Contacts of the helix formed by residues 120 - 132 (chain A) in PDB entry 1QGI
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 GLU 120 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A CYS 4.5 0.9 - - - +
51A GLU* 3.6 13.7 - - - +
52A ASP* 3.1 41.3 + - - +
59A TYR* 3.2 28.5 + - + +
119A SER* 1.3 71.4 - - - +
121A LYS* 1.3 59.1 + - - +
123A PHE* 4.5 0.7 - - - +
124A CYS* 2.8 46.2 + - + +
500A SO4 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A SER* 3.2 9.8 + - - +
120A GLU* 1.3 78.9 - - - +
122A VAL* 1.3 63.3 + - + +
124A CYS* 4.8 0.8 - - - +
125A GLY* 3.0 26.0 + - - -
500A SO4 5.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLY 5.9 0.7 - - - +
118A ASP* 3.7 30.1 - - + +
119A SER* 3.2 22.4 + - - +
121A LYS* 1.3 79.7 - - + +
123A PHE* 1.3 65.1 + - - +
125A GLY* 3.3 1.2 + - - -
126A LYS* 3.2 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A CYS* 3.6 19.3 - - - -
59A TYR* 3.6 37.7 - + + -
61A ILE* 3.5 24.0 - - + -
68A THR* 4.1 9.6 - - + -
82A PHE* 4.1 11.7 - + - -
100A LEU* 4.8 0.9 - - + -
105A ILE* 3.8 37.5 - - + -
116A ILE* 3.9 31.4 - - + -
118A ASP* 4.2 4.7 - - + +
119A SER 2.8 20.6 + - - +
120A GLU* 4.0 2.2 - - - +
122A VAL* 1.3 75.0 - - - +
124A CYS* 1.3 64.4 + - - +
126A LYS* 3.1 17.5 + - - +
127A ILE* 3.2 21.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A CYS* 2.0 68.5 - - + +
51A GLU 3.7 2.5 - - - -
59A TYR* 3.9 8.3 - - - -
120A GLU* 2.8 39.3 + - + +
121A LYS* 5.4 0.2 - - - -
123A PHE* 1.3 72.4 - - - +
125A GLY* 1.3 60.1 + - - +
127A ILE* 3.7 1.6 - - - +
128A LYS* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS 3.0 22.1 + - - -
122A VAL 3.8 2.0 - - - -
123A PHE 3.1 0.2 - - - -
124A CYS* 1.3 77.4 - - - +
126A LYS* 1.3 62.6 + - - +
128A LYS* 3.6 7.3 + - - +
129A LYS* 3.4 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 2.9 34.8 + - + +
104A GLY* 3.1 20.4 + - - +
105A ILE* 3.9 22.9 - - + -
122A VAL* 3.2 27.3 + - + +
123A PHE 3.1 7.3 + - - +
125A GLY* 1.3 76.1 - - - +
127A ILE* 1.3 66.5 + - + +
129A LYS* 3.3 21.5 + - - +
130A LEU* 3.7 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLY* 3.7 22.0 - - - +
49A TYR 4.1 0.7 - - - +
50A CYS* 3.9 22.2 - - + -
61A ILE* 4.0 25.4 - - + -
82A PHE* 4.0 32.3 - - + -
103A LEU* 5.1 0.9 - - + -
105A ILE* 4.4 7.9 - - + -
123A PHE* 3.2 27.3 + - + +
124A CYS 3.2 5.1 + - - +
126A LYS* 1.3 76.8 - - - +
128A LYS* 1.3 61.3 + - - +
130A LEU* 2.8 38.2 + - + +
136A TRP* 4.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LYS* 4.9 9.1 + - - +
48A GLY* 3.7 19.8 + - - +
124A CYS 2.9 18.6 + - - +
125A GLY* 3.7 10.3 - - - +
127A ILE* 1.3 76.1 - - - +
129A LYS* 1.3 69.4 + - + +
130A LEU 3.2 1.4 + - - -
131A GLN* 3.3 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLY* 3.4 19.6 + - - +
126A LYS* 3.3 16.4 + - - +
127A ILE 3.1 0.6 - - - -
128A LYS* 1.3 85.5 - - + +
130A LEU* 1.3 61.7 + - + +
131A GLN* 3.3 2.6 + - - +
132A ASN 4.4 3.8 + - - -
133A ASP* 5.1 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 4.0 5.2 - - + +
103A LEU* 4.0 35.4 - - + -
126A LYS 3.7 14.8 - - - +
127A ILE* 2.8 20.7 + - + +
129A LYS* 1.3 78.2 - - + +
131A GLN* 1.3 65.7 + - - +
132A ASN 3.1 3.1 - - - -
133A ASP* 2.9 42.8 + - + +
136A TRP* 3.5 59.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 3.4 19.3 - - - +
45A LYS* 2.6 55.1 + - - +
47A TYR* 3.8 18.5 - - + +
48A GLY* 4.3 6.7 - - - +
127A ILE 4.0 1.8 + - - -
128A LYS* 3.3 29.1 + - - +
129A LYS 3.3 2.0 - - - -
130A LEU* 1.3 77.1 - - - +
132A ASN* 1.3 81.7 + - - +
137A ARG* 2.9 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 5.3 1.2 - - - +
129A LYS 4.4 4.0 + - - +
130A LEU 3.1 0.4 - - - -
131A GLN* 1.3 100.2 + - - +
133A ASP* 1.3 61.5 + - - +
134A ALA* 3.5 2.8 + - - -
137A ARG* 2.7 34.3 + - - +
----------------------------------------------------------
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