Contacts of the helix formed by residues 144 - 153 (chain B) in PDB entry 2IGT
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 GLY 144 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ASN* 4.7 1.1 - - - -
141B GLY 3.0 16.8 + - - -
142B TYR* 3.1 1.0 - - - -
143B THR* 1.3 79.3 + - - +
145B VAL* 1.3 66.6 + - - +
146B ALA 3.2 3.4 - - - -
147B SER* 3.1 5.6 + - - -
148B LEU* 3.0 27.2 + - - +
159B HIS* 3.6 21.5 - - - -
170B ALA* 4.3 3.1 - - - -
186B TRP* 5.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU 5.1 1.6 - - - +
98B VAL* 4.4 13.0 - - + -
100B PHE* 3.9 41.5 - - + -
112B VAL* 4.3 11.7 - - + -
120B TRP* 3.5 42.4 - - + -
141B GLY 4.9 0.2 + - - -
143B THR* 3.5 14.0 + - - +
144B GLY* 1.3 75.6 - - - +
146B ALA* 1.3 57.3 + - - +
148B LEU* 3.2 8.7 + - + +
149B VAL* 2.9 32.7 + - + +
173B ASN* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B TRP* 3.6 32.8 - - + +
123B LEU* 3.5 13.1 - - + +
136B VAL* 6.4 0.2 - - - -
138B ASN* 3.9 15.7 - - - +
144B GLY* 3.2 0.8 - - - -
145B VAL* 1.3 77.6 - - - +
147B SER* 1.3 60.8 + - - +
149B VAL* 3.4 1.7 + - - -
150B ALA* 3.0 20.8 + - - +
209B LEU* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B VAL* 6.3 0.4 - - - -
138B ASN* 2.8 19.1 + - - +
144B GLY* 3.1 9.3 + - - -
146B ALA* 1.3 78.5 - - - +
148B LEU* 1.3 58.8 + - - +
150B ALA* 4.7 0.7 - - - -
151B ALA* 2.9 29.5 + - - +
157B VAL* 3.7 25.1 - - - +
159B HIS* 2.7 40.0 - - - +
184B ILE* 4.8 7.4 - - - -
186B TRP* 4.9 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B VAL* 3.6 30.1 - - + -
99B GLU 4.5 0.4 - - - +
100B PHE* 5.1 1.6 - - + -
144B GLY 3.0 18.6 + - - +
145B VAL* 3.2 9.6 + - - +
147B SER* 1.3 75.3 - - - +
149B VAL* 1.3 54.9 + - - +
151B ALA* 3.2 1.7 + - - -
152B ALA* 2.8 35.9 + - - +
170B ALA 4.8 1.1 - - - +
173B ASN* 3.7 38.8 - - + +
174B GLN* 3.7 22.7 - - + +
177B ALA* 4.1 2.9 - - + -
179B LEU* 3.6 16.1 - - + +
184B ILE* 3.8 22.0 - - + -
186B TRP* 4.8 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 4.0 24.0 - - + +
98B VAL* 3.8 21.3 - - + -
120B TRP* 3.7 35.2 - - + +
123B LEU* 4.4 3.1 - - + -
124B LYS* 3.8 23.9 - - + +
145B VAL* 2.9 27.9 + - + +
146B ALA* 3.7 6.5 - - - +
148B LEU* 1.3 76.1 - - - +
150B ALA* 1.3 62.6 + - - +
152B ALA* 3.3 3.3 + - - +
153B ALA* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 4.0 20.6 - - + -
124B LYS* 6.0 0.2 - - - +
127B VAL* 4.8 2.0 - - + -
136B VAL* 4.1 17.0 - - + -
146B ALA 3.0 16.5 + - - +
147B SER* 3.7 4.9 - - - +
149B VAL* 1.3 76.8 - - - +
151B ALA* 1.3 60.0 + - - +
153B ALA* 3.3 7.5 + - - +
154B GLY 3.2 5.2 + - - -
155B ALA* 3.0 32.8 + - + +
157B VAL* 3.8 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B SER 2.9 18.1 + - - +
148B LEU* 3.2 4.9 + - - +
150B ALA* 1.3 75.4 - - - +
152B ALA* 1.3 58.9 + - - +
154B GLY* 3.0 18.9 + - - -
155B ALA 4.0 7.0 - - - +
157B VAL* 3.7 8.4 - - + +
179B LEU* 4.6 6.9 - - + +
182B ALA* 3.9 19.5 - - + +
183B PRO* 5.3 2.4 - - - +
184B ILE* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLY 6.0 0.7 - - - +
98B VAL* 4.7 8.3 - - + -
148B LEU 2.8 20.2 + - - +
149B VAL* 3.7 7.2 - - - +
150B ALA 3.3 0.2 - - - -
151B ALA* 1.3 73.6 - - - +
153B ALA* 1.3 61.3 + - - +
154B GLY* 3.2 1.4 + - - -
179B LEU* 4.1 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LYS* 4.1 14.6 - - + +
127B VAL* 3.5 36.9 - - + +
128B GLU* 4.0 27.4 - - + +
149B VAL 3.1 16.4 + - - +
150B ALA* 3.8 2.2 - - - +
151B ALA 3.2 0.4 - - - -
152B ALA* 1.3 75.6 - - - +
154B GLY* 1.3 57.3 + - - +
155B ALA 3.7 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