Contacts of the helix formed by residues 105 - 119 (chain D) in PDB entry 1GN2
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 SER 105 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ILE* 4.7 0.2 - - - -
100D ALA* 3.6 14.6 + - - +
103D PHE* 2.9 4.9 + - - +
104D GLY* 1.3 79.7 - - - +
106D PHE* 1.3 63.7 + - - +
107D ASP* 3.2 8.1 + - - +
108D LYS* 2.8 38.1 + - - +
109D PHE* 3.0 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ASP 4.4 6.7 - - - -
90D LYS* 3.9 36.1 - - + +
91D PRO* 3.1 42.6 - - + -
96D ALA* 6.1 0.4 - - + +
99D ILE* 4.1 16.2 - - + +
100D ALA* 4.5 5.8 - - + +
105D SER* 1.3 73.0 - - - +
107D ASP* 1.3 66.4 + - - +
109D PHE* 3.6 15.1 - + - +
110D ARG* 3.1 58.1 + - - +
182D TRP* 4.6 2.9 - + - -
187D TRP* 3.5 25.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D LYS* 4.4 12.8 + - - -
105D SER* 3.0 7.2 + - - +
106D PHE* 1.3 87.2 - - - +
108D LYS* 1.3 58.5 + - + +
110D ARG* 3.5 27.1 + - - +
111D ALA* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ARG* 3.8 33.6 - - + +
52B ALA* 4.0 24.8 + - - +
54B GLU* 5.3 8.7 - - + -
103D PHE 3.3 22.9 - - - +
104D GLY* 4.8 4.9 - - - -
105D SER* 2.8 21.6 + - - +
107D ASP* 1.3 75.5 - - + +
109D PHE* 1.3 64.6 + - - +
111D ALA* 3.2 7.9 + - + +
112D GLN* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ILE* 4.0 14.8 - - + -
103D PHE* 3.6 47.0 - + + +
105D SER 3.0 7.9 + - - +
106D PHE* 3.6 28.5 - + - +
108D LYS* 1.3 75.4 - - - +
110D ARG* 1.3 74.4 + - + +
112D GLN* 3.1 4.3 + - - +
113D PHE* 2.9 46.5 + + - +
128D LEU* 3.8 29.4 - - + -
139D ILE* 3.8 12.9 - - + +
157D LEU* 4.4 12.8 - - + -
182D TRP* 3.6 29.2 - + - -
187D TRP* 4.3 5.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D LYS* 5.4 7.5 - - - +
106D PHE* 3.1 40.9 + - - +
107D ASP* 3.7 22.1 + - - +
109D PHE* 1.3 94.8 - - + +
111D ALA* 1.3 60.1 + - - +
113D PHE* 4.1 1.5 - - - +
114D HIS* 3.3 21.9 + - + +
179D LYS 5.3 0.4 + - - -
182D TRP* 3.3 63.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
54B GLU* 6.4 2.0 - - - -
56B HIS* 3.7 12.3 - - + +
107D ASP 3.1 13.8 + - - +
108D LYS* 3.6 11.2 - - + +
109D PHE 3.1 0.6 - - - -
110D ARG* 1.3 75.0 - - - +
112D GLN* 1.3 66.4 - - - +
114D HIS* 3.5 6.5 + - - +
115D ALA* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.8 21.4 - - - +
51B ARG* 2.6 40.1 + - + +
56B HIS* 3.2 28.2 + - + +
59B ILE* 3.9 10.7 - - + +
63B GLU* 3.5 20.2 + - - +
103D PHE* 3.8 3.6 - - - -
108D LYS 3.2 7.0 + - - +
109D PHE 3.1 8.0 + - - +
111D ALA* 1.3 79.3 - - - +
113D PHE* 1.3 66.1 + - - +
115D ALA* 2.9 5.9 + - - +
116D ALA* 2.9 20.4 + - - +
139D ILE* 3.5 25.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D PHE* 2.9 33.7 + + + +
110D ARG* 4.1 4.3 - - - +
112D GLN* 1.3 76.5 - - - +
114D HIS* 1.3 63.5 + - - +
116D ALA* 3.4 6.9 + - - +
117D ALA* 3.0 21.0 + - - +
126D ALA* 3.6 26.1 - - + +
127D ALA 4.0 4.0 - - - -
128D LEU* 3.9 27.8 - - + -
139D ILE* 3.9 20.3 - - + +
157D LEU* 4.2 21.3 - - + -
159D LEU* 3.8 34.1 - - + -
181D PHE* 4.2 8.5 - + - -
182D TRP* 3.7 23.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ARG* 3.3 17.9 + - + +
111D ALA* 3.7 7.0 + - - +
112D GLN 3.1 0.2 - - - -
113D PHE* 1.3 82.7 - - - +
115D ALA* 1.3 60.2 + - - +
117D ALA* 3.4 3.3 + - - +
118D THR* 2.7 51.5 + - + +
159D LEU* 6.1 1.3 - - - -
175D VAL* 3.8 27.8 + - + -
178D ALA* 3.7 30.7 - - + -
179D LYS* 4.0 28.9 + - + +
182D TRP* 5.0 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B HIS* 3.5 33.2 - - + +
59B ILE* 4.1 11.7 - - + -
111D ALA 3.1 12.9 + - - +
112D GLN 2.9 9.6 + - - +
114D HIS* 1.3 81.3 + - - +
116D ALA* 1.3 61.3 + - - +
118D THR* 3.4 4.6 + - - -
119D THR* 3.1 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ILE* 3.8 12.5 - - + +
63B GLU* 4.1 19.5 - - - +
112D GLN 2.9 11.9 + - - +
113D PHE* 3.6 8.1 - - - +
114D HIS 3.3 0.2 - - - -
115D ALA* 1.3 75.3 - - - +
117D ALA* 1.3 61.1 + - - +
120D VAL* 3.6 3.3 - - - +
125D TRP 5.0 0.2 - - - +
126D ALA* 4.3 9.0 - - + +
139D ILE* 4.1 13.0 - - + -
140D PHE 4.8 0.7 - - - +
141D GLN* 3.0 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D PHE 3.0 12.7 + - - +
114D HIS* 4.1 3.4 - - - +
116D ALA* 1.3 79.0 - - - +
118D THR* 1.3 64.5 + - + +
119D THR 3.4 0.7 + - - -
120D VAL* 3.7 10.5 + - - +
126D ALA* 3.4 24.4 - - + +
159D LEU* 4.1 13.5 - - + -
161D MET* 3.2 45.0 - - + +
174D LYS* 4.9 1.4 - - - -
178D ALA* 5.1 1.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
114D HIS* 2.7 39.3 + - - +
115D ALA* 3.4 7.5 + - - -
117D ALA* 1.3 77.7 - - - +
119D THR* 1.3 61.6 + - - +
120D VAL 3.6 0.7 - - - -
161D MET* 4.8 1.1 - - + -
174D LYS* 3.0 32.7 + - + +
175D VAL* 4.1 27.3 - - + +
178D ALA* 3.8 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B HIS 5.4 0.7 - - - +
57B SER 6.1 0.2 - - - +
59B ILE* 3.3 24.2 - - + +
60B LEU* 3.6 18.3 + - - +
115D ALA* 3.1 17.6 + - - +
117D ALA 3.4 0.6 - - - -
118D THR* 1.3 83.5 - - - +
120D VAL* 1.3 68.0 + - - +
121D GLN* 3.3 6.9 + - - +
141D GLN* 2.7 26.1 + - - -
174D LYS* 5.1 0.7 - - - +
----------------------------------------------------------
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