Contacts of the helix formed by residues 125 - 136 (chain A) in PDB entry 1A4Y
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 GLY 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 LEU 3.5 2.2 - - - -
124A LEU* 1.3 85.7 - - - +
126A ASP* 1.3 66.2 + - - -
127A ALA* 3.2 1.6 - - - -
129A LEU 3.1 13.0 + - - -
151A CYS 2.9 10.5 + - - -
152A SER* 3.5 21.9 - - - -
153A LEU* 3.5 11.2 - - - +
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Residues in contact with ASP 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 GLY* 1.3 71.7 - - - -
127A ALA* 1.3 62.2 + - - +
129A LEU* 3.4 1.0 + - - +
130A GLN* 3.0 41.6 + - - +
152A SER 4.2 2.8 + - - +
153A LEU* 3.7 0.7 - - - -
154A SER* 2.7 47.0 + - - -
156A ALA* 3.6 13.7 - - + +
157A SER* 2.6 31.7 + - - +
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Residues in contact with ALA 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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98A GLY* 5.7 2.5 - - - -
124A LEU 4.9 2.0 - - - +
125A GLY 3.2 0.6 - - - -
126A ASP* 1.3 77.8 - - - +
128A GLY* 1.3 64.1 + - - +
130A GLN* 3.3 11.5 + - - +
131A LEU* 3.2 21.2 + - - +
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Residues in contact with GLY 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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98A GLY* 3.6 22.1 - - - -
101A CYS* 3.3 22.9 - - - +
124A LEU* 3.2 17.2 + - - -
125A GLY 3.2 3.8 + - - -
127A ALA* 1.3 79.7 - - - +
129A LEU* 1.3 62.3 + - - +
131A LEU* 3.2 3.8 + - - +
132A LEU 3.0 17.0 + - - -
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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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101A CYS* 5.2 0.4 - - - -
124A LEU* 4.6 6.7 - - + +
125A GLY 3.1 12.0 + - - +
126A ASP 3.8 0.4 - - - +
127A ALA 3.4 0.2 - - - -
128A GLY* 1.3 74.6 - - - +
130A GLN* 1.3 53.3 + - - +
132A LEU* 3.0 23.6 + - + +
133A CYS* 2.8 42.4 + - - -
136A LEU* 5.8 0.2 - - + -
146A LEU* 5.4 0.7 - - + -
148A LEU* 3.7 30.7 - - + -
153A LEU* 3.9 12.3 - - + -
157A SER* 3.1 54.7 - - - +
160A PRO* 5.1 1.3 - - + -
161A LEU* 3.8 20.6 - - + -
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Residues in contact with GLN 130 (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 ASP* 3.0 37.9 + - - +
127A ALA* 3.4 10.4 - - - +
128A GLY 3.3 0.2 - - - -
129A LEU* 1.3 75.3 - - - +
131A LEU* 1.3 63.8 + - - +
133A CYS* 3.2 17.1 + - - +
134A GLU* 3.5 12.0 + - - +
156A ALA* 3.9 15.6 + - - +
157A SER* 4.6 1.2 - - - +
160A PRO* 3.8 29.6 - - + +
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Residues in contact with LEU 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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98A GLY 4.0 14.1 - - - +
99A ALA* 5.1 3.8 - - - +
101A CYS* 3.8 4.3 - - + +
102A GLY* 3.5 39.0 - - - +
105A SER* 2.8 25.2 + - - -
127A ALA 3.2 8.1 + - - +
128A GLY* 3.2 9.5 + - - +
130A GLN* 1.3 78.1 - - - +
132A LEU* 1.3 62.3 + - - +
134A GLU* 3.0 23.1 + - + +
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Residues in contact with LEU 132 (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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101A CYS* 4.3 9.4 - - + +
104A LEU* 3.6 39.9 - - + -
105A SER* 3.6 6.3 + - - +
108A LEU* 4.1 20.0 - - + +
117A LEU* 5.1 1.8 - - + -
119A LEU* 3.8 24.7 - - + -
124A LEU* 5.2 3.6 - - + -
128A GLY 3.0 13.4 + - - +
129A LEU* 3.2 28.3 - - + +
131A LEU* 1.3 77.5 - - - +
133A CYS* 1.3 61.3 + - - +
134A GLU 3.1 0.9 + - - -
135A GLY* 3.2 3.3 + - - -
136A LEU* 3.1 34.2 + - + +
146A LEU* 4.8 6.3 - - + -
148A LEU* 4.7 5.6 - - + -
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Residues in contact with CYS 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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129A LEU* 2.8 32.2 + - - +
130A GLN 3.6 9.9 - - - +
131A LEU 3.2 0.4 - - - -
132A LEU* 1.3 71.5 - - - +
134A GLU* 1.3 57.2 + - - +
135A GLY 3.4 0.2 - - - -
136A LEU* 3.6 17.0 - - - +
137A LEU* 2.9 39.3 + - + +
160A PRO* 3.7 40.6 - - + +
161A LEU* 4.2 7.2 - - - -
164A VAL* 4.1 13.5 - - + -
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Residues in contact with GLU 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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105A SER* 4.0 2.5 - - - +
109A ARG* 3.4 37.0 + - - +
130A GLN 3.5 8.2 + - - +
131A LEU* 3.0 24.2 + - + +
133A CYS* 1.3 79.2 - - - +
135A GLY* 1.3 60.0 + - - +
137A LEU* 3.7 7.7 + - + +
138A ASP 3.6 10.4 + - - -
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Residues in contact with GLY 135 (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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105A SER* 2.9 39.3 + - - -
108A LEU* 4.4 6.2 - - - +
109A ARG* 3.6 13.0 - - - +
132A LEU 3.2 1.3 + - - -
134A GLU* 1.3 73.7 - - - +
136A LEU* 1.3 65.2 + - - +
138A ASP* 3.0 19.2 + - - +
141A CYS* 3.3 10.6 - - - +
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Residues in contact with LEU 136 (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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108A LEU* 3.4 22.4 - - + +
129A LEU* 5.8 0.2 - - + -
132A LEU* 3.1 26.1 + - + +
133A CYS* 3.6 20.2 - - - +
135A GLY* 1.3 78.9 - - - +
137A LEU* 1.3 58.6 - - - +
138A ASP 3.4 2.1 + - - +
141A CYS* 3.7 25.2 - - - +
143A LEU* 3.9 25.6 - - + -
146A LEU* 3.9 26.0 - - + -
161A LEU* 5.2 2.0 - - + -
164A VAL* 3.7 34.3 - - + +
171A PHE* 5.8 2.5 - - + -
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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