Contacts of the helix formed by residues 76 - 87 (chain A) in PDB entry 3QJ6
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 76 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TRP* 3.6 8.0 - - - -
46A GLY* 3.4 14.9 - - - -
47A THR* 4.5 11.4 - - - -
74A ARG 3.1 0.8 + - - -
75A LYS* 1.3 71.3 - - - +
77A PHE* 1.3 57.7 + - - +
79A GLU* 3.4 25.2 + - - +
80A GLY* 3.1 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PRO* 4.4 0.9 - - + -
20A HIS 3.3 21.8 - - - -
21A TRP* 3.5 35.4 - + + -
22A PRO* 3.7 17.3 - - + +
68A TYR 3.5 21.5 - - - -
70A LYS 3.2 21.8 - - - -
72A ASN* 3.2 47.3 - - + -
74A ARG* 2.9 17.0 + - + +
75A LYS 3.3 1.4 + - - -
76A GLY* 1.3 75.1 - - - +
78A ASN* 1.3 64.2 + - - +
80A GLY* 3.0 4.9 + - - -
81A LEU* 3.0 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PRO* 3.4 17.8 - - + +
72A ASN 2.8 43.2 + - - +
73A LYS* 4.8 3.8 - - - +
74A ARG 5.0 3.8 + - - -
77A PHE* 1.3 71.4 - - - +
79A GLU* 1.3 74.2 + - - +
81A LEU* 3.1 11.5 + - + +
82A TRP* 3.0 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLY* 4.2 12.8 - - - +
76A GLY* 3.4 33.0 + - - +
77A PHE 3.9 0.2 + - - -
78A ASN* 1.3 82.9 + - - +
80A GLY* 1.3 56.3 + - - +
82A TRP* 3.1 11.0 + - - +
83A GLU* 3.0 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO* 3.7 10.2 - - - +
45A PHE* 3.5 17.0 - - - +
46A GLY* 3.6 21.5 - - - -
76A GLY 3.1 8.6 + - - -
77A PHE 3.0 9.3 + - - -
79A GLU* 1.3 73.9 - - - +
81A LEU* 1.3 58.5 - - - +
83A GLU* 4.3 0.4 - - - -
84A ILE* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 4.5 5.2 - - + -
22A PRO* 4.2 14.4 - - + -
61A TYR* 6.0 0.7 - - + -
69A GLY* 3.1 37.7 - - - +
71A PRO* 3.6 25.6 - - + -
77A PHE* 3.0 44.5 + - + +
78A ASN* 3.1 11.0 + - - +
80A GLY* 1.3 73.6 - - - +
82A TRP* 1.3 66.7 + - - +
84A ILE* 3.3 5.6 - - + +
85A GLN* 3.0 46.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASN 3.0 11.5 + - - +
79A GLU* 3.1 12.8 + - - +
81A LEU* 1.3 76.8 - - - +
83A GLU* 1.3 75.6 - - + +
85A GLN* 3.2 2.9 + - - -
86A ASN* 2.9 76.3 + - + +
87A ASN* 5.3 5.4 - - + -
92A TYR* 4.8 9.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 3.3 18.7 - - + -
46A GLY* 2.7 30.8 + - - +
48A HIS* 2.6 34.1 + - - -
79A GLU* 3.0 19.6 + - + +
80A GLY 3.8 3.4 - - - +
81A LEU 3.3 0.2 - - - -
82A TRP* 1.3 92.0 - - + +
84A ILE* 1.3 64.0 + - - +
87A ASN 2.9 30.4 + - - -
92A TYR* 3.5 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.2 17.9 - - + +
11A VAL 3.9 5.4 - - - +
22A PRO* 3.9 9.9 - - + -
23A ALA 3.7 22.2 - - - +
45A PHE* 3.5 31.6 - - + -
61A TYR* 3.7 42.6 + - + -
80A GLY 3.0 16.7 + - - +
81A LEU* 3.3 20.9 - - + +
83A GLU* 1.3 77.1 - - - +
85A GLN* 1.3 69.2 + - + +
88A PRO* 3.5 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 3.4 23.3 + - - +
69A GLY* 4.7 4.6 + - - -
81A LEU* 3.0 49.7 + - - +
82A TRP* 3.7 3.3 - - - +
83A GLU 3.1 0.2 - - - -
84A ILE* 1.3 82.2 - - + +
86A ASN* 1.3 69.0 + - - +
88A PRO* 4.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TRP* 2.9 76.3 + - + +
85A GLN* 1.3 89.1 + - - +
87A ASN* 1.3 65.9 + - - +
88A PRO* 3.7 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TRP* 5.4 6.1 - - + -
83A GLU* 2.9 9.4 + - - +
86A ASN* 1.3 83.7 + - + +
88A PRO* 1.3 67.3 - - - +
89A HIS* 3.2 8.8 + - - +
90A ALA* 3.4 31.0 + - + +
92A TYR* 2.5 34.6 + - - +
----------------------------------------------------------
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