Contacts of the helix formed by residues 145 - 158 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A TRP* 1.3 80.2 - - - +
146A ARG* 1.3 72.2 + - - +
147A ALA 3.4 2.0 - - - -
148A LEU* 3.1 11.0 + - - +
149A ARG* 2.7 32.0 + - - +
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Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A GLY* 1.3 72.8 - - - +
147A ALA* 1.3 65.9 + - - +
149A ARG* 3.9 10.5 - - - +
150A LYS* 2.9 35.8 + - + +
365B GLU* 3.3 29.6 + - + +
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 3.5 39.2 - - + +
145A GLY 3.4 0.4 - - - -
146A ARG* 1.3 79.5 - - - +
148A LEU* 1.3 59.2 + - - +
150A LYS* 3.6 8.2 - - - +
151A ALA* 2.8 31.5 + - - +
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 4.1 11.7 - - + -
128A PHE* 4.6 6.5 - - + -
129A ILE* 4.5 9.6 - - + -
132A LYS* 3.7 40.6 - - + -
144A TRP* 3.5 42.2 - - + +
145A GLY* 3.1 15.0 + - - +
147A ALA* 1.3 77.2 - - - +
149A ARG* 1.3 64.4 + - - +
151A ALA* 3.0 5.0 + - + +
152A VAL* 2.9 40.0 + - + +
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Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A TRP* 3.9 30.7 + - + +
145A GLY* 2.7 29.4 + - - +
146A ARG* 3.7 11.6 - - - +
148A LEU* 1.3 73.5 - - - +
150A LYS* 1.3 56.0 + - - +
152A VAL 3.7 0.2 + - - -
153A SER* 2.6 34.8 + - - -
185A LEU 3.6 16.0 + - - +
186A SER* 3.7 26.1 - - - +
187A HIS* 2.6 51.1 + - - -
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Residues in contact with LYS 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ARG* 2.9 36.3 + - + +
147A ALA* 3.6 7.4 - - - +
149A ARG* 1.3 74.9 - - - +
151A ALA* 1.3 59.4 + - - +
153A SER* 3.2 4.7 + - - -
154A ASP* 2.4 64.1 + - - +
312B LYS* 4.7 4.9 - - - +
315B LYS* 5.0 6.5 - - - +
363B LEU 5.8 3.8 - - - -
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Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 3.9 37.0 - - + +
115A VAL* 4.6 17.6 - - + +
116A PRO* 5.8 2.9 - - - +
128A PHE* 5.9 0.9 - - + -
147A ALA 2.8 20.4 + - - +
148A LEU* 3.6 7.0 - - + +
150A LYS* 1.3 75.5 - - - +
152A VAL* 1.3 62.0 + - + +
154A ASP* 3.5 6.5 + - - +
155A TRP* 3.1 21.5 + - - +
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Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LEU* 4.6 8.5 - - + -
129A ILE* 3.7 21.1 - - + -
144A TRP* 3.5 24.2 - - + -
148A LEU* 2.9 21.6 + - + +
151A ALA* 1.3 74.9 - - + +
153A SER* 1.3 62.9 + - - +
155A TRP* 3.1 13.5 + - - +
156A TYR* 3.1 41.7 - - + -
182A LEU* 4.1 15.7 - - + -
186A SER* 3.5 26.9 - - - +
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Residues in contact with SER 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ARG 2.6 24.3 + - - -
150A LYS* 3.2 6.4 + - - -
152A VAL* 1.3 78.4 - - - +
154A ASP* 1.3 59.8 + - - +
156A TYR* 3.0 3.3 + - - +
157A ASN* 2.9 34.7 + - - +
186A SER* 3.8 14.9 + - - -
188A ILE* 3.8 30.0 - - - +
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Residues in contact with ASP 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PRO* 5.6 7.4 - - + +
150A LYS* 2.4 58.5 + - - +
151A ALA* 3.7 7.4 - - - +
153A SER* 1.3 79.2 - - - +
155A TRP* 1.3 56.1 + - - +
157A ASN* 4.6 1.6 - - - +
158A THR* 2.7 45.8 + - + +
312B LYS* 2.9 35.3 + - - +
315B LYS* 4.8 1.7 + - - -
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Residues in contact with TRP 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A VAL* 4.7 5.2 - - + -
116A PRO* 4.2 24.6 + - + +
119A CYS* 2.6 33.2 + - + +
120A ARG 4.1 2.9 - - - -
121A ILE 3.9 6.3 - - - -
122A PRO* 3.7 45.8 - - + -
125A LEU* 3.8 27.3 - - + +
151A ALA 3.1 13.8 + - - +
152A VAL* 3.2 13.2 - - - +
153A SER 3.1 0.6 - - - -
154A ASP* 1.3 79.2 - - - +
156A TYR* 1.3 78.6 + + - +
158A THR* 3.9 2.7 + - - -
159A LYS* 2.7 67.3 - - - +
164A LEU* 3.8 18.4 - - + -
167A ALA* 4.7 0.7 - - + -
179A HIS* 4.8 3.1 - + - -
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Residues in contact with TYR 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LEU* 4.6 1.1 - - + -
152A VAL* 3.1 40.6 - - + -
153A SER 3.0 2.2 + - - -
155A TRP* 1.3 95.0 - + - +
157A ASN* 1.3 66.8 + - - +
158A THR 3.2 2.2 - - - -
159A LYS* 3.0 22.3 + - - +
164A LEU* 3.6 33.3 - - + +
168A VAL* 4.5 1.6 - - + -
179A HIS* 2.9 50.6 - + + +
182A LEU* 3.6 16.3 - - + +
183A LEU* 3.4 32.3 - - + -
188A ILE* 3.6 18.4 - - + -
195A LEU* 3.5 13.5 - - + +
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Residues in contact with ASN 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A SER* 2.9 15.6 + - - +
154A ASP* 4.9 2.2 - - - +
156A TYR* 1.3 72.7 - - - +
158A THR* 1.3 59.4 + - - +
159A LYS 3.2 4.1 + - - +
188A ILE* 2.7 39.9 - - - +
189A LYS 2.6 26.3 + - - +
190A PRO* 4.1 5.1 - - - +
191A ALA* 3.0 29.2 + - + +
195A LEU* 3.6 20.5 - - - +
312B LYS* 4.2 20.5 - - + +
313B LEU* 4.5 9.5 - - - +
316B LYS* 4.9 0.3 - - - +
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Residues in contact with THR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PRO* 5.4 5.7 - - - +
154A ASP* 2.7 32.7 + - + +
155A TRP* 3.9 5.4 + - - -
156A TYR 3.2 0.2 - - - -
157A ASN* 1.3 75.8 - - - +
159A LYS* 1.3 64.8 + - - +
160A ASP* 4.0 0.5 - - - +
312B LYS* 4.1 27.8 - - - +
315B LYS* 6.0 1.3 - - + -
316B LYS* 3.0 39.2 - - + +
15F A 5.1 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