Contacts of the helix formed by residues 145 - 157 (chain A) in PDB entry 1X1O
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 LEU 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A TRP* 3.9 20.0 - - + -
110A LEU* 4.7 13.0 - - + -
113A ARG* 4.7 14.4 - - + +
114A LEU* 5.8 2.5 - - + -
142A THR* 2.9 27.0 + - + +
143A PRO 3.7 9.9 - - - +
144A GLY* 1.3 83.5 - - - +
146A ARG* 1.3 65.8 + - - +
147A ALA 3.4 2.2 - - - -
148A LEU* 3.2 12.9 + - + -
149A GLU* 2.9 35.2 + - + +
142B THR* 4.3 15.3 - - + -
143B PRO* 3.5 33.7 - - + +
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Residues in contact with ARG 146 (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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138A THR 5.7 0.9 - - - -
139A ARG* 3.2 34.5 + - - +
141A THR* 2.8 35.4 + - + +
142A THR 3.6 2.8 + - - -
144A GLY 3.6 0.4 - - - -
145A LEU* 1.3 77.0 - - - +
147A ALA* 1.3 63.2 + - - +
149A GLU* 3.2 1.0 + - - +
150A LYS* 2.9 49.3 + - + +
163A TYR* 2.8 50.1 + - + +
164A GLY* 3.9 0.2 - - - -
24B GLU* 3.2 31.0 + - - +
25B ASP* 2.8 47.8 + - - +
105B ARG* 4.7 1.0 - - - +
109B ASN* 4.4 7.1 - - - +
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Residues in contact with ALA 147 (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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10A TRP* 3.5 21.2 - - + +
11A GLN* 3.3 31.6 - - - +
144A GLY 5.6 0.2 + - - -
145A LEU 3.4 0.4 - - - -
146A ARG* 1.3 77.8 - - - +
148A LEU* 1.3 59.1 + - + +
150A LYS* 3.5 3.0 + - - +
151A TYR* 3.0 27.5 + - - +
154A ARG* 4.9 2.1 + - - -
163A TYR* 3.3 18.2 + - - +
24B GLU* 4.7 0.2 + - - -
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Residues in contact with LEU 148 (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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10A TRP* 3.5 27.8 - - + -
14A LEU* 3.8 28.0 - - + -
21A TRP* 4.0 25.1 - - + -
59A TRP* 5.0 0.7 - - + -
60A VAL* 4.1 27.8 - - + -
110A LEU* 4.4 14.4 - - + -
114A LEU* 3.6 27.1 - - + +
144A GLY 5.8 0.2 - - - +
145A LEU* 3.2 15.0 + - + +
147A ALA* 1.3 82.3 - - + +
149A GLU* 1.3 57.7 + - - +
151A TYR* 3.3 8.0 + - + +
152A ALA* 3.0 21.5 + - - +
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Residues in contact with GLU 149 (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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113A ARG* 2.6 25.9 + - - +
114A LEU* 4.4 6.1 - - + -
117A ILE* 3.4 23.8 - - + +
141A THR* 3.1 16.7 - - + +
142A THR* 2.5 51.1 + - - -
145A LEU* 2.9 26.8 + - + +
146A ARG* 3.9 2.9 - - - +
148A LEU* 1.3 73.3 - - - +
150A LYS* 1.3 62.3 + - - +
152A ALA* 3.2 4.3 + - - +
153A VAL* 3.0 31.3 + - - +
271A THR* 4.0 10.6 - - + -
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Residues in contact with LYS 150 (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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137A ASP* 2.8 33.9 + - - +
138A THR 4.7 3.6 + - - -
141A THR* 5.2 7.6 - - + -
146A ARG* 2.9 34.9 + - + +
147A ALA* 3.9 4.0 - - - +
149A GLU* 1.3 73.4 - - - +
151A TYR* 1.3 65.4 + - - +
153A VAL* 3.3 3.3 + - - -
154A ARG* 3.1 28.3 + - - +
160A ASN* 3.1 28.9 + - - +
161A HIS 3.0 26.1 + - - -
162A ARG 3.5 8.9 + - - -
163A TYR* 3.6 37.4 - - + +
271A THR* 5.6 0.9 - - + -
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Residues in contact with TYR 151 (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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10A TRP* 3.7 25.4 - + + -
56A ALA* 4.9 1.6 - - + -
57A GLY* 4.3 9.0 - - - -
59A TRP* 2.9 29.6 + + - -
80A GLU* 2.6 41.0 + - - +
114A LEU* 5.3 3.4 - - + -
147A ALA 3.0 15.5 + - - +
148A LEU* 3.4 15.7 - - + +
150A LYS* 1.3 78.8 - - - +
152A ALA* 1.3 65.8 + - + +
154A ARG* 3.0 32.4 + - + +
155A VAL* 2.9 38.9 + - + +
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Residues in contact with ALA 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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56A ALA* 4.6 2.7 - - + -
114A LEU* 3.5 37.2 - - + +
117A ILE* 3.7 15.5 - - + -
118A ALA* 3.6 8.5 - - - +
148A LEU 3.0 13.6 + - - +
149A GLU 3.2 9.6 + - - +
151A TYR* 1.3 82.9 - - + +
153A VAL* 1.3 61.6 + - - +
155A VAL* 3.2 8.9 + - - +
156A GLY 3.0 18.2 + - - -
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Residues in contact with VAL 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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117A ILE* 3.9 13.7 - - + -
121A THR* 3.4 20.1 - - + +
137A ASP* 4.0 21.3 - - + -
149A GLU 3.0 18.5 + - - +
150A LYS* 3.5 9.6 - - - +
151A TYR 3.2 0.4 - - - -
152A ALA* 1.3 75.5 - - - +
154A ARG* 1.3 61.4 + - - +
156A GLY 3.2 6.6 + - - -
157A GLY 3.2 0.2 + - - -
158A GLY* 2.9 42.7 + - - -
159A ARG 3.9 16.6 - - - +
160A ASN* 4.0 5.4 - - - +
270A LEU* 4.3 10.8 - - + -
271A THR* 4.1 10.1 - - + -
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Residues in contact with ARG 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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10A TRP* 4.6 7.5 - - - -
147A ALA 4.9 2.0 + - - -
150A LYS* 3.1 23.1 + - - +
151A TYR* 3.0 40.9 + - + +
153A VAL* 1.3 77.7 - - - +
155A VAL* 1.3 63.3 + - + +
157A GLY* 2.9 14.7 + - - -
158A GLY 3.6 13.6 - - - +
159A ARG* 5.5 0.2 - - - -
160A ASN* 2.7 50.5 + - - +
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Residues in contact with VAL 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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54A VAL* 4.3 0.9 - - + -
55A LEU 3.7 11.4 - - - +
56A ALA* 3.9 13.0 - - + -
80A GLU* 4.4 2.9 - - + +
81A GLY* 3.3 32.4 - - - +
118A ALA* 4.2 4.5 - - + -
122A ARG* 3.1 17.2 + - - -
151A TYR* 2.9 56.9 + - + +
152A ALA 3.2 7.4 + - - +
154A ARG* 1.3 77.1 - - + +
156A GLY* 1.3 59.2 + - - +
157A GLY* 3.3 0.9 + - - -
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Residues in contact with GLY 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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118A ALA* 3.5 26.4 - - - +
121A THR* 4.0 5.6 - - - -
122A ARG* 3.1 40.5 - - - -
125A VAL* 4.0 2.8 - - - +
152A ALA 3.0 12.7 + - - -
153A VAL 3.2 3.8 + - - -
154A ARG 3.1 0.4 - - - -
155A VAL* 1.3 76.0 - - - +
157A GLY* 1.3 58.8 + - - +
158A GLY 3.6 2.0 - - - -
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Residues in contact with GLY 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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122A ARG* 5.4 0.9 - - - -
125A VAL* 3.5 20.6 - - - +
154A ARG 2.9 12.2 + - - -
155A VAL 3.1 1.7 - - - -
156A GLY* 1.3 79.5 - - - +
158A GLY* 1.3 64.8 + - - +
159A ARG* 4.9 5.5 - - - +
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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