Contacts of the helix formed by residues 142 - 153 (chain a) in PDB entry 5A0Q
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 142 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25Z TYR* 4.2 15.6 + - - -
136a LYS* 5.4 0.4 - - - -
137a ALA* 3.4 33.4 - - - -
138a GLY* 3.7 12.0 + - - -
139a GLY 2.8 22.2 + - - -
140a SER 3.3 1.5 + - - -
141a ALA* 1.3 77.4 - - - +
143a ALA* 1.4 59.5 + - - +
146a GLN* 3.0 35.3 + - - +
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Residues in contact with ALA 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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144J GLN* 2.8 43.9 - - + +
25Z TYR* 4.0 18.2 - - + -
140a SER 4.8 3.8 + - - +
141a ALA 3.2 0.8 - - - -
142a SER* 1.4 81.6 + - - +
144a MET* 1.3 62.5 + - + +
147a PRO* 3.4 12.3 - - - +
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Residues in contact with MET 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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25I VAL* 3.7 42.0 - - + -
144J GLN* 5.2 7.4 - - - +
146J TYR* 5.4 1.3 - - + -
147J GLY* 3.6 41.7 - - - +
148J MET* 4.0 4.1 + - - +
140a SER 5.9 0.4 - - - +
141a ALA* 3.0 18.2 + - + +
143a ALA* 1.3 78.6 - - + +
145a LEU* 1.3 64.4 + - + +
147a PRO* 4.3 5.5 - - - +
148a LEU* 4.5 2.8 - - - +
182a ALA* 4.9 5.8 - - + +
185a ARG* 3.6 27.6 - - + -
186a ASP* 3.6 31.0 - - + -
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Residues in contact with LEU 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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147J GLY 5.9 1.1 - - - +
11a THR* 3.4 32.5 - - + -
13a LEU* 5.3 1.6 - - + -
137a ALA* 4.0 19.7 - - + -
141a ALA* 3.1 16.4 + - + +
142a SER 3.3 0.6 + - - +
144a MET* 1.3 81.0 - - + +
146a GLN* 1.3 67.8 + - - +
147a PRO* 3.6 0.4 - - - -
148a LEU* 3.4 5.4 + - + +
149a LEU* 3.0 33.3 + - + +
178a VAL* 3.3 47.3 - - + +
179a PHE* 4.2 14.4 - - + -
181a SER* 5.8 0.9 - - - -
182a ALA* 4.0 12.6 - - + +
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Residues in contact with GLN 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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176J ARG* 2.7 43.8 + - - +
25Z TYR* 3.2 20.2 - - + +
27Z ALA 4.9 3.4 + - - -
135a PHE* 3.8 26.6 + - - -
136a LYS* 3.5 21.6 - - - +
137a ALA* 3.0 36.4 + - + +
142a SER 3.0 15.3 + - - +
145a LEU* 1.3 75.6 - - - +
147a PRO* 1.3 58.8 - - + +
149a LEU* 4.4 6.4 - - - +
150a ASP* 2.9 25.5 + - - +
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Residues in contact with PRO 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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144J GLN* 3.6 37.9 - - - +
148J MET* 4.2 11.2 - - + -
172J ASN* 3.6 38.3 - - + +
173J ALA 4.3 0.4 - - - +
176J ARG* 3.2 11.1 - - - +
143a ALA 3.4 15.5 - - - +
144a MET 4.3 2.7 - - - +
145a LEU 3.8 1.3 - - - -
146a GLN* 1.3 90.8 - - + +
148a LEU* 1.4 57.9 + - - +
150a ASP* 3.7 4.1 - - + +
151a ASN* 3.1 26.0 + - - +
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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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202I TYR* 5.8 1.3 - - + +
147J GLY 3.6 21.3 - - - +
148J MET* 3.6 36.6 - - - +
151J SER* 3.7 21.1 - - - +
152J LEU* 4.3 12.8 - - + -
144a MET 4.5 4.5 - - - +
145a LEU* 3.4 8.7 + - + +
146a GLN 3.3 0.4 - - - -
147a PRO* 1.4 76.4 - - - +
149a LEU* 1.3 63.7 + - - +
151a ASN* 3.0 18.2 + - - +
152a GLN* 3.4 16.5 + - + +
174a LEU* 4.7 9.2 - - + -
178a VAL* 3.3 35.0 - - + -
181a SER* 5.2 3.1 - - - +
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Residues in contact with LEU 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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13a LEU* 2.9 46.9 - - + -
15a ILE* 4.1 13.0 - - + -
135a PHE* 3.5 40.4 - - + -
145a LEU* 3.0 21.2 + - + +
146a GLN* 4.1 4.3 - - - +
148a LEU* 1.3 87.0 - - + +
150a ASP* 1.4 58.0 + - - +
152a GLN 4.9 0.2 - - - +
153a VAL* 2.9 40.9 + - + +
174a LEU* 5.2 6.7 - - + +
175a VAL* 5.5 0.4 - - - -
178a VAL* 4.1 16.2 - - + -
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Residues in contact with ASP 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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176J ARG* 3.9 15.0 + - - +
135a PHE* 3.1 35.2 - - + -
146a GLN 2.9 20.5 + - - +
147a PRO* 3.7 5.8 - - + +
149a LEU* 1.4 77.1 - - - +
151a ASN* 1.4 59.9 + - - +
154a GLY* 2.8 32.2 + - - -
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Residues in contact with ASN 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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204I CYS* 4.2 15.0 - - - -
148J MET* 4.8 3.6 - - + +
152J LEU* 5.7 0.8 - - - +
168J GLN* 3.7 18.2 + - - +
172J ASN* 3.7 26.8 + - - +
147a PRO 3.1 14.2 + - - +
148a LEU* 3.0 13.6 + - - +
150a ASP* 1.4 80.4 - - - +
152a GLN* 1.3 78.9 + - + +
153a VAL 3.6 0.3 + - - -
154a GLY 4.4 6.5 + - - -
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Residues in contact with GLN 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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202I TYR* 2.0 82.1 - - + +
203I ARG 4.5 5.2 + - - +
204I CYS* 4.9 3.3 - - - -
152J LEU* 6.0 2.2 - - + -
148a LEU* 3.4 14.1 + - + +
149a LEU 3.8 0.4 + - - -
151a ASN* 1.3 96.4 + - - +
153a VAL* 1.3 59.9 + - - +
164a VAL* 5.7 2.1 - - - +
170a ARG* 3.3 36.0 + - - +
174a LEU* 3.6 12.4 - - + +
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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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15a ILE* 4.5 20.2 - - + -
134a SER* 5.3 5.0 + - - +
135a PHE* 4.0 18.3 - - + -
149a LEU* 2.9 31.3 + - + +
152a GLN* 1.3 79.5 - - - +
154a GLY* 1.3 59.2 + - - +
164a VAL* 4.3 21.3 - - + +
166a LEU* 5.7 8.5 - - + -
174a LEU* 3.2 30.1 - - + -
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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