Contacts of the helix formed by residues 154 - 163 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151D PRO* 3.9 3.9 - - - +
153D HIS* 1.3 74.4 - - - +
155D ILE* 1.3 67.2 + - - -
156D GLN 3.4 3.0 + - - -
157D VAL 3.4 0.7 + - - -
158D GLU* 2.9 27.0 + - - +
324D ASP* 2.9 20.5 + - - -
372D PRO* 3.8 11.7 - - - -
373D GLY 3.3 15.7 - - - -
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Residues in contact with ILE 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D GLY* 1.3 70.3 - - - +
156D GLN* 1.3 64.1 + - - +
158D GLU* 3.3 5.2 + - - +
159D ARG* 3.0 33.7 + - + +
324D ASP 5.4 0.4 + - - -
350D ARG* 4.0 27.4 - - + +
373D GLY* 3.2 27.0 + - - +
374D VAL 3.9 16.2 - - - +
375D LEU* 4.0 31.8 - - + +
397D ASP* 3.9 20.6 - - + +
108V ARG* 3.9 22.9 - - - +
110V VAL* 5.8 0.2 - - + -
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Residues in contact with GLN 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A SER* 3.6 27.5 - - - -
182A ALA* 4.9 1.7 + - - +
211A PHE 4.5 8.3 + - - +
154D GLY 3.4 0.6 + - - -
155D ILE* 1.3 79.2 - - - +
157D VAL* 1.3 73.6 + - + +
159D ARG* 3.4 4.7 + - - +
160D ASP* 3.0 42.2 + - - +
108V ARG 3.3 14.1 + - - +
109V GLN* 3.1 35.1 + - - +
110V VAL* 3.6 20.8 - - + +
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Residues in contact with VAL 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ALA* 5.8 4.9 - - + -
216A ASP* 3.6 38.6 - - + +
220A PHE* 5.3 3.8 - - + -
153D HIS* 3.7 40.2 - - + +
154D GLY 3.4 1.4 + - - -
156D GLN* 1.3 87.4 - - + +
158D GLU* 1.3 61.5 + - - +
160D ASP* 3.3 7.7 + - - +
161D LYS* 2.9 38.4 + - + +
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Residues in contact with GLU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D HIS* 4.7 0.4 - - - +
154D GLY 2.9 18.7 + - - +
155D ILE* 3.7 4.7 - - - +
157D VAL* 1.3 76.8 - - - +
159D ARG* 1.3 65.0 + - + +
161D LYS* 3.2 3.5 + - - +
162D LEU* 3.0 31.0 + - + +
169D LEU* 4.0 11.0 - - + +
199D PHE* 4.0 6.8 - - - -
290D LEU* 3.7 36.3 - - + +
324D ASP* 3.8 14.6 - - - +
325D HIS* 2.5 43.8 + - - -
375D LEU* 3.8 16.9 - - + +
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Residues in contact with ARG 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ILE* 3.0 26.6 + - + +
156D GLN* 3.8 3.8 - - - +
158D GLU* 1.3 78.6 - - + +
160D ASP* 1.3 57.3 + - - +
162D LEU* 5.0 2.5 - - - -
163D ASN* 2.8 26.5 + - - -
164D LYS* 2.8 53.5 + - + +
165D TYR* 3.5 28.8 + - + +
166D GLY 4.7 2.7 - - - -
167D ARG 3.1 18.6 + - - +
168D PRO* 4.7 0.4 - - - +
169D LEU* 4.4 18.9 - - + +
375D LEU* 5.4 7.8 - - + +
396D ASP* 3.0 34.1 + - - +
397D ASP* 3.0 26.5 + - - +
398D SER 4.8 0.8 + - - +
108V ARG* 5.7 0.9 - - - +
110V VAL* 5.5 9.9 - - + -
111V GLN 5.1 3.4 - - - -
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Residues in contact with ASP 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A SER* 4.6 3.6 + - - -
183A LYS* 3.5 35.7 + - + +
220A PHE* 3.7 25.3 - - + -
156D GLN* 3.0 40.3 + - - +
157D VAL* 3.7 7.1 - - - +
158D GLU 3.2 0.2 - - - -
159D ARG* 1.3 80.0 - - - +
161D LYS* 1.3 61.6 + - - +
163D ASN* 3.6 7.3 + - - +
165D TYR* 2.7 35.0 + - - -
65V ARG* 4.3 5.5 - - - +
109V GLN 4.9 1.8 - - - +
110V VAL* 5.5 2.6 - - - +
111V GLN* 5.2 3.8 + - - +
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Residues in contact with LYS 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ARG* 5.6 0.8 - - - +
216A ASP* 3.0 30.5 + - - -
219A LEU* 4.1 21.3 - - + +
220A PHE* 3.9 25.1 - - + -
153D HIS* 3.5 21.5 + - + -
157D VAL* 2.9 29.3 + - + +
158D GLU* 3.7 5.6 - - - +
160D ASP* 1.3 76.1 - - - +
162D LEU* 1.3 70.6 + - + +
235D ILE* 4.0 5.0 - - - +
288D GLY* 4.8 10.9 + - - -
290D LEU* 5.4 8.1 - - + -
60V GLY* 3.8 26.6 - - - +
62V TYR* 4.0 4.2 - - - -
65V ARG* 2.9 29.0 + - - +
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Residues in contact with LEU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D GLU* 3.0 32.5 + - + +
159D ARG* 4.4 1.8 - - - +
161D LYS* 1.3 80.0 - - + +
163D ASN* 1.3 71.6 + - - +
164D LYS* 3.4 30.3 + - + +
169D LEU* 4.8 3.1 - - + -
199D PHE* 3.7 34.8 - - + -
235D ILE* 3.5 37.9 - - + +
236D LYS 6.2 0.4 - - - -
263D PRO* 4.4 15.5 - - + -
290D LEU* 4.0 20.0 - - + -
13V GLU* 4.9 0.9 - - - +
60V GLY* 6.3 0.4 - - - -
62V TYR* 5.0 2.9 - - + -
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Residues in contact with ASN 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LYS* 3.4 23.6 + - - -
159D ARG 2.8 12.5 + - - -
160D ASP 3.6 3.4 + - - +
161D LYS 3.3 2.6 - - - -
162D LEU* 1.3 81.6 - - - +
164D LYS* 1.3 59.4 + - - +
165D TYR* 3.7 14.9 + - - -
235D ILE* 4.5 3.8 - - + -
13V GLU* 3.9 17.4 - - - +
51V VAL* 5.2 5.2 - - + +
64V GLY 5.2 1.0 + - - -
65V ARG* 4.3 36.9 + - + +
100V ARG* 4.0 23.1 + - - +
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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