Contacts of the helix formed by residues 154 - 163 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A PRO* 4.0 4.3 - - - +
153A HIS* 1.3 74.6 - - - +
155A ILE* 1.3 66.0 + - - -
156A GLN 3.5 1.8 - - - -
157A VAL 3.4 1.3 + - - -
158A GLU* 2.9 27.4 + - - +
324A ASP* 2.9 21.4 + - - -
372A PRO* 3.8 11.2 - - - -
373A GLY 3.3 15.5 - - - -
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Residues in contact with ILE 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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154A GLY* 1.3 69.7 - - - +
156A GLN* 1.3 66.5 + - - +
158A GLU* 3.3 5.0 + - - +
159A ARG* 3.1 33.8 + - + +
350A ARG* 3.9 29.2 - - + +
373A GLY* 3.3 26.0 + - - +
374A VAL 3.9 15.5 - - - +
375A LEU* 4.0 31.6 - - + +
397A ASP* 4.0 29.2 - - + +
108S ARG* 4.5 11.9 - - - +
110S VAL* 6.0 0.7 - - + -
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Residues in contact with GLN 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLY 3.5 0.8 - - - -
155A ILE* 1.3 79.7 - - - +
157A VAL* 1.3 79.0 + - + +
159A ARG* 3.4 4.8 + - - +
160A ASP* 3.1 35.1 + - - +
181B SER* 3.7 27.6 - - - -
182B ALA 5.1 1.4 + - - -
211B PHE 4.4 8.2 + - - +
108S ARG 3.3 13.3 + - - +
109S GLN* 3.1 34.5 + - - +
110S VAL* 3.7 21.2 - - + +
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Residues in contact with VAL 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 HIS* 3.8 38.1 - - + +
154A GLY 3.4 1.6 + - - -
155A ILE 3.4 0.2 - - - -
156A GLN* 1.3 90.4 - - + +
158A GLU* 1.3 58.5 + - - +
160A ASP* 3.2 7.4 + - - +
161A LYS* 2.9 39.1 + - + +
182B ALA* 5.8 4.7 - - + -
216B ASP* 3.7 40.2 - - + +
220B PHE* 5.3 2.9 - - + -
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Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A HIS* 4.7 0.6 - - - +
154A GLY 2.9 19.7 + - - +
155A ILE* 3.7 4.5 - - - +
157A VAL* 1.3 76.1 - - - +
159A ARG* 1.3 64.6 + - + +
161A LYS* 3.2 3.0 + - - +
162A LEU* 3.0 41.4 + - + +
169A LEU* 4.2 3.9 - - + +
199A PHE* 4.0 4.7 - - - -
290A LEU* 3.8 35.5 - - + +
324A ASP* 3.8 13.3 - - - +
325A HIS* 2.5 46.0 + - - -
375A LEU* 3.6 16.7 - - + +
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Residues in contact with ARG 159 (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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155A ILE* 3.1 28.3 + - + +
156A GLN* 3.8 4.3 - - - +
158A GLU* 1.3 79.3 - - + +
160A ASP* 1.3 56.7 + - - +
162A LEU* 5.0 2.5 - - - -
163A ASN* 2.8 25.5 + - - -
164A LYS* 2.8 53.6 + - + +
165A TYR* 3.5 30.0 + - + +
166A GLY 4.7 2.2 - - - -
167A ARG* 3.0 18.2 + - - +
168A PRO* 4.7 0.4 - - - +
169A LEU* 4.2 21.0 - - + +
375A LEU* 5.4 6.9 - - + +
396A ASP* 2.9 33.5 + - - +
397A ASP* 3.0 26.1 + - - +
398A SER 4.8 0.6 - - - +
108S ARG* 6.3 0.4 - - - +
110S VAL* 5.5 10.5 - - + -
111S GLN 5.0 3.6 - - - -
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Residues in contact with ASP 160 (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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156A GLN* 3.1 38.7 + - - +
157A VAL* 3.6 7.5 - - - +
158A GLU 3.2 0.2 - - - -
159A ARG* 1.3 78.4 - - - +
161A LYS* 1.3 61.9 + - - +
163A ASN* 3.7 7.4 + - - +
165A TYR* 2.6 35.9 + - - -
181B SER* 4.6 3.8 + - - -
183B LYS* 3.3 36.3 + - + +
220B PHE* 3.7 23.9 - - + -
65S ARG* 4.4 5.5 + - - +
109S GLN 5.0 1.9 - - - +
110S VAL* 5.5 3.0 - - - -
111S GLN* 5.4 2.8 + - - +
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Residues in contact with LYS 161 (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 HIS* 3.6 21.0 + - + -
157A VAL* 2.9 25.7 + - + +
158A GLU* 3.7 6.3 - - - +
160A ASP* 1.3 76.7 - - - +
162A LEU* 1.3 69.0 + - + +
163A ASN 3.7 0.2 + - - -
235A ILE* 4.0 6.6 - - - +
288A GLY* 4.7 11.7 + - - -
290A LEU* 5.4 8.7 - - + +
215B ARG* 5.8 0.4 - - - +
216B ASP* 2.9 29.2 + - - +
219B LEU* 4.3 20.8 - - + +
220B PHE* 3.9 21.1 - - + -
60S GLY* 3.8 25.0 - - - +
62S TYR* 4.1 4.7 - - - -
65S ARG* 3.0 30.9 + - - +
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Residues in contact with LEU 162 (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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158A GLU* 3.0 32.3 + - + +
159A ARG* 4.4 2.0 - - - +
161A LYS* 1.3 81.5 - - + +
163A ASN* 1.3 71.5 + - - +
164A LYS* 3.5 31.0 + - + +
169A LEU* 4.7 4.5 - - + -
199A PHE* 3.6 35.4 - - + -
235A ILE* 3.5 36.2 + - + +
236A LYS 5.8 0.7 - - - +
263A PRO* 4.5 15.5 - - + -
290A LEU* 4.1 17.7 - - + -
13S GLU* 5.0 1.0 - - - +
60S GLY* 6.5 0.4 - - - -
62S TYR* 5.2 2.2 - - + -
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Residues in contact with ASN 163 (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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159A ARG 2.8 12.4 + - - -
160A ASP 3.7 3.3 + - - +
161A LYS 3.4 2.6 - - - -
162A LEU* 1.3 81.6 - - - +
164A LYS* 1.3 58.9 + - - +
165A TYR* 3.8 14.1 + - - -
235A ILE* 4.5 4.7 - - + -
183B LYS* 3.4 22.9 + - - -
13S GLU* 3.9 18.2 - - - +
51S VAL* 5.2 5.5 - - - +
64S GLY 5.3 0.6 + - - -
65S ARG* 4.3 37.1 + - + +
100S ARG* 4.0 22.9 + - - +
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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