Contacts of the helix formed by residues 151 - 162 (chain A) in PDB entry 2ESV
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 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A SER 3.5 5.0 + - - -
148A ASN 3.6 8.5 + - - -
149A ASP 3.3 7.7 + - - -
150A ALA* 1.3 80.1 - - - +
152A GLU* 1.3 63.1 + - - +
153A ALA* 3.3 4.3 - - - +
154A GLU* 3.4 24.8 + - - +
155A HIS* 4.1 7.4 - - - -
99E ASP* 4.9 2.8 - - - +
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Residues in contact with GLU 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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133A TRP* 3.7 5.2 - - - +
147A SER* 3.2 25.7 + - - +
150A ALA* 4.2 15.8 - - + +
151A SER* 1.3 73.1 - - - +
153A ALA* 1.3 65.9 + - - +
154A GLU 3.1 2.0 - - - -
155A HIS* 3.0 20.3 + - - +
156A GLN* 3.3 13.7 + - - +
97E ASP* 4.1 6.1 - - - +
98E ARG* 3.3 16.5 + - - -
5P ARG* 2.9 43.6 + - - -
6P THR 3.7 1.9 - - - +
7P LEU* 3.5 35.6 - - + +
8P ILE 5.7 0.4 - - - -
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Residues in contact with ALA 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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126A LEU* 4.0 8.5 - - + -
130A LEU 3.4 10.6 - - - +
131A ARG* 3.3 36.8 - - - +
132A SER* 3.5 5.4 - - - +
133A TRP* 3.3 20.3 - - + +
147A SER 4.5 0.2 + - - -
151A SER* 3.3 2.0 - - - -
152A GLU* 1.3 78.4 - - - +
154A GLU* 1.3 52.1 + - - +
156A GLN* 3.1 2.4 + - - +
157A ARG* 2.7 36.7 + - - +
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Residues in contact with GLU 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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131A ARG* 5.7 4.3 + - - +
151A SER* 3.4 21.5 + - - +
152A GLU 3.1 0.8 + - - -
153A ALA* 1.3 78.5 - - - +
155A HIS* 1.3 58.6 + - + +
157A ARG* 2.8 42.8 + - - +
158A ALA* 2.9 26.9 + - - +
30D TYR* 3.1 30.3 - - + +
49D LEU* 3.7 6.6 - - - +
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Residues in contact with HIS 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 4.1 13.0 - - - -
152A GLU* 3.0 10.3 + - - +
154A GLU* 1.3 79.3 - - + +
156A GLN* 1.3 62.2 + - - +
158A ALA* 3.5 4.2 - - - +
159A TYR* 3.0 24.6 + - - +
29D ASN* 6.1 0.2 - - - +
30D TYR* 3.8 31.1 + + + +
32D TYR* 4.5 3.1 - - - -
94D SER* 2.7 34.9 + - - +
99E ASP* 2.9 39.1 + - - -
4P PRO* 5.9 0.7 - - - +
5P ARG* 3.5 42.5 + - + -
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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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114A GLU* 2.9 41.8 + - - +
126A LEU* 4.5 6.1 - - + -
133A TRP* 3.6 23.9 - - + -
152A GLU* 3.3 8.8 + - - +
153A ALA 3.1 7.6 + - - +
155A HIS* 1.3 79.3 - - - +
157A ARG* 1.3 56.4 + - - +
159A TYR* 3.0 6.9 + - - +
160A LEU* 2.7 46.0 + - + +
3P ALA* 3.9 15.6 - - - +
4P PRO* 6.0 0.6 - - - +
5P ARG* 2.6 38.1 + - - +
6P THR* 4.3 5.9 - - - +
7P LEU* 5.2 1.4 - - + +
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Residues in contact with ARG 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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130A LEU* 3.8 30.2 + - + +
131A ARG* 3.6 31.6 - - - +
153A ALA 2.7 21.1 + - - +
154A GLU* 2.8 38.9 + - - +
156A GLN* 1.3 68.5 - - - +
158A ALA* 1.3 69.0 + - - +
160A LEU 4.4 0.2 - - - +
161A GLU* 2.9 77.9 + - - +
162A ASP* 6.1 1.0 - - - +
49D LEU* 3.3 21.8 - - - +
50D LYS* 5.0 10.0 - - - +
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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 GLU 2.9 17.2 + - - +
155A HIS* 3.5 7.2 - - - +
157A ARG* 1.3 90.9 - - - +
159A TYR* 1.3 61.3 + - - +
162A ASP* 3.3 23.5 + - - +
163A THR* 3.3 12.1 + - - -
28D GLY 4.7 11.4 - - - +
29D ASN* 4.7 7.4 - - + +
30D TYR* 3.5 22.9 - - + +
49D LEU* 4.8 1.8 - - + -
94D SER* 5.3 0.7 - - - +
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Residues in contact with TYR 159 (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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5A LEU* 4.5 0.2 - - - +
7A TYR* 3.9 4.9 - - - -
99A HIS* 3.3 34.5 + + - -
114A GLU* 4.8 0.9 - - - -
155A HIS 3.0 14.7 + - - +
156A GLN* 3.0 15.6 + - - +
158A ALA* 1.3 76.7 - - - +
160A LEU* 1.3 80.9 + - + +
163A THR* 3.4 19.5 + - + +
164A CYS* 2.7 58.3 + - + +
29D ASN* 5.5 1.1 - - - +
1P VAL* 2.5 33.6 + - + -
2P MET 3.8 2.5 - - - -
3P ALA* 3.6 24.7 - - + -
4P PRO* 3.8 21.8 - - + -
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Residues in contact with LEU 160 (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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99A HIS* 4.5 0.2 - - + -
100A GLY 3.4 32.3 - - - +
101A CYS* 3.5 12.3 - - + +
109A PHE* 3.3 20.1 - - + -
112A GLY* 4.4 10.3 - - - -
113A TYR 3.8 14.8 - - - +
114A GLU* 4.0 11.0 - - - +
126A LEU* 3.7 29.6 - - + -
130A LEU* 4.0 16.8 - - + -
156A GLN 2.7 26.2 + - - +
157A ARG 4.3 2.5 - - - +
159A TYR* 1.3 95.4 - - + +
161A GLU* 1.3 59.9 + - - +
164A CYS* 3.7 3.7 - - - +
165A VAL* 3.6 5.0 - - - +
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Residues in contact with GLU 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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109A PHE* 3.8 37.9 - - + +
129A ASP 5.2 1.0 - - - +
130A LEU* 3.4 20.1 - - + +
131A ARG* 5.0 4.0 + - - -
157A ARG* 2.9 53.4 + - - +
160A LEU* 1.3 76.2 - - - +
162A ASP* 1.3 59.8 + - + +
165A VAL* 3.3 17.6 - - - +
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Residues in contact with ASP 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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157A ARG* 6.1 1.3 - - - +
158A ALA* 3.3 15.6 + - - +
161A GLU* 1.3 78.4 - - + +
163A THR* 1.3 59.9 + - - +
164A CYS 3.3 1.6 - - - -
165A VAL* 3.0 4.4 + - - +
166A GLU* 2.7 53.2 + - - +
28D GLY* 3.7 33.4 - - - +
50D LYS* 5.3 6.1 + - - -
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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