Contacts of the helix formed by residues 136 - 150 (chain B) in PDB entry 2I5T
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 136 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TRP* 2.7 30.0 + - - +
65B HIS 3.7 12.3 - - - -
66B GLY* 3.8 6.3 - - - -
135B PRO* 1.3 76.4 - - - +
137B PRO* 1.4 74.5 - - - +
138B GLN* 3.6 11.1 + - - +
139B TYR* 3.2 22.3 + - - +
140B LYS* 3.1 20.6 + - - +
165B PRO* 4.4 0.2 - - - -
166B ASN* 3.2 7.4 - - - -
168B TYR* 4.4 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B SER* 1.4 85.4 - - - +
138B GLN* 1.3 65.1 + - - +
140B LYS* 3.4 5.7 + - + +
141B LYS* 2.8 31.0 + - - +
165B PRO* 4.1 16.8 - - + -
166B ASN* 3.5 24.2 - - - +
168B TYR* 3.7 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TRP* 4.1 4.9 - - + -
136B SER* 3.2 6.4 + - - +
137B PRO* 1.3 89.5 - - - +
139B TYR* 1.3 57.3 + - - +
141B LYS* 3.2 4.0 + - - +
142B ILE* 3.0 32.4 + - - +
168B TYR* 3.8 16.1 - - - +
170B GLY 2.9 26.9 + - - -
171B LYS* 3.8 4.8 - - - +
172B VAL* 3.7 22.7 - - + +
177B GLU* 3.0 27.7 + - - +
180B ILE* 3.6 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLY* 4.3 0.7 - - - -
24B SER* 3.6 32.4 + - - -
53B PHE* 3.7 4.0 - + - -
64B TRP* 3.3 49.2 - + + -
67B GLY 3.6 14.4 - - - +
68B ILE* 3.5 14.1 - - + +
69B ALA* 3.0 40.8 + - - +
105B TYR* 4.8 1.7 + - - -
135B PRO* 3.8 10.5 - - + -
136B SER* 3.2 22.3 + - - +
138B GLN* 1.3 75.5 - - - +
140B LYS* 1.3 66.3 + - - +
142B ILE* 3.2 3.8 + - - +
143B ILE* 3.0 50.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 6.2 0.9 - - - -
135B PRO* 4.5 11.8 - - + +
136B SER 3.1 13.8 + - - +
137B PRO* 3.6 10.3 - - + +
139B TYR* 1.3 77.4 - - - +
141B LYS* 1.3 63.3 + - - +
143B ILE* 3.5 7.9 + - - +
144B CYS* 3.0 33.0 + - - -
160B LEU 3.3 17.3 - - - +
161B LYS* 2.6 33.5 + - - +
162B ALA 4.2 0.2 - - - -
163B ILE* 2.6 34.9 + - + +
165B PRO* 4.4 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B PRO 2.8 18.1 + - - +
138B GLN* 3.5 8.3 - - - +
139B TYR 3.1 0.2 - - - -
140B LYS* 1.3 80.0 - - - +
142B ILE* 1.3 63.5 + - - +
144B CYS* 3.3 8.3 + - + +
145B MSE 2.9 57.4 + - + +
180B ILE* 4.1 24.7 - - + -
183B GLY 4.3 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B SER* 3.8 33.2 - - - +
27B LEU* 4.0 16.9 - - + +
30B ARG* 4.4 6.3 - - + -
64B TRP* 3.8 22.9 - - + -
138B GLN 3.0 17.1 + - - +
139B TYR 3.8 5.6 - - - +
141B LYS* 1.3 78.3 - - - +
143B ILE* 1.3 63.8 + - - +
145B MSE 3.3 7.9 + - - +
146B GLY* 2.9 20.6 + - - -
176B ILE* 4.0 8.7 - - + -
179B ILE* 3.8 31.9 - - + -
180B ILE* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR 4.6 3.8 - - - +
23B GLY* 3.4 32.8 - - - +
24B SER* 3.7 3.8 - - - +
26B LEU* 3.7 19.6 - - + +
51B LEU* 6.0 0.4 - - + -
53B PHE* 3.7 20.9 - - + -
139B TYR* 3.0 55.0 + - + +
140B LYS* 3.9 6.5 - - - +
142B ILE* 1.3 75.1 - - - +
144B CYS* 1.3 57.9 + - - +
146B GLY* 3.1 3.1 + - - -
147B ALA* 2.9 27.2 + - - +
160B LEU* 3.9 27.6 - - + -
163B ILE* 5.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LYS* 3.0 35.6 + - - +
141B LYS* 3.7 9.2 - - + +
143B ILE* 1.3 73.8 - - - +
145B MSE 1.3 65.5 + - + +
147B ALA* 3.4 7.7 + - - +
148B LYS* 3.0 24.6 + - - +
157B GLN* 4.6 2.0 - - - +
160B LEU* 3.8 38.6 - - - -
161B LYS* 4.1 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 4.1 15.0 - - + -
141B LYS* 2.9 54.3 + - - +
142B ILE* 3.6 17.0 - - - +
144B CYS* 1.3 75.3 - - - +
146B GLY* 1.3 58.0 + - - +
148B LYS* 3.4 6.8 + - - +
149B GLU* 2.8 30.7 + - - +
179B ILE* 3.5 34.5 - - + +
180B ILE* 4.3 7.6 - - - +
183B GLY* 4.0 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.5 36.2 - - - +
27B LEU* 3.7 13.8 - - - +
142B ILE 2.9 11.5 + - - -
143B ILE 3.1 3.1 + - - -
145B MSE 1.3 77.6 - - - +
147B ALA* 1.3 62.2 + - - +
149B GLU* 3.3 1.4 + - - +
150B ASN* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.1 3.2 - - + +
143B ILE 2.9 11.4 + - - +
144B CYS* 3.7 4.9 - - - +
145B MSE 3.4 0.2 - - - -
146B GLY* 1.3 76.5 - - - +
148B LYS* 1.3 62.1 + - - +
150B ASN 3.8 0.3 - - - -
151B GLY 3.2 3.8 + - - -
152B LEU* 2.9 51.8 + - + +
157B GLN* 3.8 14.4 + - + -
160B LEU* 3.4 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B CYS 3.0 17.8 + - - +
145B MSE 3.7 6.1 - - - +
147B ALA* 1.3 75.4 - - - +
149B GLU* 1.3 67.9 + - - +
151B GLY* 3.1 12.1 + - - -
157B GLN* 3.2 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 3.7 16.5 - - + +
28B THR* 2.4 47.3 + - - -
29B GLU* 4.9 1.7 + - - +
145B MSE 2.8 21.3 + - - +
146B GLY* 3.3 4.5 + - - +
148B LYS* 1.3 74.6 - - - +
150B ASN* 1.3 71.3 + - - +
151B GLY 3.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU 2.8 24.9 - - - +
28B THR* 3.8 8.8 + - - -
40B PHE* 3.4 35.5 - - + +
43B VAL* 3.0 17.4 - - + +
82B VAL* 3.6 23.3 - - + +
84B TRP* 4.1 3.3 - - - -
146B GLY 3.0 9.9 + - - +
149B GLU* 1.3 95.8 + - - +
151B GLY* 1.3 63.9 + - - +
152B LEU* 3.4 3.8 - - + -
----------------------------------------------------------
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