Contacts of the helix formed by residues 126 - 132 (chain B) in PDB entry 2E52
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 VAL 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B GLN 5.2 0.2 + - - -
124B PHE* 3.8 22.2 - - + -
125B LYS* 1.3 77.7 - - - +
127B LYS* 1.3 60.4 + - - +
129B LEU* 3.6 4.4 - - - +
130B SER 3.0 22.9 + - - -
141B LEU* 4.1 12.8 - - + -
155B ILE* 4.1 13.9 - - + -
158B GLN* 3.6 43.2 + - + +
159B SER* 3.8 11.2 - - - +
164B VAL* 3.6 33.5 - - + +
166B LEU* 4.3 7.2 - - + -
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Residues in contact with LYS 127 (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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127A LYS* 4.4 37.6 - - + +
131A GLU* 4.1 23.4 + - - +
162A GLU* 5.6 3.2 + - - -
126B VAL* 1.3 78.1 - - - +
128B ALA* 1.3 61.6 + - - +
130B SER* 3.3 8.6 - - - -
131B GLU* 3.2 27.4 + - - +
158B GLN* 3.9 39.6 + - + +
161B ASP* 4.4 17.7 + - - +
162B GLU* 3.8 31.8 + - + +
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Residues in contact with ALA 128 (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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121A GLN* 3.9 17.3 - - - +
154A GLN* 3.8 11.9 - - - +
158A GLN* 5.1 5.8 - - - +
125B LYS* 3.4 12.6 + - + +
126B VAL 3.3 0.4 - - - -
127B LYS* 1.3 75.1 - - - +
129B LEU* 1.3 66.1 + - - +
131B GLU* 3.1 10.5 + - - +
132B TRP* 3.0 50.5 + - + -
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Residues in contact with LEU 129 (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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92B GLY* 4.5 4.9 - - - -
106B VAL* 4.2 17.7 - - + +
107B ALA 4.8 0.2 - - - -
108B ASP* 3.8 29.6 - - + +
124B PHE 5.1 0.4 - - - +
125B LYS 3.0 18.1 + - - +
126B VAL 3.6 4.0 - - - +
128B ALA* 1.3 77.0 - - - +
130B SER* 1.3 63.7 + - - +
132B TRP* 3.0 41.4 + - + +
133B ARG 3.5 4.5 + - - -
139B ALA* 4.1 10.1 - - + +
140B VAL 4.0 7.4 - - - +
141B LEU* 3.8 39.5 - - + +
164B VAL* 3.8 13.5 - - + -
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Residues in contact with SER 130 (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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126B VAL 3.0 8.9 + - - -
127B LYS 3.3 10.8 - - - -
128B ALA 3.3 0.2 - - - -
129B LEU* 1.3 75.2 - - - +
131B GLU* 1.3 61.1 + - - +
133B ARG* 2.7 59.8 + - - +
139B ALA* 4.2 1.6 - - - -
162B GLU* 2.7 33.2 + - - -
164B VAL* 3.6 15.0 - - - +
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Residues in contact with GLU 131 (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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127A LYS* 3.7 26.0 + - - +
157A LYS* 4.4 18.0 + - - +
158A GLN* 5.6 2.8 - - - +
161A ASP* 4.2 8.6 - - - +
127B LYS 3.2 18.2 - - - +
128B ALA* 3.1 9.8 + - - +
130B SER* 1.3 71.7 - - - +
132B TRP* 1.3 65.8 + - + +
133B ARG 3.1 6.3 + - - -
134B GLU* 3.3 17.3 + - - +
162B GLU* 5.4 5.0 - - - +
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Residues in contact with TRP 132 (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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154A GLN* 3.4 13.8 + - - -
90B ASN* 3.1 39.6 + - - -
91B ALA* 3.4 26.4 - - - -
92B GLY* 3.7 14.6 + - - +
106B VAL* 4.0 11.1 - - + +
108B ASP* 3.8 19.5 - - - -
125B LYS* 4.0 17.7 - - + -
128B ALA* 3.0 29.9 + - + -
129B LEU* 3.0 39.8 + - + +
131B GLU* 1.3 78.3 - - + +
133B ARG* 1.3 63.3 + - - +
134B GLU* 3.1 13.9 + - - +
136B LYS* 5.5 1.4 - - - -
4G A 3.4 42.2 - - - -
5G A 5.6 0.7 - - - -
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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