SER* 3.1 3.5 - - - -
18H VAL* 2.8 48.9 + - + +
20H ILE* 5.4 1.6 - - + -
48H ILE* 5.2 1.8 - - + -
63H PHE* 5.4 2.9 - - + -
66H LYS* 3.2 19.1 - - + +
67H ALA* 3.9 20.0 - - + -
80H MET* 4.2 22.9 - - + +
81H GLN* 1.3 80.9 - - - +
82H SER* 1.3 59.8 + - - +
86H ASP* 5.3 0.9 - - + +
90H TYR* 3.4 46.2 - - + +
109H VAL* 5.0 2.5 - - + -
----------------------------------------------------------
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