Contacts of the helix formed by residues 70 - 86 (chain A) in PDB entry 3QZS
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 70 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR* 6.4 0.7 - - + -
68A PRO* 4.4 6.5 - - + +
69A LEU* 1.3 78.0 - - - +
71A GLU* 1.3 66.0 + - - +
72A LYS* 3.5 6.9 + - - +
73A ASP* 3.1 33.5 + - - +
74A TYR* 3.1 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A THR* 1.3 73.9 - - - +
72A LYS* 1.3 63.5 + - - +
74A TYR* 3.2 19.5 + - - +
75A GLU* 3.6 9.8 + - - +
125A ARG* 2.8 51.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A THR* 3.3 7.7 + - - +
71A GLU* 1.3 77.3 - - - +
73A ASP* 1.3 63.4 + - - +
75A GLU* 3.0 23.2 + - + +
76A GLY 3.4 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PRO 4.2 2.9 - - - +
69A LEU* 3.6 28.1 - - + +
70A THR* 3.1 41.1 + - - +
72A LYS* 1.3 75.2 - - - +
74A TYR* 1.3 59.6 + - - +
76A GLY* 3.0 4.1 + - - +
77A LEU* 2.9 26.1 + - - +
172A PHE* 3.4 20.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 4.0 21.3 - - + -
70A THR 3.1 20.1 + - - -
71A GLU* 3.4 12.6 - - - +
72A LYS 3.1 0.4 - - - -
73A ASP* 1.3 80.6 - - - +
75A GLU* 1.3 62.9 + - - +
77A LEU* 3.5 15.9 + - + +
78A LYS* 3.1 22.2 + - - +
122A VAL* 3.4 42.1 - - + +
125A ARG* 3.3 52.7 + - + +
127A TYR* 2.5 53.8 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU* 3.6 11.1 + - - +
72A LYS* 3.0 15.5 + - + +
74A TYR* 1.3 80.6 - - - +
76A GLY* 1.3 59.9 + - - +
78A LYS* 3.3 18.0 + - - +
79A ARG* 3.1 22.4 + - - +
125A ARG* 3.7 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS 3.4 5.6 + - - -
73A ASP 3.0 8.0 + - - -
75A GLU* 1.3 75.4 - - - +
77A LEU* 1.3 62.5 + - - +
79A ARG* 3.5 9.8 + - - +
80A VAL* 3.1 27.7 + - - +
172A PHE* 3.6 17.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.9 29.2 - - + -
73A ASP 2.9 15.1 + - - +
74A TYR* 3.9 24.0 - - + +
75A GLU 3.4 0.2 - - - -
76A GLY* 1.3 72.2 - - - +
78A LYS* 1.3 61.9 + - - +
80A VAL* 3.2 7.5 + - + +
81A LEU* 2.9 28.8 + - - +
122A VAL* 5.0 5.2 - - + -
127A TYR* 5.1 2.0 - - + -
130A LEU* 3.8 19.5 - - + -
133A PHE* 3.6 55.0 - - + -
169A LEU* 6.0 0.4 - - + -
172A PHE* 3.6 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TYR 3.1 14.0 + - - +
75A GLU* 3.4 22.0 - - - +
76A GLY 3.3 0.2 - - - -
77A LEU* 1.3 77.2 - - - +
79A ARG* 1.3 52.0 + - - +
81A LEU* 3.3 10.9 + - + -
82A ARG* 2.7 88.8 + - + +
119A GLU* 4.6 15.0 - - - -
122A VAL* 4.5 20.8 - - + +
123A GLN* 5.8 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLU 3.1 10.0 + - - +
76A GLY* 3.6 12.8 - - - +
78A LYS* 1.3 80.4 - - - +
80A VAL* 1.3 63.7 + - + +
82A ARG* 3.8 6.3 - - - +
83A SER* 3.0 25.3 + - - -
168A LYS* 6.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLY 3.1 16.1 + - - +
77A LEU* 3.2 11.2 + - + +
79A ARG* 1.3 78.9 - - + +
81A LEU* 1.3 63.5 + - - +
83A SER* 2.8 24.9 + - - -
84A LEU* 3.1 19.7 + - + +
133A PHE* 4.6 8.3 - - + -
137A MET* 5.4 0.2 - - + -
165A PHE* 4.1 28.7 - - + -
168A LYS* 4.1 32.8 - - + +
169A LEU* 5.1 1.8 - - + +
172A PHE* 4.2 16.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
77A LEU 2.9 15.6 + - - +
78A LYS* 3.7 12.3 - - + +
80A VAL* 1.3 77.4 - - - +
82A ARG* 1.3 61.6 + - - +
84A LEU* 3.2 7.7 + - - +
85A GLN* 3.0 32.6 + - - +
115A LEU* 3.9 35.4 - - + +
118A MET* 4.0 10.8 - - + +
119A GLU* 3.4 43.5 - - + +
122A VAL* 4.4 11.9 - - + -
133A PHE* 4.5 8.5 - - + -
137A MET* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 2.7 62.5 + - + +
79A ARG* 3.9 6.5 - - - +
81A LEU* 1.3 72.3 - - - +
83A SER* 1.3 62.1 + - - +
85A GLN* 2.9 26.6 + - - +
86A ALA* 3.1 24.9 + - - +
119A GLU* 3.0 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 3.0 17.8 + - - -
80A VAL 2.8 14.8 + - - -
82A ARG* 1.3 75.7 - - - +
84A LEU* 1.3 65.5 + - - +
86A ALA* 3.5 6.7 + - - +
87A HIS* 3.4 14.6 + - - +
164A PHE* 3.5 29.6 - - - -
168A LYS* 3.7 26.7 - - - +
----------------------------------------------------------
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 VAL* 3.1 24.9 + - + +
81A LEU 3.2 8.7 + - - +
83A SER* 1.3 86.1 + - - +
85A GLN* 1.3 64.6 + - - +
86A ALA 3.0 2.0 - - - -
87A HIS* 3.1 15.4 + - - +
90A ALA* 3.1 18.3 - - - +
115A LEU* 4.3 13.0 - - + -
137A MET* 3.6 34.5 - - + -
141A PHE* 4.1 12.6 - - + -
161A LEU* 4.0 16.9 - - + +
164A PHE* 4.0 16.2 - - + -
165A PHE* 4.1 32.8 - - + -
168A LYS* 4.8 1.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
81A LEU* 3.0 29.3 + - + +
82A ARG* 2.9 37.6 + - - +
84A LEU* 1.3 75.4 - - - +
86A ALA* 1.3 59.7 + - - +
87A HIS 3.7 1.0 + - - +
90A ALA* 4.3 2.9 - - - +
94A LEU* 3.7 32.0 + - + +
115A LEU* 3.8 40.7 + - + +
116A ALA* 4.6 2.2 - - - +
119A GLU* 3.2 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ARG 3.1 15.1 + - - +
83A SER* 4.0 6.7 - - - +
84A LEU 3.0 1.0 - - - -
85A GLN* 1.3 77.5 - - - +
87A HIS* 1.3 62.3 + - - +
88A LYS* 3.7 1.9 + - - +
----------------------------------------------------------
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