Contacts of the helix formed by residues 154 - 163 (chain B) in PDB entry 1IR1
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 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B PRO* 4.0 4.1 - - - +
153B HIS* 1.3 74.8 - - - +
155B ILE* 1.3 64.6 + - - -
156B GLN 3.5 2.5 - - - -
157B VAL 3.4 1.4 + - - -
158B GLU* 3.0 27.1 + - - +
324B ASP* 2.9 21.0 + - - -
372B PRO* 3.8 12.1 - - - -
373B GLY 3.3 15.3 - - - -
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Residues in contact with ILE 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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154B GLY* 1.3 69.5 - - - +
156B GLN* 1.3 65.9 + - - +
158B GLU* 3.3 5.4 + - - +
159B ARG* 3.0 33.9 + - + +
350B ARG* 4.0 39.3 - - + +
372B PRO* 5.2 0.2 - - - +
373B GLY* 3.3 24.3 + - - +
374B VAL* 4.1 6.0 - - - +
375B LEU* 3.9 32.4 - - + +
397B ASP* 4.0 28.7 - - + +
108T ARG* 4.3 12.1 - - - +
110T VAL* 5.7 0.4 - - + -
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Residues in contact with GLN 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B GLY 3.5 0.8 - - - -
155B ILE* 1.3 78.2 - - - +
157B VAL* 1.3 78.9 + - + +
159B ARG* 3.4 4.4 + - - +
160B ASP* 3.0 36.4 + - - +
181C SER* 3.6 26.3 - - - -
182C ALA 5.0 1.2 + - - -
211C PHE 4.5 7.7 + - - +
108T ARG 3.3 13.5 + - - +
109T GLN* 3.2 24.3 + - - +
110T VAL* 3.4 30.2 - - + +
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Residues in contact with VAL 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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153B HIS* 3.7 39.0 - - + +
154B GLY 3.4 1.8 + - - +
156B GLN* 1.3 90.4 - - + +
158B GLU* 1.3 57.7 + - - +
160B ASP* 3.2 8.5 + - - +
161B LYS* 2.8 38.8 + - + +
182C ALA* 5.9 3.8 - - + -
216C ASP* 3.6 39.9 - - + +
220C PHE* 5.4 2.9 - - + -
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B HIS* 4.7 0.4 - - + +
154B GLY 3.0 18.6 + - - +
155B ILE* 3.7 4.7 - - - +
157B VAL* 1.3 77.5 - - - +
159B ARG* 1.3 64.8 + - + +
161B LYS* 3.2 3.1 + - - +
162B LEU* 3.0 39.0 + - + +
169B LEU* 4.0 3.9 - - + +
199B PHE* 4.0 3.8 - - - -
290B LEU* 3.8 39.4 - - + +
324B ASP* 3.8 14.0 - - - +
325B HIS* 2.5 44.5 + - - -
375B LEU* 3.8 17.0 - - + +
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Residues in contact with ARG 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ILE* 3.0 27.9 + - + +
156B GLN* 3.8 4.0 - - - +
158B GLU* 1.3 77.4 - - + +
160B ASP* 1.3 53.3 + - - +
162B LEU* 5.0 1.8 - - - -
163B ASN* 2.8 29.6 + - - -
164B LYS* 2.9 41.0 + - - +
165B TYR* 3.5 33.2 - - + +
166B GLY 4.8 2.7 - - - -
167B ARG* 3.2 17.2 + - - +
169B LEU* 3.8 21.2 - - + +
375B LEU* 5.2 6.3 - - + +
396B ASP* 2.9 32.7 + - - +
397B ASP* 2.9 27.3 + - - +
398B SER 4.7 0.4 - - - +
108T ARG* 6.1 0.9 - - - +
110T VAL* 5.5 9.6 - - + -
111T GLN 5.1 3.4 - - - -
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Residues in contact with ASP 160 (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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156B GLN* 3.0 38.7 + - - +
157B VAL* 3.6 7.3 - - - +
158B GLU 3.2 0.2 - - - -
159B ARG* 1.3 76.5 - - - +
161B LYS* 1.3 63.9 + - - +
163B ASN* 3.6 8.0 + - - -
165B TYR* 2.6 34.3 + - - -
181C SER* 4.6 2.9 + - - -
183C LYS* 3.5 42.3 + - + +
220C PHE* 3.6 20.4 - - + -
65T ARG* 4.2 5.5 - - - -
109T GLN 5.0 2.0 - - - +
110T VAL* 5.5 2.6 - - - +
111T GLN* 5.4 3.6 + - - +
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Residues in contact with LYS 161 (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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153B HIS* 3.6 21.3 + - + -
157B VAL* 2.8 25.4 + - + +
158B GLU* 3.7 5.8 - - - +
160B ASP* 1.3 76.3 - - - +
162B LEU* 1.3 69.2 + - + +
288B GLY* 4.7 11.1 + - - -
290B LEU* 5.5 8.5 - - + +
215C ARG* 5.6 0.8 - - - +
216C ASP* 2.8 30.7 + - - +
219C LEU* 4.2 21.4 - - + +
220C PHE* 3.9 24.2 - - + -
60T GLY* 3.7 26.7 - - - +
62T TYR* 4.0 9.6 - - - -
65T ARG* 2.9 28.2 + - - +
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Residues in contact with LEU 162 (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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158B GLU* 3.0 32.5 + - + +
159B ARG* 4.4 0.9 - - - +
161B LYS* 1.3 79.7 - - + +
163B ASN* 1.3 70.5 + - - +
164B LYS* 3.4 30.1 + - + +
169B LEU* 4.8 3.4 - - + -
199B PHE* 3.6 36.3 - - + -
235B ILE* 3.5 39.1 - - + +
236B LYS 5.7 0.9 - - - +
263B PRO* 4.4 16.8 - - + -
290B LEU* 4.0 16.6 - - + -
13T GLU* 4.9 1.2 - - - +
60T GLY* 6.4 0.7 - - - -
62T TYR* 5.1 2.7 - - + -
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Residues in contact with ASN 163 (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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159B ARG 2.8 12.1 + - - -
160B ASP 3.6 3.3 + - - +
161B LYS 3.3 3.0 - - - -
162B LEU* 1.3 81.3 - - - +
164B LYS* 1.3 58.1 + - - +
165B TYR* 3.7 15.7 + - - -
235B ILE* 4.5 3.8 - - + -
183C LYS* 3.3 23.4 + - - -
13T GLU* 4.0 17.1 - - - +
51T VAL* 5.1 5.9 - - - +
64T GLY 5.2 0.8 + - - -
65T ARG* 4.2 38.1 + - + +
100T ARG* 4.0 23.9 + - - +
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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