Contacts of the helix formed by residues 141 - 155 (chain s) in PDB entry 3J7Y
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 ALA 141 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140s ALA* 1.3 79.5 - - - +
142s LEU* 1.3 57.9 + - + +
144s ALA* 3.2 9.1 + - - +
145s VAL* 2.9 35.0 + - + +
187s LEU* 4.5 9.0 - - + -
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Residues in contact with LEU 142 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140s ALA 3.2 6.9 - - - +
141s ALA* 1.3 79.8 - - + +
143s ARG* 1.3 59.0 + - - +
145s VAL* 3.2 4.2 + - - +
146s ALA* 2.9 28.6 + - - +
184s LEU* 3.5 24.1 - - + +
187s LEU* 3.3 28.9 - - + -
188s LEU* 3.4 30.7 - - + -
191s HIS* 6.3 1.6 - - + +
418s LEU* 4.6 6.7 - - + -
422s VAL* 4.1 24.5 - - + -
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Residues in contact with ARG 143 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140s ALA* 3.2 19.8 + - - +
142s LEU* 1.3 78.7 - - - +
144s ALA* 1.3 60.0 + - - +
146s ALA* 3.2 4.3 + - - +
147s CYS* 2.9 38.5 + - - -
413s PHE* 3.7 46.7 + - + +
415s ASP* 5.1 18.7 + - - +
418s LEU* 3.7 16.7 - - + +
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Residues in contact with ALA 144 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140s ALA 2.9 12.8 + - - +
141s ALA* 3.3 12.6 - - - +
143s ARG* 1.3 77.5 - - - +
145s VAL* 1.3 57.0 + - + +
147s CYS* 3.2 10.2 + - - +
148s ASP* 2.9 33.5 + - - +
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Residues in contact with VAL 145 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1995 ALA 5.8 1.6 - - - +
2025 ILE* 6.4 0.2 - - + -
2855 TYR* 3.7 23.3 - - + +
141s ALA* 2.9 17.2 + - + +
142s LEU 3.2 9.4 + - - +
144s ALA* 1.3 77.7 - - + +
146s ALA* 1.3 55.3 + - - +
148s ASP* 3.2 9.0 + - - +
149s CYS* 2.9 32.9 + - - -
180s LEU* 5.9 0.7 - - + -
183s THR* 3.6 35.7 - - + +
184s LEU* 5.2 5.4 - - + +
187s LEU* 3.9 26.0 - - + -
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Residues in contact with ALA 146 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142s LEU 2.9 12.2 + - - +
143s ARG 3.4 8.7 - - - +
145s VAL* 1.3 77.4 - - - +
147s CYS* 1.3 57.4 + - - +
149s CYS* 3.2 5.4 + - - +
150s LEU* 2.9 35.0 + - + +
176s PHE* 4.4 1.0 - - - -
180s LEU* 4.3 19.5 - - + -
184s LEU* 6.1 0.6 - - + +
401s LEU* 5.9 1.6 - - + -
413s PHE* 3.7 21.3 - - + -
418s LEU* 3.9 18.8 - - + -
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Residues in contact with CYS 147 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143s ARG* 2.9 32.4 + - - -
144s ALA* 3.2 11.2 + - - +
146s ALA* 1.3 75.4 - - - +
148s ASP* 1.3 55.6 + - - +
150s LEU* 3.2 12.0 + - - +
151s LEU* 2.9 42.8 + - + +
410s VAL* 4.7 14.7 - - + +
413s PHE* 4.1 26.0 - - - -
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Residues in contact with ASP 148 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2025 ILE* 6.2 2.7 - - + -
2335 LYS* 4.8 1.2 - - - -
2835 TYR* 5.3 4.5 - - + -
2845 PRO* 3.3 38.1 - - - +
2855 TYR* 3.2 31.6 + - + -
144s ALA 2.9 15.1 + - - +
145s VAL* 3.4 11.2 - - - +
147s CYS* 1.3 76.9 - - - +
149s CYS* 1.3 57.6 + - - +
151s LEU* 3.2 15.6 + - - +
152s GLN* 2.9 32.4 + - - +
156s TYR* 5.0 1.7 - - - -
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Residues in contact with CYS 149 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2025 ILE* 4.6 9.0 - - - -
145s VAL* 2.9 27.1 + - - -
146s ALA* 3.4 10.8 - - - +
148s ASP* 1.3 78.5 - - - +
150s LEU* 1.3 63.7 + - - +
151s LEU 3.4 0.2 + - - -
152s GLN* 3.6 18.0 + - - +
153s GLU* 3.9 7.4 + - - +
176s PHE* 3.6 30.5 - - + +
179s GLN* 4.1 21.3 - - + -
180s LEU* 4.2 8.1 - - + -
183s THR* 3.9 25.4 - - - -
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Residues in contact with LEU 150 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146s ALA 2.9 14.0 + - - +
147s CYS* 3.4 8.5 - - - +
149s CYS* 1.3 76.1 - - - +
151s LEU* 1.3 62.5 - - - +
154s HIS* 3.1 37.4 + - - +
176s PHE* 3.3 35.7 - - + -
364s GLY 4.4 0.9 - - - +
401s LEU* 3.6 13.7 - - + -
402s TYR* 3.3 38.1 - - + +
405s ILE* 4.4 9.4 - - + -
410s VAL* 4.5 9.6 - - + -
413s PHE* 3.6 33.9 - - + -
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Residues in contact with LEU 151 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147s CYS* 2.9 29.0 + - + +
148s ASP* 3.5 15.5 - - - +
150s LEU* 1.3 76.4 - - + +
152s GLN* 1.3 61.1 + - - +
154s HIS* 3.0 4.3 + - - -
155s PHE* 2.7 35.1 + - + +
156s TYR* 3.4 34.6 + - + +
405s ILE* 4.6 12.6 - - + -
407s ASP 4.8 0.9 - - - +
408s ASN* 3.5 44.6 - - + +
409s ASP* 3.9 4.9 - - - +
410s VAL* 5.3 5.2 - - + +
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Residues in contact with GLN 152 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2025 ILE* 4.5 7.3 - - + +
2045 VAL* 3.0 23.6 - - - +
2795 PHE* 4.0 4.2 - - + -
2835 TYR* 2.7 37.6 + - + -
148s ASP 2.9 20.2 + - - +
149s CYS* 3.7 8.3 + - - +
150s LEU 3.6 0.2 - - - -
151s LEU* 1.3 73.8 - - - +
153s GLU* 1.3 84.5 + - + +
156s TYR* 3.3 14.7 + - - -
157s LEU* 2.7 40.4 + - + +
176s PHE* 5.8 0.2 - - - +
179s GLN* 3.6 29.1 - - - +
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Residues in contact with GLU 153 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2045 VAL* 6.0 0.2 - - - +
2065 ASN* 4.3 3.5 + - - -
149s CYS 3.9 4.5 + - - +
151s LEU 3.2 0.6 - - - -
152s GLN* 1.3 104.0 + - + +
154s HIS* 1.3 72.9 + - + +
155s PHE 3.4 0.7 + - - -
157s LEU* 3.5 20.9 - - - +
159s ARG* 2.5 54.8 + - - +
171s VAL 3.4 10.2 - - - +
172s ILE* 3.5 26.6 - - + +
175s PRO* 3.7 16.6 - - - +
176s PHE* 4.0 19.5 - - + +
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Residues in contact with HIS 154 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150s LEU* 3.1 33.6 - - + +
151s LEU* 3.0 4.0 + - - +
153s GLU* 1.3 80.7 - - + +
155s PHE* 1.3 60.5 + - + +
172s ILE* 3.4 33.4 - - + +
176s PHE* 5.1 8.2 - - + -
364s GLY* 5.3 8.4 + - - -
402s TYR* 3.2 23.3 + - - -
405s ILE* 3.6 25.7 - - + +
407s ASP 5.1 0.7 - - - +
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Residues in contact with PHE 155 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2805 GLN* 4.1 35.3 - - + +
2815 GLU* 4.7 3.4 - - + -
151s LEU* 2.7 18.2 + - + +
152s GLN 3.8 0.2 - - - -
153s GLU 3.3 1.6 - - - -
154s HIS* 1.3 75.6 - - + +
156s TYR* 1.3 112.4 + + - +
157s LEU 3.3 11.7 + - - +
158s ARG* 5.1 0.9 - - - +
405s ILE* 5.9 0.4 - - + -
407s ASP* 3.0 37.2 - - + +
408s ASN* 3.6 28.5 - - + -
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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