Contacts of the helix formed by residues 142 - 155 (chain A) in PDB entry 5Y3R
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 SER 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A TYR* 1.3 80.8 - - - +
143A LEU* 1.3 59.5 + - - +
145A GLU* 2.7 41.6 + - - +
146A VAL* 3.0 14.8 - - - +
182A LYS* 2.4 24.1 + - - +
185A ARG* 2.2 31.8 + - - +
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Residues in contact with LEU 143 (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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141A TYR* 3.7 14.9 - - + -
142A SER* 1.3 69.8 - - - +
144A SER* 1.3 73.8 + - - +
146A VAL* 2.4 40.2 + - - +
147A LEU* 2.9 5.4 + - - +
175A PRO* 4.5 9.6 - - + -
176A HIS* 3.2 32.5 - - + +
182A LYS* 2.9 33.0 - - + +
185A ARG* 2.9 15.4 - - - +
186A ALA* 3.1 30.3 - - + +
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Residues in contact with SER 144 (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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143A LEU* 1.3 86.6 - - - +
145A GLU* 1.3 66.2 + - - +
147A LEU* 2.8 38.7 + - - +
148A TRP* 2.9 25.0 + - - -
185A ARG* 2.6 45.5 + - - -
186A ALA* 3.6 1.0 + - - -
189A LYS* 3.5 11.9 - - - -
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Residues in contact with GLU 145 (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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99A PHE* 6.4 1.6 - - + -
142A SER* 2.7 42.3 + - - +
144A SER* 1.3 71.1 + - - +
146A VAL* 1.3 54.7 + - + -
148A TRP* 3.3 37.3 + - + +
149A VAL* 2.8 32.6 + - + +
182A LYS* 4.5 0.2 + - - -
185A ARG* 2.5 38.1 + - - -
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Residues in contact with VAL 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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41A LEU* 4.2 12.1 - - + -
88A TYR* 3.3 67.1 - - + -
101A ASN 5.5 0.7 - - - +
102A ILE* 6.2 1.1 - - + -
141A TYR* 4.5 1.1 - - + -
142A SER 3.0 22.7 - - - +
143A LEU* 2.4 17.2 + - - +
145A GLU* 1.3 68.9 - - + +
147A LEU* 1.3 68.2 + - - +
149A VAL* 2.8 24.8 + - + +
150A CYS* 3.0 10.4 + - - +
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Residues in contact with LEU 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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143A LEU 2.9 7.6 + - - +
144A SER* 2.8 43.1 + - - +
146A VAL* 1.3 80.0 - - - +
148A TRP* 1.3 56.7 + - - +
150A CYS* 3.0 1.8 + - - +
151A ALA* 2.8 25.0 + - - +
186A ALA* 5.4 1.1 - - - -
189A LYS* 3.0 19.5 - - + +
190A ALA* 3.4 32.3 - - + +
193A LEU* 3.7 21.9 - - + +
200A LEU* 6.2 7.4 - - + -
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Residues in contact with TRP 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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97A VAL* 5.5 4.5 - - + +
99A PHE* 4.7 22.7 - + - -
144A SER* 2.9 35.4 + - - -
145A GLU* 3.3 48.4 + - + +
147A LEU* 1.3 69.4 - - - +
149A VAL* 1.3 67.6 + - + +
151A ALA* 3.5 11.4 - - + -
152A ASN* 2.4 55.1 + - - +
185A ARG* 4.9 4.0 - - + -
189A LYS* 3.3 24.5 - - + +
2383C PHE* 4.7 11.7 - + + -
2415C LEU* 5.0 25.1 - - + -
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Residues in contact with VAL 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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86A VAL* 4.8 8.5 - - + -
88A TYR* 5.4 2.0 - - + -
95A ASN* 6.1 0.7 - - + -
97A VAL* 4.8 15.4 - - + +
99A PHE* 6.0 0.9 - - + -
102A ILE* 4.3 40.6 - - + -
104A VAL* 6.5 0.9 - - + -
145A GLU* 2.8 27.7 + - + +
146A VAL* 2.8 21.9 + - + +
148A TRP* 1.3 83.6 - - + +
150A CYS* 1.3 68.5 + - - +
152A ASN* 2.6 26.6 + - - +
153A LEU* 2.9 14.9 + - + +
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Residues in contact with CYS 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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39A ILE* 5.0 7.2 - - + +
40A PHE 5.7 0.2 - - - -
41A LEU* 3.5 43.7 - - + -
86A VAL* 4.4 4.7 - - - -
88A TYR* 6.2 0.2 - - - -
146A VAL* 3.0 14.0 + - - +
147A LEU* 4.1 1.6 - - - +
149A VAL* 1.3 85.9 - - - +
151A ALA* 1.3 59.2 + - - +
153A LEU* 2.6 47.1 + - + +
154A PHE* 3.0 3.5 + - - +
166A ILE* 4.6 23.4 - - + +
200A LEU* 6.3 0.2 - - + -
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Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A LEU 2.8 17.2 + - - +
148A TRP* 3.5 10.5 - - - -
150A CYS* 1.3 75.1 - - - +
152A ASN* 1.3 55.1 + - - +
154A PHE* 2.1 43.7 + - - +
166A ILE* 4.8 2.0 - - - +
189A LYS* 4.6 1.3 - - - +
193A LEU* 3.6 31.1 - - + +
198A ILE* 4.8 4.5 - - - -
2384C PHE* 2.8 20.5 - - + -
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Residues in contact with ASN 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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97A VAL* 5.0 15.1 - - + +
148A TRP* 2.4 50.7 + - - +
149A VAL* 2.6 11.6 + - - +
151A ALA* 1.3 70.5 - - - +
153A LEU* 1.3 59.8 + - - +
154A PHE 3.3 0.2 - - - -
155A SER* 2.9 33.4 + - - +
156A ASP* 3.0 7.1 - - - +
2383C PHE* 3.3 21.8 - - - -
2384C PHE* 3.1 17.7 - - - -
2422C GLN* 5.0 10.9 + - - +
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Residues in contact with LEU 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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39A ILE* 5.9 5.4 - - + -
84A ALA* 5.6 6.7 - - + -
86A VAL* 3.6 39.7 - - + -
104A VAL* 5.0 13.9 - - + -
106A GLN 5.9 0.9 - - - +
107A GLU* 6.1 0.2 - - - -
108A LEU* 3.2 19.9 - - + +
149A VAL* 3.5 10.3 - - + +
150A CYS* 2.6 35.9 + - + +
152A ASN* 1.3 73.5 - - - +
154A PHE* 1.3 56.2 + - - -
155A SER 2.9 1.1 - - - -
156A ASP* 2.7 53.5 + - - +
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Residues in contact with PHE 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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37A SER* 4.7 5.4 - - - -
39A ILE* 6.3 2.9 - - + +
108A LEU* 4.9 3.6 - - + -
150A CYS 3.0 4.6 + - - +
151A ALA* 2.1 28.0 + - - +
153A LEU* 1.3 65.1 - - - +
155A SER* 1.3 63.1 + - - -
156A ASP 3.0 0.2 - - - -
157A VAL* 3.0 24.6 - - + +
161A MET* 3.2 33.9 - - - -
164A LYS* 3.3 37.5 - - + -
166A ILE* 6.1 1.1 - - + -
196A THR* 5.1 3.1 - - + -
198A ILE* 3.4 28.5 - - + -
2384C PHE* 3.5 27.9 - + + -
2388C LYS* 4.6 19.5 - - + -
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Residues in contact with SER 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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151A ALA 2.9 0.2 + - - -
152A ASN* 2.9 30.8 + - - +
153A LEU 2.9 0.2 - - - -
154A PHE* 1.3 79.2 - - - +
156A ASP* 1.3 52.4 + - - +
157A VAL* 2.6 23.9 + - - +
2384C PHE* 2.8 32.6 - - - -
2387C PRO* 5.7 8.7 - - - +
2388C LYS* 5.2 7.3 - - - +
2422C GLN* 5.0 9.7 + - - -
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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