Contacts of the helix formed by residues 114 - 127 (chain C) in PDB entry 1QGN
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 PRO 114 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ARG 5.3 1.2 - - - +
71C GLY 6.1 0.2 - - - -
72C ILE* 4.1 30.4 - - + +
82C VAL* 3.4 34.1 - - + -
87C TYR* 3.3 19.1 - - + +
106C PHE* 3.2 14.7 - - + -
113C ASN* 1.3 91.7 - - - +
115C THR* 1.3 58.5 + - - +
117C VAL* 3.0 26.2 + - + +
118C VAL* 3.8 12.0 + - - +
74D THR* 5.4 3.8 - - + -
75D ASP* 5.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ILE* 5.7 0.2 - - - +
79C THR* 3.7 15.7 - - - +
80C PRO 2.9 25.6 + - - -
81C VAL* 4.0 3.9 - - - -
82C VAL 3.3 16.6 - - - +
113C ASN* 2.5 30.6 + - - +
114C PRO* 1.3 75.3 - - - +
116C THR* 1.3 55.9 + - - +
118C VAL* 4.3 1.3 - - - +
297C PRO* 3.3 40.7 + - + -
300C ALA* 3.7 6.1 - - - +
301C TYR* 4.5 8.5 - - - +
304C ILE* 3.6 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLY* 6.0 1.1 - - - -
113C ASN* 3.1 25.7 + - - +
114C PRO 3.0 0.8 - - - -
115C THR* 1.3 78.4 - - - +
117C VAL* 1.3 68.0 + - + +
118C VAL 3.1 2.0 - - - -
119C LEU* 3.1 6.6 + - - +
120C GLU* 3.0 31.2 + - - +
134C LEU* 4.5 11.0 - - + +
295C LEU* 4.0 28.8 + - + +
297C PRO* 4.4 2.9 - - - +
300C ALA* 3.3 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ARG 5.1 7.6 - - - +
106C PHE* 3.8 28.7 - - + -
112C GLY* 6.0 0.4 - - - -
113C ASN 3.0 12.3 + - - +
114C PRO* 3.0 26.0 - - + +
116C THR* 1.3 72.2 - - + +
118C VAL* 1.3 55.9 + - + +
120C GLU* 2.7 24.0 + - - +
121C GLU* 2.7 50.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLY* 3.6 20.1 - - - +
66C GLU* 3.6 20.6 - - + +
70C ARG* 3.3 38.1 - - + +
72C ILE* 5.8 0.9 - - + -
79C THR* 3.7 9.6 - - + +
114C PRO 3.8 14.6 - - - +
115C THR 4.3 1.3 - - - +
116C THR 3.1 0.2 - - - -
117C VAL* 1.3 78.4 - - + +
119C LEU* 1.3 58.7 + - - +
121C GLU* 3.1 6.8 + - - +
122C LYS* 2.8 31.3 + - - +
304C ILE* 3.6 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C THR 4.7 1.1 - - - +
116C THR* 3.1 10.8 + - - +
118C VAL* 1.3 79.5 - - - +
120C GLU* 1.3 61.5 + - - +
122C LYS* 4.2 6.5 - - + -
123C ILE* 3.2 36.1 + - + +
134C LEU* 3.3 34.5 - - + -
300C ALA* 3.8 22.7 - - + +
303C ILE* 3.5 35.4 - - + -
304C ILE* 3.5 25.6 - - + +
307C MET* 3.8 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C THR* 3.0 19.1 + - + +
117C VAL* 2.7 32.4 + - - +
119C LEU* 1.3 79.2 - - - +
121C GLU* 1.3 56.8 + - + +
123C ILE 3.6 0.2 + - - -
124C SER* 3.1 31.7 + - - -
132C THR* 3.1 34.6 - - - +
133C LEU* 4.5 0.5 - - - +
134C LEU* 3.6 30.5 + - + +
285C ARG* 3.0 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C TYR* 5.4 6.1 - - + -
64C ALA* 4.7 0.9 - - - +
65C GLY* 4.3 21.1 + - - +
70C ARG 5.7 1.6 - - - +
117C VAL* 2.7 34.1 + - + +
118C VAL* 3.7 5.6 - - - +
120C GLU* 1.3 71.5 - - + +
122C LYS* 1.3 64.7 + - - +
124C SER* 3.7 7.4 - - - -
125C ALA* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C VAL 4.6 0.2 - - - +
61C ALA* 3.0 23.4 + - - +
62C ILE 2.9 17.5 + - - -
64C ALA* 2.9 38.7 + - + +
66C GLU* 2.7 28.2 + - - -
118C VAL* 2.8 15.4 + - - +
119C LEU* 3.7 11.4 - - + +
120C GLU 3.2 0.2 - - - -
121C GLU* 1.3 78.9 - - - +
123C ILE* 1.3 61.9 + - - +
125C ALA* 3.3 13.0 + - - +
126C LEU* 3.3 14.4 + - - +
304C ILE* 4.1 14.8 + - - +
307C MET* 4.1 26.5 - - + -
308C LYS* 3.4 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LEU* 3.2 39.6 + - + +
120C GLU 4.2 2.5 - - - +
122C LYS* 1.3 76.5 - - - +
124C SER* 1.3 66.9 + - - +
126C LEU* 3.2 8.8 + - + +
127C GLU* 3.0 30.5 + - + +
132C THR* 3.9 7.4 - - + +
134C LEU* 4.4 7.0 - - + -
242C PRO* 5.9 2.7 - - + -
257C HIS* 5.8 2.0 - - + -
259C ALA* 5.8 0.4 - - + -
263C LEU* 4.3 15.3 - - + -
273C CYS* 3.6 29.2 - - - -
275C SER* 3.6 21.8 - - - +
303C ILE* 5.3 1.3 - - + -
307C MET* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C GLU 3.1 13.1 + - - -
121C GLU* 3.7 9.6 - - - -
123C ILE* 1.3 78.4 - - - +
125C ALA* 1.3 56.5 + - - +
128C GLY* 2.9 6.9 + - - -
129C ALA* 2.7 46.2 + - - +
130C GLU 5.1 0.7 - - - -
131C SER* 3.3 7.4 - - - -
132C THR* 2.6 42.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C MET 5.8 3.1 - - - -
50C TYR* 4.5 17.5 - - + +
60C VAL* 3.8 10.7 - - + +
64C ALA* 3.7 20.6 - - + -
121C GLU 3.2 13.4 + - - +
122C LYS 3.4 10.3 - - - +
123C ILE 3.1 0.4 - - - -
124C SER* 1.3 75.0 - - - +
126C LEU* 1.3 67.3 + - - +
128C GLY* 3.0 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ASP* 3.6 33.9 - - - +
60C VAL* 3.8 16.2 - - + -
61C ALA* 3.9 9.0 - - + +
122C LYS 3.3 8.4 + - - +
123C ILE* 3.2 10.4 + - + +
125C ALA* 1.3 79.4 - - - +
127C GLU* 1.3 60.8 + - - +
242C PRO* 4.0 29.8 - - + +
243C LEU* 4.1 14.1 - - + -
246C LYS* 3.0 28.6 + - - +
307C MET* 3.5 31.4 - - + -
310C LEU* 4.0 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ILE* 3.0 21.6 + - + +
126C LEU* 1.3 74.8 - - - +
128C GLY* 1.3 63.8 + - - +
129C ALA* 3.2 14.9 + - + +
242C PRO* 3.0 29.2 - - + +
245C GLN 4.5 6.2 - - - +
246C LYS* 4.7 17.8 - - - +
247C ALA 4.7 2.3 + - - -
248C LEU* 3.5 24.0 - - + +
249C ALA 5.4 0.2 + - - -
255C VAL* 3.8 19.3 - - + +
257C HIS* 2.7 33.7 + - - -
275C SER* 4.1 13.2 - - - +
----------------------------------------------------------
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