Contacts of the helix formed by residues 125 - 134 (chain A) in PDB entry 4B23
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 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A LYS 3.9 1.4 + - - -
124A MET* 1.3 77.4 - - - +
126A GLU* 1.3 65.0 + - - +
127A GLU* 3.4 16.8 + - - +
128A GLU* 2.9 36.4 + - - +
129A LEU* 2.9 18.5 + - - +
154A ARG* 3.6 2.0 - - - +
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Residues in contact with GLU 126 (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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125A SER* 1.3 73.9 - - - +
127A GLU* 1.3 70.2 + - - +
129A LEU* 3.2 7.4 + - - +
130A MET* 2.8 60.8 + - + +
144A ILE* 4.0 3.8 - - - +
145A GLU* 4.5 2.3 - - + -
148A SER* 2.7 30.8 + - - -
154A ARG* 3.4 21.4 + - - +
157A ILE* 3.4 29.3 - - + +
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Residues in contact with GLU 127 (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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125A SER* 3.2 15.7 + - - +
126A GLU* 1.3 90.4 + - - +
128A GLU* 1.3 62.4 + - + +
130A MET* 3.4 8.8 + - - +
131A GLU* 3.1 23.8 + - - +
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Residues in contact with GLU 128 (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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123A LYS 4.0 3.5 - - - +
124A MET* 3.0 33.3 - - + +
125A SER* 2.9 37.1 + - - +
127A GLU* 1.3 75.6 - - + +
129A LEU* 1.3 60.6 + - - +
131A GLU* 3.3 11.4 + - - +
132A SER 2.9 24.6 + - - -
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Residues in contact with LEU 129 (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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121A ILE* 4.0 23.8 - - + -
124A MET* 3.6 20.4 - - + +
125A SER 2.9 12.3 + - - +
126A GLU* 3.4 25.6 - - - +
128A GLU* 1.3 78.0 - - - +
130A MET* 1.3 57.0 + - - +
133A LEU* 2.9 69.6 + - + +
144A ILE* 4.2 8.5 - - + +
147A TYR* 4.7 2.0 - - + -
148A SER* 3.8 7.9 - - - +
152A LEU* 3.5 29.4 - - + -
154A ARG* 3.9 9.0 - - - +
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Residues in contact with MET 130 (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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126A GLU* 2.8 45.5 + - + +
127A GLU* 3.5 9.2 - - - +
129A LEU* 1.3 77.3 - - - +
131A GLU* 1.3 58.8 + - - +
134A SER* 2.5 36.6 + - - +
141A ARG* 3.5 41.3 - - + +
144A ILE* 3.7 26.5 - - + -
145A GLU* 3.7 15.7 - - + +
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Residues in contact with GLU 131 (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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127A GLU 3.1 13.3 + - - +
128A GLU* 3.7 10.3 - - - +
130A MET* 1.3 79.3 - - - +
132A SER* 1.3 60.9 + - - +
134A SER* 4.1 4.3 + - - -
135A LYS* 2.8 40.6 + - - +
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Residues in contact with SER 132 (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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116A PRO* 3.4 29.1 - - - +
124A MET* 3.4 18.9 - - - +
128A GLU 2.9 17.1 + - - -
129A LEU* 3.8 1.8 - - - -
131A GLU* 1.3 77.3 - - - +
133A LEU* 1.3 63.3 + - - +
135A LYS* 2.9 33.1 + - - +
136A ILE* 5.0 1.9 - - - +
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Residues in contact with LEU 133 (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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45A ILE* 4.2 17.0 - - + -
115A ILE* 4.7 1.6 - - + -
116A PRO* 4.1 25.6 - - + -
121A ILE* 5.0 4.3 - - + -
129A LEU* 2.9 44.9 + - + +
132A SER* 1.3 72.7 - - - +
134A SER* 1.3 57.7 + - - +
135A LYS 2.9 5.6 - - - -
136A ILE* 2.9 46.7 + - + +
139A VAL* 3.7 12.1 - - + +
144A ILE* 3.8 21.8 - - + -
147A TYR* 4.0 26.5 - - + -
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Residues in contact with SER 134 (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 MET* 2.5 27.8 + - - +
131A GLU* 4.4 5.6 - - - -
132A SER 3.3 0.6 - - - -
133A LEU* 1.3 75.9 - - - +
135A LYS* 1.3 57.4 + - - +
136A ILE 3.1 2.0 - - - -
139A VAL 3.3 11.9 - - - -
140A LYS* 3.0 41.1 + - - +
141A ARG 4.7 1.0 + - - -
144A ILE* 3.3 12.7 - - - +
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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