Contacts of the helix formed by residues 133 - 159 (chain D) in PDB entry 3V5I
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 ALA 133 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D GLY 3.9 1.2 + - - -
132D GLN* 1.3 71.6 - - - +
134D THR* 1.3 57.3 + - - +
136D ILE* 3.3 11.7 + - - +
137D GLU* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D GLN* 3.3 4.0 - - - +
133D ALA* 1.3 77.2 - - - +
135D GLU* 1.3 63.0 + - - +
137D GLU* 3.4 15.7 + - - +
138D ILE* 3.1 30.5 + - + +
171E ARG* 3.5 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ALA* 5.5 0.7 - - - -
130D GLN 4.0 10.4 - - - +
131D GLY* 3.6 7.4 - - - -
132D GLN* 2.9 34.7 + - + +
134D THR* 1.3 75.3 - - - +
136D ILE* 1.3 63.6 + - - +
138D ILE* 3.2 10.9 + - + +
139D ALA* 3.1 21.0 + - - +
171E ARG* 3.5 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ALA* 4.1 31.6 - - + +
130D GLN 4.5 0.2 - - - -
131D GLY 3.5 33.4 - - - +
132D GLN 2.9 13.0 + - - +
133D ALA* 3.7 10.3 - - - +
135D GLU* 1.3 71.6 - - - +
137D GLU* 1.3 61.0 + - - +
139D ALA* 3.1 2.4 + - - +
140D ALA* 2.8 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D ALA 2.9 17.0 + - - +
134D THR* 3.5 15.1 + - - +
136D ILE* 1.3 78.1 - - - +
138D ILE* 1.3 65.3 + - + +
140D ALA* 3.3 6.2 + - + +
141D ASN* 3.0 44.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D THR* 3.1 26.4 + - + +
135D GLU* 3.2 8.7 + - + +
137D GLU* 1.3 76.9 - - + +
139D ALA* 1.3 64.2 + - - +
141D ASN* 3.4 8.8 + - - +
142D HIS* 3.0 21.3 + - - +
171E ARG* 3.5 37.5 - - + -
172E ASP* 3.6 33.7 - - + +
174E PHE* 4.3 13.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D GLY 4.3 7.2 - - - +
129D ALA* 3.5 31.2 - - + -
135D GLU 3.1 11.4 + - - +
136D ILE 3.1 2.4 + - - +
138D ILE* 1.3 77.6 - - - +
140D ALA* 1.3 63.9 + - - +
142D HIS* 3.2 7.4 + - - +
143D ILE* 3.0 25.6 + - - +
174E PHE* 5.4 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ALA* 5.4 0.4 - - - +
136D ILE* 2.8 22.3 + - + +
137D GLU* 3.7 7.6 - - + +
139D ALA* 1.3 77.1 - - - +
141D ASN* 1.3 61.7 + - - +
143D ILE* 3.4 9.1 - - - +
144D LEU* 3.0 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D GLU* 3.0 39.4 + - - +
138D ILE* 3.7 8.8 - - - +
140D ALA* 1.3 80.2 - - - +
142D HIS* 1.3 61.6 + - - +
144D LEU* 3.4 13.2 + - - +
145D LYS* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D ILE 3.0 16.6 + - - +
139D ALA* 3.2 6.4 + - - +
141D ASN* 1.3 78.0 - - - +
143D ILE* 1.3 59.7 + - - +
145D LYS* 3.3 8.6 + - + +
146D THR* 3.0 42.0 + - - -
95E MET* 4.5 4.3 - - + -
119E GLU* 2.9 33.7 + - - -
174E PHE* 3.3 60.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D PRO* 4.0 24.2 - - + +
126D LEU 3.7 10.3 - - - +
127D GLY* 3.7 33.2 - - - +
139D ALA 3.0 16.1 + - - +
140D ALA* 3.4 15.9 - - - +
142D HIS* 1.3 80.1 - - - +
144D LEU* 1.3 69.7 + - + +
146D THR* 3.2 8.5 + - + -
147D ARG* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D ALA* 3.0 29.9 + - + +
141D ASN* 3.8 11.9 - - - +
143D ILE* 1.3 80.3 - - + +
145D LYS* 1.3 63.1 + - - +
147D ARG* 3.1 16.1 + - + +
148D GLU* 3.1 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D ASN 2.9 18.1 + - - +
142D HIS* 3.6 10.1 - - + +
144D LEU* 1.3 76.3 - - - +
146D THR* 1.3 58.6 + - - +
148D GLU* 3.3 17.4 + - - +
149D LYS* 3.0 26.5 + - - +
174E PHE 5.8 0.8 + - - -
176E THR* 3.7 28.5 - - + +
179E GLU* 3.9 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D VAL* 3.7 33.7 - - + -
75D PHE* 5.2 3.4 - - + -
125D PRO* 4.9 4.7 - - + -
142D HIS* 3.0 28.2 + - - -
143D ILE* 3.2 14.3 + - + -
145D LYS* 1.3 73.2 - - - +
147D ARG* 1.3 59.1 + - - +
149D LYS* 3.2 8.1 + - + +
150D LEU* 2.9 35.8 + - + +
119E GLU* 3.5 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D GLN* 3.5 36.6 + - - +
125D PRO* 3.8 23.5 - - + +
143D ILE 3.0 12.6 + - - +
144D LEU* 3.1 19.1 + - + +
146D THR* 1.3 77.4 - - - +
148D GLU* 1.3 57.3 + - - +
150D LEU* 3.3 3.2 + - + +
151D ASN* 2.8 46.9 + - - +
166D GLN* 2.9 62.0 + - - +
169D THR* 3.0 28.9 + - - -
170D ASP* 3.6 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D LEU* 3.1 18.0 + - - +
145D LYS* 3.3 20.3 + - - +
147D ARG* 1.3 75.6 - - - +
149D LYS* 1.3 58.5 + - - +
151D ASN* 3.9 5.5 - - - +
152D ARG* 2.8 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D PHE* 3.6 35.1 - - + -
145D LYS 3.0 13.4 + - - +
146D THR* 3.2 11.4 + - - +
148D GLU* 1.3 76.1 - - - +
150D LEU* 1.3 63.6 + - - +
152D ARG* 3.6 23.9 - - - +
153D ILE* 3.1 26.1 + - + +
117E ASN* 2.8 49.5 + - - +
118E ALA 4.7 0.6 + - - -
119E GLU* 3.3 32.6 + - - +
176E THR* 6.1 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D VAL* 4.3 4.7 - - + -
75D PHE* 3.7 23.6 - - + -
99D MET* 3.6 33.7 - - + -
102D PHE* 3.6 31.5 - - + -
125D PRO* 4.0 28.3 - - + -
146D THR* 2.9 27.9 + - + +
147D ARG* 3.7 4.5 - - + +
149D LYS* 1.3 77.8 - - - +
151D ASN* 1.3 60.6 + - - +
153D ILE 3.3 0.3 + - - -
154D LEU* 2.9 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D ARG* 2.8 33.0 + - - +
148D GLU* 3.9 5.5 - - - +
150D LEU* 1.3 77.3 - - - +
152D ARG* 1.3 57.4 + - - +
154D LEU* 3.3 3.8 + - - +
155D SER* 2.8 31.6 + - - -
162D ILE* 4.3 15.1 + - + +
165D ILE* 3.4 30.3 - - + +
166D GLN* 2.9 43.0 + - - +
169D THR* 4.3 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D GLU* 2.8 25.0 + - - +
149D LYS* 3.6 36.7 - - - +
151D ASN* 1.3 72.6 - - - +
153D ILE* 1.3 71.1 + - - +
155D SER* 3.2 6.4 + - - -
156D GLU* 3.2 39.3 + - + +
162D ILE* 4.3 21.7 - - + +
117E ASN* 3.9 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D PHE* 3.8 19.3 - - + -
78D TYR* 3.1 34.3 - - + +
102D PHE* 3.8 13.9 - - + -
149D LYS* 3.1 17.4 + - + +
150D LEU 4.0 2.2 - - - +
152D ARG* 1.3 87.1 - - - +
154D LEU* 1.3 62.3 + - - +
156D GLU* 3.3 19.0 + - - +
157D ARG* 3.2 26.3 + - - +
117E ASN* 3.5 38.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D PHE* 4.0 27.9 - - + +
105D ALA* 4.3 15.0 - - + -
122D ILE* 5.1 14.1 - - + -
150D LEU* 2.9 18.4 + - + +
151D ASN* 3.6 7.4 - - - +
153D ILE* 1.3 75.5 - - - +
155D SER* 1.3 62.7 - - - +
157D ARG* 3.1 4.0 + - + +
158D THR* 2.8 36.7 + - + +
165D ILE* 4.0 28.3 - - + -
169D THR* 5.3 5.8 - - + -
183D TYR* 5.9 0.9 - - + -
185D LEU* 4.2 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D ASN 2.8 13.6 + - - -
152D ARG 3.2 10.8 - - - -
154D LEU* 1.3 76.2 - - - +
156D GLU* 1.3 57.8 + - - +
158D THR* 3.9 1.8 - - - -
159D GLY* 2.9 31.7 + - - -
160D GLN 2.7 25.1 + - - +
161D SER* 3.9 1.4 - - - -
162D ILE* 3.6 28.4 + - - +
165D ILE* 4.5 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D TYR* 5.2 1.6 + - - -
109D LYS* 3.7 11.0 + - - -
152D ARG* 3.2 34.6 + - + +
153D ILE* 3.5 25.1 - - - +
154D LEU 3.2 0.4 - - - -
155D SER* 1.3 79.2 - - - +
157D ARG* 1.3 63.6 + - + +
159D GLY* 4.4 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D TYR* 3.3 29.6 + - - -
82D GLN* 3.6 31.8 - - - +
102D PHE 5.8 0.2 - - - -
105D ALA* 3.6 36.3 + - + +
106D ALA* 4.1 9.3 + - - +
107D GLY 3.7 14.8 + - - -
108D ALA* 5.7 0.6 - - - +
109D LYS* 3.7 36.8 + - - +
112D ARG* 3.1 25.0 + - - +
153D ILE* 3.2 18.6 - - + +
154D LEU* 3.1 7.5 + - + +
156D GLU* 1.3 82.5 - - + +
158D THR* 1.3 61.5 + - - +
184D GLY 3.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ALA* 5.0 0.9 - - + -
154D LEU* 2.8 31.0 + - + +
155D SER* 3.6 1.4 + - - -
157D ARG* 1.3 79.5 - - + +
159D GLY* 1.3 61.6 + - - +
160D GLN* 3.2 22.0 + - - +
165D ILE* 4.1 2.6 - - - +
183D TYR* 3.6 27.0 - - + +
184D GLY* 3.3 26.7 - - - +
185D LEU* 3.8 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D SER 2.9 11.7 + - - -
156D GLU 4.3 2.8 + - - -
157D ARG 3.6 1.8 - - - +
158D THR* 1.3 77.4 - - - +
160D GLN* 1.3 64.5 + - - +
161D SER 4.0 0.5 + - - -
----------------------------------------------------------
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