Contacts of the helix formed by residues 144 - 155 (chain B) in PDB entry 2HEI
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 GLU 144 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B ARG* 4.7 12.0 - - - +
142B MET* 4.0 8.5 + - - +
143B VAL* 1.3 75.7 - - - +
145B TYR* 1.3 66.4 + - - +
146B GLU* 4.1 14.3 - - + +
147B GLU* 3.0 30.4 + - + +
148B ALA* 3.0 21.0 + - - +
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Residues in contact with TYR 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B TYR* 5.4 0.2 - - - -
141B ARG* 4.1 10.8 - - - +
143B VAL 3.3 4.8 + - - -
144B GLU* 1.3 71.1 + - - +
146B GLU* 1.3 71.1 + - + +
148B ALA* 3.2 6.5 + - - +
149B GLN* 2.7 52.8 + - + +
159B PHE* 3.6 22.1 + + - -
160B MET* 4.8 3.6 - - - -
161B GLU* 3.1 59.5 + - + +
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B GLU* 4.1 14.5 - - + +
145B TYR* 1.3 98.4 + - + +
147B GLU* 1.3 60.2 + - - +
149B GLN* 4.2 6.0 - - - +
150B ALA* 3.0 31.2 + - - +
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Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B PHE* 3.4 30.6 - - + -
112B LYS* 4.1 11.8 + - - +
143B VAL* 5.5 0.8 - - + +
144B GLU* 3.0 29.6 + - + +
146B GLU* 1.3 78.0 - - - +
148B ALA* 1.4 58.8 + - - +
150B ALA* 3.8 3.5 - - - +
151B TYR* 2.9 31.1 + - + +
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B TYR* 3.2 28.0 - - + +
108B PHE* 3.8 23.5 - - + -
130B LEU* 4.0 4.3 - - + +
143B VAL* 4.6 1.3 - - + -
144B GLU 3.0 11.8 + - - +
145B TYR* 3.5 5.2 - - - +
147B GLU* 1.4 75.1 - - - +
149B GLN* 1.3 59.9 + - - +
151B TYR* 3.3 2.8 + - - +
152B ALA* 2.8 29.1 + - - +
159B PHE* 3.4 19.7 - - + -
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Residues in contact with GLN 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B TYR* 2.7 41.0 + - + +
146B GLU* 4.2 6.3 - - - +
148B ALA* 1.3 72.0 - - - +
150B ALA* 1.3 57.9 + - - +
152B ALA* 3.1 2.4 + - - +
153B ASP* 2.8 64.0 + - - +
157B LEU 5.5 0.5 - - - +
159B PHE* 3.6 37.1 + - + +
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B GLU 3.0 20.3 + - - +
147B GLU* 3.8 5.2 - - - +
149B GLN* 1.3 75.8 - - - +
151B TYR* 1.3 64.2 + - - +
153B ASP* 3.3 8.7 + - - +
154B ASP* 3.0 33.2 + - - +
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Residues in contact with TYR 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B PHE* 4.0 14.1 - + + -
111B ALA* 5.9 0.2 - - + -
112B LYS* 3.4 53.5 + - + +
115B VAL* 3.2 34.2 - - + +
116B LYS* 4.7 9.8 + - - +
130B LEU* 3.8 22.7 - - + -
147B GLU* 2.9 20.2 + - + +
148B ALA 3.5 2.0 - - - +
150B ALA* 1.3 76.6 - - - +
152B ALA* 1.3 62.6 + - - +
154B ASP* 3.3 7.4 + - + +
155B ASN* 3.1 55.3 + - - +
157B LEU* 3.8 17.9 - - + -
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Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LEU* 4.4 4.3 - - + -
148B ALA 2.8 20.4 + - - +
149B GLN* 3.5 7.4 - - - +
151B TYR* 1.3 72.7 - - - +
153B ASP* 1.3 64.6 + - - +
155B ASN 3.1 1.6 + - - -
156B SER 3.0 4.2 + - - -
157B LEU* 2.9 55.5 + - + +
159B PHE* 3.5 29.8 - - + -
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Residues in contact with ASP 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B GLN* 2.8 47.8 + - - +
150B ALA* 3.6 7.9 - - - +
152B ALA* 1.3 79.1 - - - +
154B ASP* 1.3 63.5 + - - +
155B ASN 3.2 1.0 + - - -
156B SER* 3.3 12.0 + - - +
157B LEU 5.0 3.6 - - - +
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Residues in contact with ASP 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ALA* 3.0 20.4 + - - +
151B TYR* 3.3 11.3 + - + +
153B ASP* 1.3 77.6 - - - +
155B ASN* 1.3 66.8 + - - +
156B SER* 3.5 1.4 + - - -
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Residues in contact with ASN 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B VAL* 4.3 2.3 - - + +
116B LYS* 5.8 3.9 + - - +
119B GLN* 3.1 32.9 + - - +
151B TYR* 3.1 52.7 + - - +
152B ALA 3.1 1.4 + - - -
153B ASP 3.1 0.8 - - - -
154B ASP* 1.3 86.5 - - - +
156B SER* 1.3 70.9 + - - +
157B LEU* 3.2 30.3 - - + +
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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