Contacts of the helix formed by residues 104 - 127 (chain D) in PDB entry 1GQA
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 104 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR* 3.0 23.3 + - - -
100D ALA 4.1 0.5 - - - +
102D GLY 3.5 0.4 - - - -
103D ALA* 1.3 79.9 - - - +
105D GLN* 1.3 60.3 + - - -
107D GLU* 3.3 10.7 - - - +
108D LEU* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D MET 3.2 24.9 - - - +
28D ALA* 3.4 18.2 - - - +
30D GLY* 4.7 3.3 + - - -
34D TYR* 3.8 38.4 - - + +
104D GLY* 1.3 72.7 - - - -
106D LYS* 1.3 71.9 + - + +
107D GLU* 3.9 0.2 + - - -
108D LEU* 3.7 2.6 - - + +
109D ALA* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D GLY 3.4 0.2 - - - -
105D GLN* 1.3 84.2 - - + +
107D GLU* 1.3 78.6 + - - +
109D ALA* 3.2 5.2 + - - +
110D ALA* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ALA* 3.9 18.4 - - + +
103D ALA* 3.5 27.1 - - + +
104D GLY* 3.3 24.1 - - - +
105D GLN 3.9 0.2 + - - -
106D LYS* 1.3 92.8 + - - +
108D LEU* 1.3 62.9 + - - +
110D ALA* 3.3 7.4 + - - +
111D ALA* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 3.7 30.1 - - + +
27D MET* 3.5 36.1 - - + -
28D ALA* 4.0 7.6 - - + +
34D TYR* 4.1 6.5 - - + -
39D ALA* 4.7 0.2 - - + -
97D LEU* 4.1 11.4 - - + -
100D ALA 3.8 8.0 + - - +
101D ALA* 3.9 26.2 - - + +
104D GLY 2.9 20.2 + - - +
105D GLN* 3.7 4.7 - - - +
107D GLU* 1.3 76.4 - - - +
109D ALA* 1.3 59.9 + - - +
111D ALA* 3.3 2.9 + - - -
112D VAL* 2.8 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ALA* 3.8 33.7 - - + +
105D GLN* 2.9 23.8 + - - +
106D LYS* 3.2 7.2 + - - +
108D LEU* 1.3 75.1 - - - +
110D ALA* 1.3 59.5 + - - +
112D VAL* 3.8 1.4 - - - +
113D GLY* 2.9 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D LYS 3.0 12.2 + - - +
107D GLU* 3.4 12.6 - - - +
109D ALA* 1.3 77.0 - - - +
111D ALA* 1.3 64.1 + - - +
113D GLY* 3.2 3.2 + - - -
114D LYS* 3.1 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ALA 5.1 0.7 - - - +
96D ALA* 4.6 3.4 - - + +
97D LEU* 3.9 24.9 - - + -
100D ALA* 4.0 19.7 - - + -
107D GLU 3.0 14.0 + - - +
108D LEU* 3.8 3.6 - - - +
110D ALA* 1.3 78.8 - - - +
112D VAL* 1.3 64.7 + - - +
114D LYS* 3.1 10.4 + - - +
115D VAL* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D PHE* 3.9 22.4 - - + -
24D LEU* 3.7 18.4 - - + +
25D ALA* 4.0 20.9 - - + -
28D ALA* 4.0 9.0 - - + -
97D LEU* 3.8 11.2 - - + -
108D LEU* 2.8 48.3 + - + +
109D ALA 3.9 3.1 - - - +
111D ALA* 1.3 73.1 - - - +
113D GLY* 1.4 60.3 + - - +
115D VAL* 3.2 5.4 + - - +
116D GLY* 2.8 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D ALA 2.9 16.1 + - - -
110D ALA 3.2 4.9 + - - -
111D ALA 3.2 0.2 - - - -
112D VAL* 1.4 77.3 - - - +
114D LYS* 1.3 65.0 + - - +
116D GLY* 3.3 2.5 + - - -
117D GLY* 3.1 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ALA* 4.4 13.7 - - + +
110D ALA 3.1 17.3 + - - +
111D ALA* 3.1 12.6 + - - +
113D GLY* 1.3 75.9 - - - +
115D VAL* 1.3 65.5 + - - +
117D GLY* 3.2 11.2 + - - -
118D THR* 3.3 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D PHE* 3.4 28.3 - - + -
46D LEU* 5.4 3.4 - - + -
90D PHE* 4.4 11.7 - - + -
93D ALA* 3.6 31.2 - - - +
94D VAL* 4.4 8.5 - - + +
97D LEU* 4.2 19.5 - - + -
111D ALA 3.0 14.2 + - - +
112D VAL 3.5 6.1 - - - +
114D LYS* 1.3 75.5 - - - +
116D GLY* 1.3 55.0 + - - +
118D THR* 2.7 36.3 + - - +
119D CYS* 3.0 5.4 + - - -
131D HEC 3.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D PHE* 4.0 17.0 - - - -
112D VAL 2.8 18.4 + - - -
113D GLY* 3.6 4.5 - - - -
115D VAL* 1.3 71.4 - - - +
117D GLY* 1.3 61.2 + - - +
119D CYS* 3.0 18.2 + - - +
120D LYS* 3.1 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D GLY 3.1 12.5 + - - -
114D LYS* 3.7 4.9 - - - -
115D VAL 3.2 0.4 - - - -
116D GLY* 1.3 73.5 - - - +
118D THR* 1.3 57.9 + - - +
120D LYS* 3.4 5.5 + - - +
121D SER* 2.9 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D LYS* 5.1 1.5 - - - +
89D ALA* 3.6 31.9 - - + +
90D PHE* 3.4 34.5 - - - -
93D ALA* 3.9 9.4 - - + +
114D LYS 3.3 13.2 + - - +
115D VAL* 2.7 25.9 + - - -
117D GLY* 1.3 69.0 - - - +
119D CYS* 1.3 66.0 + - - +
121D SER* 3.9 6.7 - - - -
122D CYS* 3.3 20.3 + - - +
131D HEC 3.8 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D PHE* 4.5 4.7 - - - -
115D VAL* 3.0 16.6 + - - -
116D GLY* 3.0 15.9 + - - +
118D THR* 1.3 78.3 + - - +
120D LYS* 1.3 60.2 + - + +
122D CYS* 3.4 2.4 + - - +
123D HIS* 3.1 37.6 + - + -
131D HEC 1.9 74.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D GLY 3.1 11.5 + - - +
117D GLY* 4.2 4.5 - - - +
119D CYS* 1.3 80.3 - - + +
121D SER* 1.3 60.7 + - - +
123D HIS* 4.3 8.1 - - + -
124D ASP* 2.7 65.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D LYS* 2.6 44.9 + - - +
117D GLY 2.9 18.0 + - - -
118D THR* 3.9 7.9 - - - -
119D CYS 3.4 0.2 - - - -
120D LYS* 1.3 79.2 - - - +
122D CYS* 1.3 61.5 + - - +
124D ASP* 3.4 15.2 + - - +
125D ASP* 3.6 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 3.6 17.5 - - - -
86D LYS* 4.0 18.1 - - + +
118D THR 3.3 5.5 + - - +
119D CYS 3.9 0.4 - - - +
120D LYS 3.2 0.4 - - - -
121D SER* 1.3 79.5 - - - +
123D HIS* 1.3 56.5 + - - +
125D ASP 3.3 1.6 + - - -
126D PHE* 2.9 31.2 + - - +
131D HEC 1.9 75.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D CYS* 3.1 24.3 + - + +
120D LYS* 3.8 8.1 - - + +
122D CYS* 1.3 74.1 - - - +
124D ASP* 1.3 66.1 + - - +
127D ARG* 3.1 71.0 + - + +
129D LYS* 4.8 2.8 + - - -
131D HEC 2.0 85.9 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D LYS* 4.7 7.8 + - - -
120D LYS* 2.7 65.2 + - - +
121D SER* 3.6 8.7 - - - +
122D CYS 3.3 0.2 - - - -
123D HIS* 1.3 74.5 - - - +
125D ASP* 1.3 66.8 + - - +
127D ARG 4.9 0.7 - - - +
129D LYS* 3.2 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D LYS* 3.5 17.5 + - - +
75D ALA* 4.1 6.6 - - - +
86D LYS* 3.1 31.2 + - - -
121D SER 3.6 2.4 + - - +
122D CYS 3.3 2.6 + - - +
123D HIS 3.2 0.2 - - - -
124D ASP* 1.3 83.8 - - - +
126D PHE* 1.3 91.2 + - + +
127D ARG 3.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ALA 3.9 1.0 - - - +
72D ALA* 4.0 0.9 - - - -
73D LYS* 3.1 29.8 + - - -
75D ALA* 3.4 27.1 - - + -
76D ILE* 3.5 39.7 - - + +
79D ASP* 4.1 16.8 - - + -
82D GLY 4.0 3.1 - - - -
83D PHE* 3.6 43.5 - + + -
86D LYS* 3.7 26.0 - - + -
122D CYS* 2.9 18.1 + - - +
125D ASP* 1.3 103.0 - - + +
127D ARG* 1.3 61.1 + - - +
131D HEC 4.0 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ALA* 3.4 19.3 - - + +
73D LYS* 4.1 8.7 - - - -
122D CYS 4.0 0.2 + - - -
123D HIS* 3.1 74.7 + - + +
124D ASP 4.9 0.7 - - - +
125D ASP 3.8 0.2 - - - -
126D PHE* 1.3 79.9 - - - +
128D VAL* 1.3 77.7 + - - +
129D LYS* 3.2 8.5 + - - +
131D HEC 3.6 49.0 - - + +
----------------------------------------------------------
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