Contacts of the helix formed by residues 150 - 162 (chain A) in PDB entry 2E4Y
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 TYR 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A PRO* 4.2 13.7 - - + -
49A GLU* 3.4 19.9 + - - -
61A ASN* 4.1 7.0 + - - -
64A ARG* 5.9 0.2 - - - -
100A SER* 3.3 30.2 + - - -
149A SER* 1.3 82.7 - - - +
151A SER* 1.3 66.2 + - - +
152A SER* 4.0 5.6 - - - +
153A VAL* 3.0 29.4 + - + +
154A SER* 3.0 6.8 + - - -
173A SER* 3.4 1.8 + - - -
277A ARG* 3.3 63.9 - - + +
278A SER* 4.1 16.3 - - - -
279A ASP* 3.8 4.3 + - - -
1001A 52A 3.4 37.3 + - - +
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Residues in contact with SER 151 (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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150A TYR* 1.3 70.7 - - - +
152A SER* 1.3 65.6 + - - +
154A SER* 2.8 13.0 + - - -
155A ILE* 3.0 21.9 + - - +
173A SER* 3.7 12.8 - - - -
174A THR 3.0 15.4 + - - -
175A SER* 3.0 28.6 + - - -
178A LEU* 5.2 0.4 - - - -
221A ASP 4.8 0.4 - - - -
222A TYR* 3.6 18.0 - - - -
1001A 52A 2.8 28.7 + - - -
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Residues in contact with SER 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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100A SER 6.0 0.2 - - - -
102A ASP* 3.8 22.8 - - - +
150A TYR* 4.0 6.1 - - - +
151A SER* 1.3 78.7 - - - +
153A VAL* 1.3 60.2 + - - +
155A ILE* 3.9 2.6 + - - +
156A GLN* 3.6 16.8 + - - +
220A GLY* 4.8 5.5 - - - -
221A ASP* 4.4 24.3 + - - +
222A TYR* 4.1 17.7 + - - +
277A ARG* 3.6 26.5 + - - -
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Residues in contact with VAL 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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44A LEU* 4.9 1.6 - - + -
98A THR* 4.7 13.7 - - + +
100A SER 5.2 3.4 - - - +
101A ARG 4.6 0.9 - - - +
102A ASP* 3.9 22.7 - - - +
105A ALA* 3.2 31.9 - - + -
148A GLY* 4.9 5.8 - - - -
149A SER 4.6 5.6 - - - +
150A TYR* 3.0 41.1 - - + +
152A SER* 1.3 73.6 - - - +
154A SER* 1.3 67.7 + - - +
155A ILE 3.1 2.2 - - - -
156A GLN* 3.8 1.3 - - + -
157A VAL* 2.8 38.3 + - + +
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Residues in contact with SER 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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147A GLY 3.3 6.6 + - - -
148A GLY* 2.7 23.9 + - - -
150A TYR 3.0 4.9 + - - -
151A SER 2.8 9.8 + - - -
153A VAL* 1.3 73.9 - - - +
155A ILE* 1.3 52.7 + - - +
157A VAL* 4.3 0.9 - - - -
158A ALA* 2.7 35.1 + - - +
168A GLN* 3.4 15.5 + - - +
170A SER* 3.8 1.7 - - - -
173A SER* 2.6 34.1 + - - -
178A LEU* 4.2 4.5 - - - -
187A PHE* 4.0 8.5 - - - -
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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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151A SER 3.0 14.5 + - - +
152A SER 4.1 2.7 - - - +
154A SER* 1.3 73.3 - - - +
156A GLN* 1.3 69.8 + - + +
157A VAL 2.8 1.6 - - - -
158A ALA* 2.6 16.5 + - - +
159A ASN* 2.9 23.9 + - - +
175A SER* 4.6 5.8 - - - +
177A LYS* 4.4 18.8 - - + +
178A LEU* 3.7 24.9 - - + -
184A TYR* 3.4 31.6 - - + +
221A ASP* 3.5 42.8 - - + +
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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
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102A ASP* 3.8 34.9 + - + +
103A THR* 5.0 7.5 - - - +
106A LEU* 3.3 43.8 - - + +
152A SER 3.6 11.9 + - - +
153A VAL* 3.5 4.8 + - - +
155A ILE* 1.3 79.3 - - + +
157A VAL* 1.3 62.6 + - + +
159A ASN* 3.5 28.0 + - - +
160A LEU 4.0 2.4 + - - -
221A ASP* 6.2 0.4 - - - +
162B ARG* 5.0 2.8 + - - -
163B LEU* 4.3 16.8 + - - +
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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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44A LEU* 4.0 15.5 - - + -
105A ALA* 4.3 4.9 - - + -
106A LEU* 4.5 7.9 - - - +
109A SER* 3.7 29.4 - - - +
153A VAL* 2.8 41.9 + - + +
154A SER* 3.5 5.8 - - - +
155A ILE 2.7 4.4 + - - -
156A GLN* 1.3 73.2 - - + +
158A ALA* 1.3 66.4 + - - +
159A ASN 3.0 1.6 - - - -
160A LEU* 2.8 18.0 + - - +
161A LEU* 3.2 32.8 + - + +
168A GLN* 3.9 7.6 - - - +
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Residues in contact with ALA 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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154A SER 2.7 17.6 + - - +
155A ILE* 2.6 12.4 + - - +
157A VAL* 1.3 71.9 - - - +
159A ASN* 1.3 63.6 + - - +
160A LEU 2.8 1.7 + - - -
161A LEU* 3.3 10.9 + - - +
162A ARG* 3.4 18.7 + - - +
168A GLN* 3.2 18.5 + - - +
178A LEU* 4.8 0.2 - - + -
184A TYR* 4.1 23.8 - - + -
186A TYR* 6.1 0.6 - - - +
187A PHE* 4.5 15.9 - - + -
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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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155A ILE* 2.9 24.9 + - - +
156A GLN* 3.5 25.9 + - - +
157A VAL 3.0 0.2 - - - -
158A ALA* 1.3 76.7 - - - +
160A LEU* 1.3 55.5 + - - +
162A ARG* 3.5 10.4 - - - +
163A LEU* 3.4 23.2 - - - +
183A ARG* 4.6 2.9 + - - +
184A TYR* 3.3 26.0 + - - -
159B ASN 4.6 0.3 - - - +
162B ARG* 4.3 12.7 - - - +
163B LEU* 3.4 27.7 - - + +
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Residues in contact with LEU 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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106A LEU* 4.6 7.9 - - + +
109A SER* 3.9 27.1 - - - +
110A LEU* 3.7 28.3 - - + +
113A VAL* 3.5 21.5 - - + -
156A GLN 4.5 2.7 - - - +
157A VAL* 2.8 10.5 + - - +
159A ASN* 1.3 79.2 - - - +
161A LEU* 1.3 63.9 + - + +
162A ARG 3.2 2.2 - - - -
163A LEU* 3.2 7.6 + - + +
164A PHE* 3.1 32.8 - - + -
160B LEU* 3.4 32.5 - - + -
163B LEU* 3.4 16.4 - - + +
164B PHE* 4.3 3.1 - - + -
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Residues in contact with LEU 161 (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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109A SER* 4.9 2.2 - - - +
112A PHE* 4.8 8.3 - - + -
113A VAL* 3.9 22.4 - - + -
145A VAL* 4.4 15.7 - - + -
157A VAL* 3.2 38.5 + - + +
158A ALA* 4.2 3.1 - - - +
160A LEU* 1.3 83.2 - - + +
162A ARG* 1.3 60.5 + - - +
164A PHE* 3.1 4.3 + - - +
165A GLN 2.9 9.4 + - - -
166A ILE* 2.9 63.5 + - + +
168A GLN* 3.5 24.7 - - + +
186A TYR* 5.5 1.6 - - + -
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Residues in contact with ARG 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 ALA 3.4 11.9 + - - +
159A ASN* 3.5 18.8 - - - +
161A LEU* 1.3 72.9 - - - +
163A LEU* 1.3 95.0 + - + +
164A PHE 2.8 10.8 + - - -
165A GLN* 2.9 17.6 + - - +
182A SER 5.2 5.3 + - - -
183A ARG* 3.7 20.0 + - - -
184A TYR* 5.4 1.1 - - - +
185A ASP* 2.9 42.2 + - - +
186A TYR* 4.2 22.2 - - + +
156B GLN* 5.5 1.6 + - - -
159B ASN* 4.8 10.5 - - - +
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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