Contacts of the helix formed by residues 142 - 153 (chain A) in PDB entry 1AQJ
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 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A LEU* 3.8 27.8 - - + -
107A PRO* 3.7 30.3 - - + +
108A TYR 5.5 0.4 - - - -
109A GLY* 2.7 26.0 + - - +
110A ILE* 4.9 4.7 - - - +
111A VAL* 3.6 30.9 - - + +
129A TYR* 4.1 9.9 - - + -
136A TRP* 4.8 3.4 - - + -
141A ASN* 1.3 71.8 + - - +
143A TYR* 1.3 61.3 + - - +
145A ALA* 3.2 6.7 + - + +
146A PHE* 3.1 32.7 + - + -
500A SFG 5.8 3.4 - - - +
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Residues in contact with TYR 143 (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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106A PRO* 4.0 23.4 - - + +
107A PRO 3.3 16.8 + - - +
108A TYR* 4.1 7.0 - + + -
141A ASN* 3.0 40.3 + - + -
142A LEU* 1.3 76.3 - - - +
144A GLY* 1.3 65.3 + - - +
146A PHE* 3.9 1.7 - - - +
147A LEU* 3.2 29.0 + - + +
164A VAL* 3.9 15.3 - - + -
165A PRO* 3.6 28.7 + - + -
167A THR* 2.8 27.4 + - - -
168A TRP* 3.0 47.8 + + + +
174A PHE* 3.6 13.4 - + - -
177A LEU* 5.2 0.4 - - + -
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Residues in contact with GLY 144 (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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135A THR* 4.9 0.2 - - - -
140A TYR* 3.4 29.7 + - - -
141A ASN* 2.9 10.8 + - - +
143A TYR* 1.3 86.7 - - - +
145A ALA* 1.3 60.5 + - - +
147A LEU* 3.2 5.4 + - - +
148A GLU* 3.1 20.6 + - - +
174A PHE* 4.8 1.1 - - - -
177A LEU* 4.0 14.8 - - - +
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Residues in contact with ALA 145 (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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91A LEU* 3.7 25.1 - - + +
133A PHE* 3.9 26.7 - - + -
136A TRP* 4.3 17.3 - - + -
140A TYR* 3.7 5.5 - - - -
141A ASN 3.6 3.2 + - - -
142A LEU* 3.2 10.7 + - - +
144A GLY* 1.3 74.2 - - - +
146A PHE* 1.3 64.2 + - - +
148A GLU* 3.4 3.2 + - - +
149A LYS* 2.9 25.5 + - - +
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Residues in contact with PHE 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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46A PRO* 4.5 8.5 - - + -
47A ALA* 4.3 11.9 - - + -
90A PHE* 3.4 38.9 - + + -
91A LEU* 3.7 30.3 - - + -
106A PRO* 3.7 24.5 - - + -
107A PRO* 3.5 35.2 - - + -
142A LEU* 3.1 34.3 + - + +
143A TYR 3.9 1.6 - - - +
144A GLY 3.4 0.2 - - - -
145A ALA* 1.3 74.5 - - - +
147A LEU* 1.3 53.6 + - - +
149A LYS* 3.7 0.9 - - - +
150A ALA* 2.6 38.9 + - - +
162A PHE* 4.2 4.9 - - + -
500A SFG 3.5 29.4 - + - -
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Residues in contact with LEU 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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143A TYR* 3.2 29.6 + - + +
144A GLY 3.3 8.5 - - - +
146A PHE* 1.3 76.4 - - - +
148A GLU* 1.3 57.6 + - - +
150A ALA* 3.1 4.1 + - - +
151A VAL* 2.8 36.5 + - - +
160A LEU* 4.0 22.2 - - + -
162A PHE* 3.8 23.6 - - + -
164A VAL* 4.9 10.1 - - + -
168A TRP* 5.4 4.9 - - + -
177A LEU* 3.8 29.4 - - + -
180A PHE* 5.0 0.7 - - - -
181A LEU* 4.8 13.5 - - + -
206A ILE* 4.1 20.4 - - + -
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Residues in contact with GLU 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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133A PHE* 3.5 16.7 - - + +
134A SER* 2.9 27.8 + - - -
135A THR* 2.6 42.5 + - + +
144A GLY 3.1 10.5 + - - +
145A ALA* 3.4 6.7 + - - +
147A LEU* 1.3 79.0 - - - +
149A LYS* 1.3 63.6 + - - +
151A VAL* 3.3 2.4 + - - +
152A ARG* 2.7 54.0 + - - +
177A LEU* 4.6 1.5 - - + +
180A PHE* 3.7 29.8 - - + -
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Residues in contact with LYS 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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90A PHE* 3.3 41.5 - - + +
91A LEU* 3.9 21.4 + - + +
92A LEU 4.5 1.0 - - - -
93A TRP 2.8 29.3 + - - +
94A GLU* 3.6 18.0 + - - -
133A PHE* 4.1 13.6 - - + -
145A ALA 2.9 17.5 + - - +
146A PHE 3.7 2.7 - - - +
148A GLU* 1.3 76.1 - - - +
150A ALA* 1.3 55.1 + - - +
152A ARG* 2.7 31.8 + - + +
153A LEU* 3.2 29.4 + - + +
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Residues in contact with ALA 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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90A PHE* 4.1 9.6 - - + -
102A ILE* 3.3 30.1 - - + +
146A PHE 2.6 23.9 + - - +
147A LEU 3.3 4.3 - - - +
149A LYS* 1.3 72.8 - - - +
151A VAL* 1.3 61.4 + - - +
153A LEU* 3.1 11.7 + - - -
154A LEU* 3.4 4.7 + - - +
160A LEU* 3.5 21.1 - - + -
162A PHE* 3.9 18.4 - - + -
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Residues in contact with VAL 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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147A LEU* 2.8 24.8 + - + +
148A GLU 3.7 5.2 - - - +
150A ALA* 1.3 72.5 - - - +
152A ARG* 1.3 59.0 + - + +
154A LEU* 3.4 16.3 - - - +
160A LEU* 3.8 16.2 - - + -
180A PHE* 3.8 28.3 - - + -
181A LEU* 4.1 13.7 - - + -
184A GLU* 4.1 10.5 - - + +
208A PHE* 3.6 34.8 - - + -
210A LYS* 3.0 27.1 + - - -
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Residues in contact with ARG 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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98A ALA* 5.9 0.3 - - - +
132A ALA 4.3 12.1 + - - -
133A PHE* 5.4 2.0 - - - -
134A SER* 3.1 25.7 + - - +
148A GLU* 2.7 37.0 + - - +
149A LYS* 2.7 23.5 + - + +
151A VAL* 1.3 72.3 - - + +
153A LEU* 1.3 63.2 + - + +
154A LEU 3.3 4.4 + - - +
180A PHE* 4.1 20.8 - - + -
210A LYS* 4.1 10.1 + - - +
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 4.3 5.2 - - + -
90A PHE* 3.5 36.1 - - + -
93A TRP* 3.9 21.3 - - + -
94A GLU* 4.8 7.0 - - - +
95A PRO* 3.9 26.5 - - + +
97A GLU 5.0 1.8 - - - +
98A ALA* 3.4 8.0 - - - +
99A PHE* 2.5 42.6 + - + +
102A ILE* 4.1 7.0 - - + -
149A LYS* 3.7 25.8 - - + +
150A ALA 3.1 8.3 + - - +
152A ARG* 1.3 82.1 - - + +
154A LEU* 1.3 55.7 + - - +
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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