Contacts of the helix formed by residues 78 - 90 (chain A) in PDB entry 2QXU
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 MET 78 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLY* 3.9 1.7 - - - -
12A ILE* 3.3 54.3 - - + +
45A THR 4.4 5.2 - - - +
46A GLY* 3.3 27.1 - - - +
47A THR* 6.1 0.2 - - - -
48A ASN* 5.6 0.9 - - - +
76A HIS 3.2 0.4 + - - -
77A SER* 1.3 80.9 + - - +
79A GLY* 1.3 62.2 + - - +
80A GLY 3.0 0.4 - - - -
81A ALA* 3.0 25.7 + - - +
82A ASN* 3.0 15.3 + - - +
105A ALA* 4.3 7.3 - - + +
108A LEU* 3.3 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.8 16.1 - - - +
10A HIS 3.4 22.2 + - - -
75A ALA* 3.5 6.5 - - - -
76A HIS 2.8 11.2 + - - -
78A MET* 1.3 77.7 - - - +
80A GLY* 1.3 56.7 + - - +
82A ASN* 3.3 5.6 + - - +
83A THR* 2.8 33.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
75A ALA* 3.6 15.7 - - - +
76A HIS 4.0 1.0 + - - -
77A SER 2.8 9.7 + - - -
79A GLY* 1.3 78.0 - - - +
81A ALA* 1.3 60.9 + - - +
83A THR* 3.3 3.4 + - - -
84A LEU* 3.1 28.5 + - - +
101A THR* 4.2 9.5 - - - +
104A GLY* 4.8 0.4 - - - -
106A ASN* 3.3 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 3.4 7.3 - - - +
77A SER 3.9 1.8 + - - -
78A MET* 3.0 27.8 + - - +
80A GLY* 1.3 77.4 - - - +
82A ASN* 1.3 62.8 + - - +
84A LEU* 3.3 1.8 + - - -
85A TYR 3.0 13.3 + - - -
105A ALA 3.5 22.9 + - - +
106A ASN* 3.9 4.7 + - - -
108A LEU* 4.1 6.5 - - + -
109A THR* 2.7 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.7 0.2 - - + -
10A HIS 4.6 1.2 + - - -
11A GLY 6.2 0.2 - - - -
41A PHE* 3.7 18.3 - - + -
46A GLY* 3.0 18.8 + - - +
47A THR 3.8 0.3 - - - +
48A ASN* 2.8 25.8 - - - +
51A ASN* 3.0 43.5 - - + +
52A GLY* 4.8 2.4 - - - +
55A LEU* 4.0 7.8 - - + +
78A MET* 3.0 20.8 + - - +
79A GLY* 3.6 10.8 - - - +
81A ALA* 1.3 76.0 - - - +
83A THR* 1.3 56.7 + - - +
85A TYR* 3.3 5.9 + - - +
86A TYR* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.9 8.3 - - - +
55A LEU* 3.9 9.9 - - - +
73A ILE* 3.6 36.5 - - + +
75A ALA* 3.6 12.9 - - - +
79A GLY 2.8 22.3 + - - -
80A GLY* 3.5 7.4 - - - -
82A ASN* 1.3 77.1 - - - +
84A LEU* 1.3 64.7 + - + +
86A TYR* 3.2 5.2 + - - +
87A ILE* 3.1 34.8 + - + +
99A VAL* 4.3 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLY 3.1 17.9 + - - +
81A ALA 3.3 3.8 + - - +
83A THR* 1.3 79.8 - - + +
85A TYR* 1.3 52.2 + - - +
87A ILE* 3.3 6.4 + - + +
88A LYS* 2.8 37.1 + - - +
106A ASN* 3.5 46.4 - - + +
109A THR* 3.8 11.7 - - + -
110A THR* 3.9 20.2 - - + -
112A LYS 4.2 8.1 - - - +
114A LEU* 3.8 6.9 - - + +
125A TYR* 3.7 36.8 - - + +
143A LEU* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 3.5 56.2 + - + -
49A TYR* 4.6 12.2 + - - -
52A GLY* 3.9 11.4 - - - -
53A PRO* 4.7 3.9 - - + +
81A ALA 3.0 13.7 + - - +
82A ASN 3.4 8.1 - - - +
84A LEU* 1.3 76.5 - - - +
86A TYR* 1.3 56.8 + - - +
88A LYS* 4.4 2.5 - - - -
89A ASN* 2.8 65.9 + - + +
90A LEU* 3.6 24.6 + - + +
109A THR* 3.5 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLY* 4.8 1.8 - - - +
55A LEU* 3.9 21.5 - - + -
56A SER* 3.4 28.3 + - - -
59A VAL* 3.2 41.9 - - + +
73A ILE* 4.6 4.7 - - + -
82A ASN 3.0 13.9 + - - +
83A THR 3.3 10.8 - - - +
85A TYR* 1.3 76.9 - - - +
87A ILE* 1.3 65.0 + - + +
90A LEU* 3.2 31.2 + - + -
91A ASP* 3.4 21.5 + - - -
92A GLY* 3.1 42.0 + - - -
95A LYS* 3.7 13.9 - - - +
96A VAL* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A THR* 3.1 30.0 + - + +
84A LEU* 3.7 8.3 - - - +
86A TYR* 1.3 86.4 - - + +
88A LYS* 1.3 61.5 + - - +
90A LEU 4.4 3.6 - - - +
92A GLY 4.3 10.3 - - - +
93A GLY* 3.8 23.8 + - - +
96A VAL* 4.4 6.3 - - + -
99A VAL* 4.3 12.1 - - + -
114A LEU* 4.0 22.0 - - + +
116A GLY* 4.6 3.6 - - - -
123A ILE* 3.8 30.1 - - + -
125A TYR* 3.6 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU 2.8 22.2 + - - +
85A TYR* 4.0 2.0 - - - +
87A ILE* 1.3 77.6 - - - +
89A ASN* 1.3 84.7 + - - +
90A LEU 5.0 0.7 - - - +
109A THR* 4.5 23.6 + - + +
110A THR* 5.1 5.5 - - - -
114A LEU* 3.3 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 2.8 56.2 + - + +
88A LYS* 1.3 109.0 + - - +
90A LEU* 1.3 69.4 + - + +
109A THR* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLY* 3.3 42.8 - - - +
53A PRO* 3.7 14.1 - - + -
56A SER* 4.3 3.4 - - - -
85A TYR* 3.6 20.2 + - + +
86A TYR* 3.2 29.9 + - + +
87A ILE 4.4 5.2 - - - +
88A LYS 5.0 0.5 - - - +
89A ASN* 1.3 88.9 - - + +
91A ASP* 1.3 68.9 + - - +
92A GLY 3.7 1.0 + - - -
93A GLY 4.8 0.9 + - - -
----------------------------------------------------------
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