Contacts of the helix formed by residues 106 - 126 (chain I) in PDB entry 1GD2
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 106 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I GLU* 1.3 81.3 - - + +
107I GLN* 1.3 66.0 + - + +
108I VAL 3.2 2.5 - - - -
109I VAL* 3.3 27.1 - - - +
110I THR* 3.3 18.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 107 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I GLU 3.4 3.9 - - - +
106I THR* 1.3 83.1 - - + +
108I VAL* 1.3 64.1 + - + +
109I VAL 3.5 0.2 - - - -
110I THR* 3.3 14.6 + - - +
111I LEU* 3.3 40.2 + - + +
108J VAL* 4.7 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 108 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I GLU 4.0 25.6 - - - +
106I THR 3.2 0.6 - - - -
107I GLN* 1.3 81.8 - - + +
109I VAL* 1.3 65.5 + - + +
112I LYS* 3.4 43.1 + - + +
107J GLN* 3.4 49.1 - - + +
108J VAL 5.6 0.4 - - - +
111J LEU* 3.7 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I GLU 4.6 5.4 - - - +
106I THR* 3.3 27.6 - - - +
108I VAL* 1.3 83.4 - - + +
110I THR* 1.3 61.7 + - + +
111I LEU 3.4 0.2 - - - -
112I LYS* 4.0 8.9 - - + +
113I GLU* 3.2 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 110 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I THR* 3.3 19.1 - - - +
107I GLN* 3.3 20.8 + - - +
109I VAL* 1.3 82.2 - - + +
111I LEU* 1.3 68.9 + - - +
112I LYS 3.4 0.7 - - - -
113I GLU* 3.6 7.0 + - - +
114I LEU* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I GLN* 3.3 40.5 + - + +
108I VAL 3.8 0.2 + - - -
110I THR* 1.3 90.6 + - - +
112I LYS* 1.3 59.9 + - - +
113I GLU 3.3 0.7 - - - -
114I LEU* 3.7 21.4 - - + +
115I HIS* 3.1 23.2 + - - +
108J VAL* 4.3 14.1 - - + +
111J LEU* 3.5 53.5 - - + +
112J LYS* 4.3 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H LYS* 5.7 0.8 + - - -
108I VAL* 3.4 38.7 + - + +
109I VAL* 3.9 8.5 + - + +
110I THR 3.4 0.2 - - - -
111I LEU* 1.3 76.9 - - - +
113I GLU* 1.3 53.4 + - - +
114I LEU 3.3 0.4 - - - -
115I HIS* 3.7 9.8 + - - +
116I SER* 2.7 35.7 + - - -
107J GLN* 4.2 12.1 + - - +
111J LEU* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H LYS* 5.0 13.2 - - - +
109I VAL 3.2 18.8 + - - +
110I THR* 3.8 8.1 - - - +
111I LEU 3.3 0.2 - - - -
112I LYS* 1.3 78.7 - - - +
114I LEU* 1.3 59.4 + - - +
115I HIS 3.2 0.4 - - - -
116I SER* 3.9 6.9 - - - +
117I SER* 3.3 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110I THR 3.0 16.8 + - - +
111I LEU* 3.8 23.1 - - + +
113I GLU* 1.3 77.5 - - - +
115I HIS* 1.3 59.3 + - - +
117I SER* 3.3 6.5 + - - +
118I THR* 3.0 37.4 + - + +
115J HIS* 5.7 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 115 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111I LEU 3.1 19.2 + - - +
112I LYS* 3.7 12.1 + - - +
113I GLU 3.2 0.2 - - - -
114I LEU* 1.3 75.7 - - - +
116I SER* 1.3 65.3 + - - +
117I SER 3.2 0.4 - - - -
118I THR* 3.3 10.9 - - + +
119I THR* 2.8 50.0 + - + -
111J LEU* 4.5 11.9 - - + +
114J LEU 4.5 16.2 + - - -
115J HIS* 5.9 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 116 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H LYS* 4.6 25.8 + - - +
116H SER* 4.3 9.7 + - - -
112I LYS 2.7 22.5 + - - -
113I GLU* 4.2 8.0 - - - -
114I LEU 3.4 0.2 - - - -
115I HIS* 1.3 79.0 + - - +
117I SER* 1.3 59.1 + - - +
119I THR* 4.3 3.9 - - - -
120I LEU* 3.9 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113I GLU 3.3 17.3 + - - -
114I LEU* 3.3 10.4 + - - +
116I SER* 1.3 78.2 - - - +
118I THR* 1.3 63.5 + - - +
119I THR 3.2 1.8 - - - -
120I LEU* 3.4 11.9 + - - +
121I GLU* 3.4 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I LEU* 3.0 39.0 + - + +
115I HIS* 3.3 24.2 - - + +
117I SER* 1.3 76.6 + - - +
119I THR* 1.3 63.9 + - - +
120I LEU 3.3 0.2 - - - -
121I GLU* 3.9 18.1 + - - +
122I ASN* 3.6 17.7 + - - +
115J HIS* 5.8 10.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115I HIS* 2.8 43.6 + - + +
116I SER* 4.7 4.0 - - - -
118I THR* 1.3 77.8 - - - +
120I LEU* 1.3 60.6 + - - +
121I GLU 3.3 0.4 - - - -
122I ASN* 3.4 13.8 + - + +
123I ASP* 2.9 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H HIS* 4.3 23.8 - - + +
116H SER* 3.6 45.3 - - - +
119H THR* 4.5 12.8 - - + -
120H LEU* 4.9 5.2 - - + -
116I SER 3.9 13.7 + - - +
117I SER* 3.4 15.1 + - - +
118I THR 3.3 0.2 - - - -
119I THR* 1.3 77.2 - - - +
121I GLU* 1.3 65.4 + - + +
123I ASP* 3.2 7.5 + - + +
124I GLN* 3.0 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 121 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I SER* 3.4 18.5 + - - +
118I THR* 3.9 18.9 + - - +
120I LEU* 1.3 77.9 - - + +
122I ASN* 1.3 57.9 + - - +
124I GLN* 3.8 14.6 - - - +
125I LEU* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 122 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I THR 3.6 12.4 + - - +
119I THR* 3.4 17.9 + - - +
121I GLU* 1.3 80.0 - - - +
123I ASP* 1.3 61.8 + - - +
125I LEU* 3.8 4.4 - - - +
126I ARG* 3.1 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H LEU* 3.4 27.8 - - + +
119I THR* 2.9 17.6 + - + +
120I LEU* 3.6 10.5 - - + +
122I ASN* 1.3 80.5 - - - +
124I GLN* 1.3 56.8 + - - +
126I ARG* 3.2 30.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 124 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H THR* 3.6 20.7 - - - +
120H LEU* 3.7 11.5 - - + +
123H ASP* 2.7 44.5 + - + +
120I LEU* 3.0 34.4 + - - +
121I GLU* 3.8 16.7 - - - +
123I ASP* 1.3 74.5 - - - +
125I LEU* 1.3 65.3 + - - +
126I ARG 3.8 4.2 - - - +
129I VAL 4.8 1.4 + - - -
130I ARG* 4.0 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121I GLU 2.9 22.1 + - - +
122I ASN* 3.8 7.4 - - - +
124I GLN* 1.3 80.7 - - - +
126I ARG* 1.3 61.3 + - - +
129I VAL* 4.1 27.6 - - + +
130I ARG* 3.7 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 126 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122I ASN* 3.1 48.9 + - - +
123I ASP* 3.2 27.9 - - - +
124I GLN 3.8 5.2 - - - +
125I LEU* 1.3 83.4 - - - +
130I ARG* 5.0 6.2 - - - +
----------------------------------------------------------
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