Contacts of the helix formed by residues 126 - 149 (chain G) in PDB entry 1QGH
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 ASP 126 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G ASP* 6.4 0.2 - - - +
124G GLY* 3.3 10.3 + - - +
125G ASP* 1.3 72.6 + - - +
127G VAL* 1.3 64.9 + - + +
129G ASN* 3.3 9.3 - - - +
130G ASP* 3.0 20.4 + - - +
114L LYS* 2.4 37.5 + - - +
117L ILE* 3.8 20.7 - - + +
121L ASP* 5.4 3.6 - - - +
133L ILE* 3.6 34.2 - - + +
136L LYS* 5.1 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G ARG* 3.3 39.9 - - - +
125G ASP* 3.2 1.2 + - - -
126G ASP* 1.3 81.0 - - + +
128G THR* 1.3 61.9 + - - +
130G ASP* 3.2 4.7 + - - +
131G MET* 3.0 23.4 + - + +
133L ILE* 3.5 32.5 - - + +
136L LYS* 3.7 26.6 - - + +
137L ALA* 3.6 32.8 - - + +
140L ASP* 4.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 128 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G THR* 3.9 5.1 - - + +
13G LEU* 3.7 37.0 - - + +
63G ARG* 2.9 22.1 + - - +
67G ILE* 4.6 0.7 - - - +
120G THR* 3.7 15.0 - - - +
125G ASP* 2.6 33.5 + - - -
127G VAL* 1.3 76.9 - - - +
129G ASN* 1.3 62.7 + - - +
131G MET* 3.1 13.2 + - + +
132G LEU* 3.0 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 129 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP* 5.7 0.2 + - - -
117G ILE* 2.9 44.1 + - - +
120G THR* 2.8 28.4 - - + +
121G ASP* 3.8 14.4 - - - +
125G ASP 3.0 3.1 + - - +
126G ASP* 3.3 14.1 - - - +
128G THR* 1.3 77.6 - - - +
130G ASP* 1.3 69.2 + - - +
132G LEU* 3.3 4.4 + - - +
133G ILE* 3.0 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP* 3.6 23.6 - - - +
126G ASP 3.0 10.7 + - - +
127G VAL 3.9 3.4 - - - +
129G ASN* 1.3 87.4 - - - +
131G MET* 1.3 66.6 + - - +
133G ILE* 3.2 8.3 + - - +
134G ALA* 3.1 23.6 + - - +
130L ASP* 3.4 30.5 - - - +
133L ILE* 3.9 24.7 - - + +
134L ALA* 5.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 131 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G LEU* 4.3 5.2 - - + -
59G GLU* 4.1 17.9 - - - +
60G VAL* 4.2 15.7 - - + -
63G ARG* 4.0 36.6 - - + -
127G VAL* 3.0 19.0 + - + +
128G THR* 3.1 15.9 + - + +
130G ASP* 1.3 76.3 - - - +
132G LEU* 1.3 86.5 + - + +
134G ALA* 3.2 6.5 + - - +
135G PHE* 3.0 47.7 + - + -
137L ALA* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G PHE* 3.9 32.3 - - + -
13G LEU* 4.3 3.8 - - + -
16G GLN* 6.0 0.7 - - + -
60G VAL* 5.2 2.9 - - + -
113G TYR* 4.0 17.6 - - + +
116G GLY 4.0 12.6 - - - -
117G ILE* 3.6 20.8 - - + +
120G THR* 3.9 12.1 - - - +
128G THR* 3.0 29.9 + - + +
129G ASN* 3.6 1.6 - - - +
131G MET* 1.3 100.7 - - + +
133G ILE* 1.3 58.9 + - - +
135G PHE* 3.2 16.4 + - + +
136G LYS* 2.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP* 3.7 45.3 - - + +
127B VAL* 3.5 11.6 - - + +
130B ASP* 3.9 22.4 - - + +
117G ILE* 3.8 23.1 - - + -
129G ASN* 3.0 40.3 + - - +
130G ASP* 3.6 14.4 - - - +
131G MET 3.2 0.2 - - - -
132G LEU* 1.3 76.1 - - - +
134G ALA* 1.3 57.3 + - - +
136G LYS* 3.0 4.0 + - - +
137G ALA* 2.9 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP* 5.4 1.8 + - - +
130G ASP 3.1 12.6 + - - +
131G MET* 3.2 9.6 + - - +
133G ILE* 1.3 76.2 - - - +
135G PHE* 1.3 69.0 + - + +
137G ALA* 3.2 21.0 + - - +
138G SER* 3.3 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 135 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G GLN* 3.5 52.2 + - + +
59G GLU* 3.8 28.0 - - + -
60G VAL* 3.5 26.9 - - + -
113G TYR* 3.4 27.1 - + + -
131G MET* 3.0 41.5 + - + -
132G LEU* 3.6 8.7 - - + +
134G ALA* 1.3 79.4 - - + +
136G LYS* 1.3 66.0 + - - +
138G SER* 3.0 5.9 + - - -
139G ILE* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 136 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 4.5 6.0 - - - +
125B ASP* 5.5 1.1 + - - -
126B ASP* 5.2 4.5 - - - +
127B VAL* 3.7 22.0 - - + +
110G ARG* 4.1 35.5 - - + +
113G TYR* 4.2 5.8 - - + -
114G LYS* 4.7 16.3 - - + +
117G ILE* 4.1 21.1 - - + -
132G LEU 2.8 14.2 + - - +
133G ILE 3.0 8.0 + - - +
135G PHE* 1.3 77.6 - - - +
137G ALA* 1.3 65.5 + - - +
139G ILE* 3.0 8.8 + - - +
140G ASP* 2.8 54.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 4.9 0.7 + - - -
127B VAL* 3.6 30.9 - - + +
131B MET* 6.5 0.2 - - + -
133G ILE* 2.9 11.0 + - + +
134G ALA* 3.3 14.1 - - - +
135G PHE 3.1 0.2 - - - -
136G LYS* 1.3 77.3 - - - +
138G SER* 1.3 63.1 + - - +
140G ASP* 3.3 4.9 + - - +
141G LYS* 3.2 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G GLU* 2.6 28.8 + - - -
53G PHE* 5.2 0.3 - - - -
56G GLN* 4.9 2.8 + - - -
134G ALA 3.3 6.2 + - - -
135G PHE* 3.0 10.8 + - - -
137G ALA* 1.3 79.2 - - - +
139G ILE* 1.3 67.7 + - - +
141G LYS* 3.1 11.2 + - - +
142G HIS* 2.9 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 139 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G PHE* 3.9 29.2 - - + -
56G GLN* 4.5 2.0 - - - +
106G LEU* 3.7 22.4 - - + +
109G LEU* 4.3 15.5 - - + -
110G ARG* 3.9 13.7 - - + +
113G TYR* 3.7 32.1 - - + -
135G PHE 3.0 20.1 + - - +
136G LYS* 3.5 7.6 - - - +
138G SER* 1.3 75.5 - - - +
140G ASP* 1.3 59.0 + - - +
142G HIS* 3.1 9.8 + - - +
143G ILE* 2.8 49.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 2.8 34.9 + - - +
66B ALA* 4.0 14.9 - - + +
127B VAL* 4.2 1.2 - - - +
110G ARG* 3.2 34.3 + - - +
136G LYS* 2.8 41.7 + - - +
137G ALA 3.5 3.8 - - - +
138G SER 3.1 0.2 - - - -
139G ILE* 1.3 77.6 - - - +
141G LYS* 1.3 54.7 + - - +
143G ILE* 3.2 7.8 + - - +
144G TRP* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLU* 3.0 30.7 + - + +
66B ALA* 4.7 4.7 - - - +
43D HIS* 5.5 2.0 + - - -
137G ALA 3.2 8.8 + - - +
138G SER* 3.1 12.7 + - - +
140G ASP* 1.3 74.2 - - - +
142G HIS* 1.3 68.7 + - + +
144G TRP* 3.0 26.0 + - + +
145G MET* 3.0 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 142 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G LYS* 4.4 5.8 + - - -
49G LEU* 3.7 23.7 - - + +
52G GLU* 2.8 27.8 + - - -
53G PHE* 4.1 20.8 - + - -
106G LEU* 3.9 16.6 - - + -
138G SER* 2.9 36.5 + - - -
139G ILE* 3.5 6.5 - - - +
141G LYS* 1.3 79.3 - - + +
143G ILE* 1.3 64.9 + - - +
145G MET* 3.9 21.4 - - + +
146G PHE* 2.8 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 143 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G VAL* 5.0 4.3 - - + +
106G LEU* 3.8 21.3 - - + -
107G GLU* 4.0 26.9 - - + +
110G ARG* 3.8 35.7 - - - +
139G ILE* 2.8 36.0 + - + +
140G ASP* 3.5 10.1 - - - +
141G LYS 3.1 0.2 - - - -
142G HIS* 1.3 76.8 - - - +
144G TRP* 1.3 64.9 + - - +
146G PHE* 4.2 1.9 - - - +
147G LYS* 3.1 29.8 + - + +
154G PRO* 4.0 23.6 - - + +
155G LEU* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 144 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLU* 3.7 43.7 - - + -
65B LEU* 3.8 30.5 - - + +
66B ALA* 4.0 20.0 - - + -
31D HIS 4.7 0.7 - - - -
32D TRP* 4.2 11.5 + + - -
34D MET 5.5 0.8 + - - -
39D PHE* 4.0 16.3 - + - -
43D HIS* 3.6 27.8 - + - -
140G ASP 2.9 13.5 + - - +
141G LYS* 3.0 20.8 + - + +
143G ILE* 1.3 77.1 - - - +
145G MET* 1.3 80.3 + - + +
147G LYS* 3.9 1.7 - - - +
148G ALA* 3.1 32.8 + - + +
152G LYS 5.2 0.2 - - - +
154G PRO* 3.9 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 145 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D PHE* 3.6 35.5 - - + -
40D PHE* 3.8 13.6 - - + -
43D HIS* 4.6 11.2 - - - -
45G LYS* 3.9 15.5 - - - +
141G LYS* 3.0 40.7 + - + +
142G HIS* 3.8 28.9 - - + +
144G TRP* 1.3 98.7 - - + +
146G PHE* 1.3 60.5 + - + +
148G ALA* 3.3 3.1 + - - +
149G PHE* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 146 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D PHE* 3.5 31.2 - + - -
42G LEU* 4.7 1.3 - - + -
45G LYS* 3.9 21.8 - - + -
46G MET* 3.6 22.7 - - + -
49G LEU* 4.0 11.2 - - + -
99G MET* 3.6 36.1 - - + +
102G LEU* 3.7 18.8 - - + -
103G VAL* 3.3 24.7 - - + -
106G LEU* 4.4 3.1 - - + -
142G HIS* 2.8 45.6 + - + +
145G MET* 1.3 73.0 - - + +
147G LYS* 1.3 57.4 + - - +
149G PHE* 3.3 6.5 - - + +
150G LEU* 3.1 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 147 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G VAL* 3.8 22.4 - - + -
107G GLU* 3.4 26.0 + - - -
143G ILE* 3.1 21.9 + - + +
144G TRP 3.9 2.9 - - - +
146G PHE* 1.3 74.1 - - - +
148G ALA* 1.3 65.6 + - - +
150G LEU* 2.9 11.2 + - + +
151G GLY 2.9 5.4 + - - -
152G LYS* 2.7 39.0 + - + +
153G ALA 3.0 29.4 - - - +
154G PRO* 3.2 12.2 + - + +
155G LEU 4.9 0.4 - - - -
156G GLU* 2.4 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D MET 3.8 11.0 - - - +
35D ARG* 3.3 9.7 - - + +
36D GLY 2.7 24.4 + - - -
39D PHE* 3.6 31.9 - - + -
144G TRP* 3.1 24.7 + - + +
145G MET 3.3 2.7 + - - +
147G LYS* 1.3 73.6 - - - +
149G PHE* 1.3 57.7 + - - +
151G GLY 2.8 10.6 + - - -
152G LYS 3.6 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 149 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D GLY 3.2 25.6 - - - -
37D HIS* 3.1 60.5 + - + -
39D PHE* 3.9 4.1 - - + +
40D PHE* 3.7 27.8 - + + -
38G ASN* 4.0 4.0 - - - -
42G LEU* 3.5 28.5 - - + -
95G MET* 4.0 6.7 - - + -
96G ASP* 3.6 16.8 - - - -
99G MET* 3.5 30.3 - - + -
145G MET 2.9 14.0 + - - +
146G PHE* 3.3 9.9 - + - +
148G ALA* 1.3 76.5 - - - +
150G LEU* 1.3 69.4 + - + +
151G GLY 3.4 0.2 + - - -
----------------------------------------------------------
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