Contacts of the helix formed by residues 157 - 172 (chain A) in PDB entry 1R42
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 ASP 157 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A SER* 3.1 9.4 + - - +
156A LEU* 1.3 77.0 - - - +
158A TYR* 1.3 65.9 + - - +
159A ASN* 2.7 21.4 + - - +
160A GLU* 2.5 41.6 + - + +
161A ARG* 3.1 23.2 + - - +
252A TYR* 4.5 0.2 - - - -
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Residues in contact with TYR 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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156A LEU 3.7 4.8 + - - -
157A ASP* 1.3 72.8 + - - +
159A ASN* 1.3 70.2 + - - +
162A LEU* 3.0 43.1 + - + +
252A TYR* 4.0 13.4 - + + -
255A TYR* 3.5 74.4 + + + +
263A PRO* 4.8 1.9 - - + +
265A HIS* 3.2 38.3 - + - -
266A LEU* 3.8 23.1 - - + -
490A PRO* 5.0 1.4 - - - +
612A PRO* 3.6 26.0 - - - +
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Residues in contact with ASN 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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157A ASP* 2.7 16.7 + - - +
158A TYR* 1.3 84.0 - - - +
160A GLU* 1.3 59.6 + - - +
162A LEU* 3.2 10.2 + - - +
163A TRP* 2.8 29.3 + - - +
255A TYR* 4.2 12.7 + - - -
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Residues in contact with GLU 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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151A ILE* 3.9 28.6 - - + +
155A SER* 2.8 26.9 + - - -
157A ASP* 2.5 28.2 + - - +
159A ASN* 1.3 71.9 - - - +
161A ARG* 1.3 62.8 + - - +
163A TRP* 3.2 12.9 + - + +
164A ALA* 3.0 23.7 + - - +
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Residues in contact with ARG 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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151A ILE* 3.5 7.4 + - + +
152A MET* 2.7 60.6 + - - +
153A ALA 4.5 1.4 + - - -
154A ASN 4.5 1.0 - - - +
155A SER* 3.0 36.2 + - - +
157A ASP 3.1 20.6 + - - +
158A TYR 3.9 3.4 - - - +
160A GLU* 1.3 76.0 - - - +
162A LEU* 1.3 57.8 + - - +
164A ALA 3.4 0.3 + - - -
165A TRP* 2.9 30.5 + - - +
252A TYR* 3.4 22.2 + - - -
265A HIS* 2.7 37.0 + - + +
266A LEU* 3.7 13.9 - - - +
267A LEU 3.8 1.6 - - - +
268A GLY* 3.2 23.1 - - - +
269A ASP 4.3 0.2 - - - +
278A LEU* 6.3 0.2 - - - -
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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 TYR* 3.0 35.3 + - + +
159A ASN* 3.6 11.0 - - - +
160A GLU 3.2 0.2 - - - -
161A ARG* 1.3 73.3 - - - +
163A TRP* 1.3 68.1 + - - +
165A TRP* 4.8 1.6 - - + -
166A GLU* 3.0 28.6 + - + +
265A HIS* 3.4 14.8 - - + +
490A PRO* 3.3 37.7 - - + +
491A VAL* 4.2 20.0 - - + -
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Residues in contact with TRP 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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132A VAL* 3.7 29.8 - - + -
133A CYS 3.5 24.1 + - - -
134A ASN* 4.0 11.2 - - + -
135A PRO* 3.7 32.1 - - + +
142A LEU* 4.0 15.0 - - + -
148A LEU* 4.3 5.8 - - + -
151A ILE* 4.1 23.1 - - + -
159A ASN 2.8 14.4 + - - +
160A GLU* 3.2 21.1 + - + +
162A LEU* 1.3 79.1 - - - +
164A ALA* 1.3 65.5 + - + +
166A GLU* 4.4 1.9 - - - +
167A SER* 2.5 61.2 + - - -
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Residues in contact with ALA 164 (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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148A LEU* 4.1 23.5 - - + +
151A ILE* 4.2 11.2 - - + -
152A MET* 3.9 16.6 - - + -
160A GLU 3.0 16.3 + - - +
161A ARG 3.9 3.1 - - - +
163A TRP* 1.3 89.7 - - + +
165A TRP* 1.3 65.9 + - - +
167A SER* 4.0 2.2 - - - -
168A TRP* 3.1 26.3 + - - +
270A MET* 3.7 4.5 - - - +
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Residues in contact with TRP 165 (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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152A MET* 4.2 6.4 - - + -
161A ARG 2.9 18.3 + - - +
162A LEU* 3.8 3.4 - - + +
164A ALA* 1.3 79.4 - - - +
166A GLU* 1.3 84.7 + - + +
168A TRP* 3.6 0.5 - - - +
169A ARG* 3.2 69.7 + - - +
264A ALA* 3.6 32.7 + - + +
265A HIS* 3.6 25.8 - - + -
270A MET* 3.5 21.2 + - - -
271A TRP* 5.1 1.0 + - - +
478A TRP* 3.6 22.0 - + - -
489A GLU* 3.9 3.1 - - + -
490A PRO* 3.3 30.3 - - + -
491A VAL* 4.6 2.5 - - + -
493A HIS* 3.4 32.3 - + - -
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Residues in contact with GLU 166 (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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162A LEU* 3.0 15.9 + - + +
163A TRP* 4.4 2.2 - - - +
165A TRP* 1.3 86.1 - - + +
167A SER* 1.3 56.8 + - - +
169A ARG* 3.3 1.5 + - - +
170A SER* 2.6 46.2 + - - -
491A VAL* 3.6 26.2 - - + +
493A HIS* 2.6 29.9 + - - -
497A TYR* 2.5 31.0 + - - -
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Residues in contact with SER 167 (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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132A VAL* 3.5 24.6 - - - +
163A TRP* 2.5 48.5 + - - -
164A ALA 4.0 2.2 - - - -
166A GLU* 1.3 74.6 - - - +
168A TRP* 1.3 60.0 + - - +
170A SER* 4.3 2.7 - - - +
171A GLU* 2.7 48.8 + - - +
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Residues in contact with TRP 168 (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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126A ILE 4.8 0.4 - - - -
127A TYR* 3.6 37.0 - + - -
130A GLY 3.8 17.5 - - - -
131A LYS* 4.8 0.4 - - - -
132A VAL* 3.8 6.0 - - + +
144A LEU* 3.7 37.9 - - + +
148A LEU* 3.7 18.6 - - + -
164A ALA 3.1 20.7 + - - +
165A TRP 3.6 3.4 - - - +
166A GLU 3.3 0.2 - - - -
167A SER* 1.3 74.7 - - - +
169A ARG* 1.3 64.4 + - - +
172A VAL* 3.0 71.0 + - + +
270A MET* 3.5 32.9 - - + +
271A TRP* 4.6 0.4 - - - -
502A SER* 3.1 40.3 + - - -
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Residues in contact with ARG 169 (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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165A TRP* 3.2 71.3 + - - +
166A GLU 3.9 5.4 - - - +
168A TRP* 1.3 80.8 - - + +
170A SER* 1.3 60.5 + - - +
173A GLY* 3.4 7.9 + - - +
174A LYS 3.3 20.6 + - - -
270A MET* 2.9 33.9 + - - +
271A TRP* 3.2 20.4 - - - +
493A HIS* 4.1 3.4 - - - +
497A TYR* 3.7 13.9 - - + -
499A ASP* 3.3 25.2 - - - +
502A SER* 3.9 19.4 + - - +
803A CL 3.2 32.1 - - - +
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Residues in contact with SER 170 (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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166A GLU* 2.6 39.6 + - - -
167A SER* 3.2 4.0 + - - -
169A ARG* 1.3 75.8 - - - +
171A GLU* 1.3 72.4 + - - +
174A LYS* 3.3 40.4 + - - +
497A TYR* 3.9 7.9 + - - -
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Residues in contact with GLU 171 (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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131A LYS 4.4 13.5 - - - +
132A VAL* 4.3 14.5 - - + +
133A CYS 5.6 0.9 + - - +
167A SER* 2.7 41.4 + - - +
170A SER* 1.3 87.1 + - - +
172A VAL* 1.3 62.2 + - + +
174A LYS* 4.6 0.7 - - - +
175A GLN* 3.1 27.5 + - - +
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Residues in contact with VAL 172 (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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126A ILE* 3.5 21.3 - - + +
127A TYR* 6.0 0.2 - - + -
130A GLY* 3.9 23.3 - - - -
131A LYS 4.2 4.5 - - - +
168A TRP* 3.0 69.3 + - + +
171A GLU* 1.3 82.4 - - + +
173A GLY* 1.3 75.4 + - - +
174A LYS 3.2 2.0 - - - -
175A GLN* 2.8 25.2 + - - +
176A LEU* 3.2 11.0 + - + +
502A SER* 5.1 1.3 - - - -
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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