Contacts of the helix formed by residues 73 - 80 (chain B) in PDB entry 3QFR
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 VAL 73 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B SER* 3.0 6.8 + - - +
72B PHE* 1.3 93.3 - - + +
74B GLU* 1.3 65.7 + - - +
76B MET* 3.1 8.5 + - - +
77B LYS* 3.0 31.0 + - - +
124B ASP* 3.4 29.8 - - + +
127B SER* 3.8 26.5 - - - +
128B LEU* 4.2 11.2 - - + +
130B GLU* 3.9 15.5 - - - +
131B ILE* 3.6 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B SER 4.1 5.4 - - - +
71B SER* 3.0 27.6 + - - +
73B VAL* 1.3 76.4 - - - +
75B LYS* 1.3 56.8 + - - +
76B MET 3.0 5.2 - - - -
77B LYS* 3.6 32.2 + - - +
78B LYS* 2.9 48.0 + - - +
127B SER* 5.8 0.2 - - - -
130B GLU* 3.7 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B SER 4.8 12.5 + - - +
71B SER 3.0 13.9 + - - +
72B PHE* 3.9 9.9 - - - +
73B VAL 3.3 0.2 - - - -
74B GLU* 1.3 77.1 - - - +
76B MET* 1.3 51.5 + - - +
78B LYS* 4.0 6.7 - - + -
79B THR* 2.7 38.8 + - + +
81B ARG* 6.3 0.2 - - - +
113B MET* 4.5 15.1 - - + +
120B TYR* 3.3 29.2 + - + +
357B GLU* 2.8 34.0 + - + +
358B SER* 4.3 3.4 - - - +
359B ASN* 3.3 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 2.9 26.2 + - - +
73B VAL* 3.1 3.5 + - - +
74B GLU 3.0 0.4 - - - -
75B LYS* 1.3 77.6 - - - +
77B LYS* 1.3 66.2 + - - +
78B LYS 3.1 0.7 - - - -
79B THR* 3.3 4.2 + - - -
80B GLY* 2.9 20.6 + - - -
81B ARG* 2.9 36.3 + - + +
82B ASN* 3.4 27.1 - - - +
83B ILE 3.8 12.3 - - - +
84B ILE* 4.0 16.6 - - + +
113B MET* 3.8 18.4 - - - -
128B LEU* 4.0 21.1 - - + -
131B ILE* 3.3 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL* 3.0 19.1 + - - +
74B GLU* 3.6 27.9 + - - +
76B MET* 1.3 76.4 - - - +
78B LYS* 1.3 65.8 + - - +
80B GLY* 3.3 9.9 + - - -
130B GLU* 2.8 59.9 + - - +
131B ILE* 3.9 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLU* 2.9 37.2 + - - +
75B LYS* 3.9 9.0 - - + +
77B LYS* 1.3 80.1 - - - +
79B THR* 1.3 59.4 + - + +
80B GLY 3.8 0.2 + - - -
357B GLU* 3.5 24.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LYS* 2.7 26.8 + - + +
76B MET 3.3 0.7 + - - -
78B LYS* 1.3 76.4 - - + +
80B GLY* 1.3 58.5 + - - +
81B ARG* 2.9 43.4 + - - +
111B ARG* 2.9 21.0 + - - -
113B MET* 4.8 0.5 - - - -
355B ASP* 4.7 1.1 - - - +
357B GLU* 3.7 47.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B MET 2.9 7.1 + - - -
77B LYS* 3.3 10.4 + - - -
78B LYS 3.4 0.4 - - - -
79B THR* 1.3 80.7 - - - +
81B ARG* 1.3 59.3 + - - +
82B ASN* 4.1 0.5 + - - +
111B ARG* 2.8 31.4 - - - +
----------------------------------------------------------
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