Contacts of the helix formed by residues 145 - 158 (chain B) in PDB entry 2I91
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 145 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B TRP* 1.3 79.8 - - - +
146B ARG* 1.3 71.6 + - - +
147B ALA 3.4 2.0 - - - -
148B LEU* 3.1 11.1 + - - +
149B ARG* 2.7 32.2 + - - +
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Residues in contact with ARG 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A GLU* 3.0 31.4 - - + +
145B GLY* 1.3 73.1 - - - +
147B ALA* 1.3 63.4 + - - +
149B ARG* 3.6 15.0 - - - +
150B LYS* 2.9 36.4 + - + +
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 3.6 39.1 - - + +
145B GLY 3.4 0.2 - - - -
146B ARG* 1.3 79.0 - - - +
148B LEU* 1.3 57.6 + - - +
150B LYS* 3.6 8.2 - - - +
151B ALA* 2.9 31.4 + - - +
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 4.1 14.1 - - + -
128B PHE* 4.6 7.0 - - + -
129B ILE* 4.5 9.6 - - + -
132B LYS* 3.8 39.7 - - + -
144B TRP* 3.5 42.6 - - + +
145B GLY* 3.1 14.5 + - - +
147B ALA* 1.3 77.8 - - - +
149B ARG* 1.3 64.3 + - - +
151B ALA* 3.0 4.2 + - + +
152B VAL* 2.9 39.6 + - + +
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Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B TRP* 3.9 24.5 + - + +
145B GLY* 2.7 31.4 + - - +
146B ARG* 3.6 13.0 - - - +
148B LEU* 1.3 72.9 - - - +
150B LYS* 1.3 57.0 + - - +
152B VAL 3.7 0.2 + - - -
153B SER* 2.6 35.0 + - - -
185B LEU 3.7 21.0 + - - +
186B SER* 3.7 22.3 + - - +
187B HIS* 2.6 50.6 + - - +
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Residues in contact with LYS 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A LYS* 4.7 4.6 - - - +
315A LYS* 5.0 6.5 - - - +
363A LEU 5.8 4.3 - - - -
146B ARG* 2.9 34.3 + - + +
147B ALA* 3.6 8.1 - - - +
149B ARG* 1.3 74.4 - - - +
151B ALA* 1.3 59.9 + - - +
153B SER* 3.2 5.3 + - - -
154B ASP* 2.5 63.3 + - - +
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 3.9 37.7 - - + +
115B VAL* 4.6 18.4 - - + +
116B PRO* 5.8 2.7 - - - +
128B PHE* 6.0 0.9 - - + -
147B ALA 2.9 21.0 + - - +
148B LEU* 3.5 5.6 - - + +
150B LYS* 1.3 74.2 - - - +
152B VAL* 1.3 62.9 + - + +
154B ASP* 3.4 6.9 + - - +
155B TRP* 3.1 21.8 + - - +
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LEU* 4.6 9.2 - - + -
129B ILE* 3.8 20.4 - - + -
144B TRP* 3.5 23.1 - - + -
148B LEU* 2.9 22.5 + - + +
151B ALA* 1.3 76.2 - - + +
153B SER* 1.3 61.4 + - - +
155B TRP* 3.1 12.6 + - - +
156B TYR* 3.1 41.4 - - + -
182B LEU* 4.1 16.2 - - + +
186B SER* 3.5 27.6 - - - +
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Residues in contact with SER 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ARG 2.6 23.5 + - - -
150B LYS* 3.2 6.0 + - - -
152B VAL* 1.3 78.0 - - - +
154B ASP* 1.3 60.8 + - - +
156B TYR* 3.0 2.8 + - - -
157B ASN* 2.9 35.5 + - - +
186B SER* 3.8 15.1 + - - -
188B ILE* 3.8 31.1 - - - +
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Residues in contact with ASP 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A LYS* 2.8 37.1 + - - +
315A LYS* 4.8 1.9 + - - -
116B PRO* 5.6 7.8 - - + +
150B LYS* 2.5 58.6 + - - +
151B ALA* 3.7 7.6 - - - +
153B SER* 1.3 78.5 - - - +
155B TRP* 1.3 56.7 + - - +
157B ASN* 4.6 1.3 - - - +
158B THR* 2.7 45.7 + - + +
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Residues in contact with TRP 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B VAL* 4.7 4.7 - - + -
116B PRO* 4.2 25.7 + - + +
119B CYS* 2.6 32.5 + - + +
120B ARG 4.1 2.7 - - - -
121B ILE 4.0 6.3 - - - -
122B PRO* 3.8 45.1 - - + -
125B LEU* 3.9 25.5 - - + +
151B ALA 3.1 13.4 + - - +
152B VAL* 3.2 14.8 - - - +
153B SER 3.1 0.8 - - - -
154B ASP* 1.3 78.9 - - - +
156B TYR* 1.3 77.6 + + - +
158B THR* 3.9 2.8 + - - -
159B LYS* 2.7 70.0 - - - +
164B LEU* 3.8 18.2 - - + -
167B ALA* 4.7 1.3 - - + -
179B HIS* 4.8 2.9 - + - -
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Residues in contact with TYR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LEU* 4.7 0.9 - - + -
152B VAL* 3.1 42.0 - - + -
153B SER 3.0 2.4 + - - -
155B TRP* 1.3 95.8 - + - +
157B ASN* 1.3 65.8 + - - +
158B THR 3.2 2.2 - - - -
159B LYS* 3.1 21.9 + - - +
164B LEU* 3.6 32.4 - - + +
168B VAL* 4.5 1.3 - - + -
179B HIS* 2.9 49.8 - + + +
182B LEU* 3.6 16.0 - - + +
183B LEU* 3.4 31.2 - - + -
186B SER* 5.8 0.2 - - - -
188B ILE* 3.6 18.2 - - + -
195B LEU* 3.5 14.3 - - + +
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Residues in contact with ASN 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A LYS* 4.1 20.2 - - + +
313A LEU* 4.4 9.7 - - - +
316A LYS* 5.0 0.2 - - - +
153B SER* 2.9 18.3 + - - +
154B ASP* 4.9 1.3 - - - +
156B TYR* 1.3 73.2 - - - +
158B THR* 1.3 60.8 + - - +
159B LYS 3.2 2.7 + - - +
188B ILE* 2.6 43.6 - - - +
189B LYS 2.7 12.8 - - - +
190B PRO* 4.2 2.7 - - - +
191B ALA* 2.7 44.4 + - + +
195B LEU* 3.6 19.6 - - - +
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Residues in contact with THR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A LYS* 4.0 29.6 - - - +
315A LYS* 5.9 1.1 - - + -
316A LYS* 3.0 39.6 - - + +
116B PRO* 5.5 5.4 - - - +
154B ASP* 2.7 29.8 + - + +
155B TRP* 3.9 6.1 + - - -
156B TYR 3.2 0.4 - - - -
157B ASN* 1.3 75.6 - - - +
159B LYS* 1.3 64.3 + - - +
160B ASP* 4.0 0.2 - - - +
15D A 4.2 0.5 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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