Contacts of the helix formed by residues 141 - 152 (chain G) in PDB entry 6S1M
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 141 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139G MET 3.3 2.0 + - - -
140G PRO* 1.3 71.4 - - - +
142G GLY* 1.3 58.1 + - - +
144G PHE* 3.2 3.6 + - - +
145G ALA* 2.8 30.8 + - - +
219G THR* 3.5 21.1 + - - +
222G SER 2.5 29.0 + - - -
223G SER* 2.8 14.2 + - - -
224G THR 4.1 3.8 - - - -
225G VAL* 3.8 11.4 - - - -
239G TYR* 4.0 20.1 + - - -
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Residues in contact with GLY 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G PRO* 3.2 3.7 - - - +
141G SER* 1.3 79.6 + - - +
143G GLU* 1.3 58.5 + - - +
145G ALA* 3.4 6.7 + - - +
146G ARG* 2.9 30.1 + - - +
219G THR* 4.0 7.8 - - - +
223G SER 4.5 0.6 + - - -
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Residues in contact with GLU 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F GLU* 4.5 13.3 - - - +
110F LYS* 3.9 32.5 + - + +
139G MET* 4.2 1.6 - - - +
140G PRO* 3.3 38.1 + - + +
142G GLY* 1.3 71.9 - - - +
144G PHE* 1.3 68.5 + - - +
146G ARG* 3.2 7.3 + - - +
147G ILE* 2.9 31.8 + - + +
182G LEU* 4.0 21.1 - - + +
193G GLU 5.1 1.9 - - - +
195G VAL* 3.7 16.0 - - - +
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Residues in contact with PHE 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139G MET* 4.1 15.0 - - + -
140G PRO 3.2 10.8 + - - +
141G SER 3.5 7.0 - - - +
143G GLU* 1.3 78.9 - - - +
145G ALA* 1.3 64.4 + - - +
147G ILE* 3.1 10.2 + - + +
148G CYS* 3.0 41.8 + - - -
160G ILE* 6.0 1.8 - - + -
169G PHE* 4.5 14.4 - + - -
212G LEU* 4.4 20.6 - - + -
215G PHE* 5.4 0.9 - - + -
216G THR* 4.0 16.8 - - + -
225G VAL* 3.8 20.2 - - + -
227G LEU* 3.7 41.7 - - + -
235G LEU* 5.9 0.4 - - + -
237G VAL* 4.1 9.6 - - + -
239G TYR* 3.8 19.3 - - - -
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Residues in contact with ALA 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G SER 2.8 20.2 + - - +
142G GLY* 3.5 9.0 - - - +
144G PHE* 1.3 74.0 - - - +
146G ARG* 1.3 63.6 + - - +
148G CYS* 3.1 5.7 + - - +
149G ARG* 3.0 23.1 + - - +
213G ASN* 4.9 0.5 - - - +
216G THR* 3.8 22.4 + - - +
219G THR* 3.8 19.3 - - + +
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Residues in contact with ARG 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F LYS* 4.8 2.2 - - - +
80F LYS 2.8 25.6 + - - -
81F CYS 3.7 1.4 - - - -
82F ALA 3.2 28.4 + - - +
83F GLY* 4.5 11.6 - - - -
110F LYS* 4.4 11.0 - - - +
142G GLY 2.9 18.0 + - - +
143G GLU* 3.2 7.2 + - - +
145G ALA* 1.3 74.7 - - - +
147G ILE* 1.3 64.7 + - - +
149G ARG* 3.0 41.3 + - - +
150G ASP* 2.7 52.3 + - - +
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Residues in contact with ILE 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F LYS* 4.2 14.1 - - - +
139G MET* 4.6 1.3 - - - -
143G GLU* 2.9 24.5 + - + +
144G PHE* 3.3 15.0 - - + +
146G ARG* 1.3 74.8 - - - +
148G CYS* 1.3 62.7 + - - +
150G ASP* 3.3 2.4 + - - +
151G LEU* 3.0 44.1 + - + +
169G PHE* 3.7 43.1 - - + -
180G ILE* 3.7 27.6 - - + -
182G LEU* 4.0 23.1 - - + -
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Residues in contact with CYS 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G PHE* 3.0 43.7 + - - +
145G ALA 3.6 7.4 - - - +
147G ILE* 1.3 80.6 - - - +
149G ARG* 1.3 57.4 + - - +
152G SER* 2.6 33.8 + - - -
169G PHE* 6.4 0.7 - - - -
209G LEU* 4.0 14.1 - - + +
212G LEU* 3.7 26.0 - - + -
213G ASN* 3.3 18.2 + - - +
216G THR* 4.5 7.6 - - + -
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Residues in contact with ARG 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F LYS* 4.9 3.0 + - - +
145G ALA 3.0 11.3 + - - +
146G ARG* 3.0 52.6 + - - +
148G CYS* 1.3 75.0 - - - +
150G ASP* 1.3 73.0 + - - +
152G SER* 3.1 18.8 - - - -
153G HIS* 3.7 26.6 + - - +
213G ASN* 3.9 8.0 + - - +
16T G 5.7 9.4 - - - -
17T G 4.7 16.4 + - - -
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Residues in contact with ASP 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F LYS 3.9 1.4 - - - +
81F CYS* 3.2 41.4 - - + +
110F LYS* 4.4 5.5 + - - -
112F SER* 5.7 0.5 + - - -
114F TYR* 3.7 17.2 + - - +
146G ARG* 2.7 56.0 + - - +
147G ILE* 3.6 7.6 + - - +
149G ARG* 1.3 79.3 + - - +
151G LEU* 1.3 63.8 + - - +
153G HIS* 2.9 25.5 + - - +
154G ILE* 3.9 1.9 + - - +
180G ILE* 4.3 7.9 - - + +
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Residues in contact with LEU 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F TYR* 4.4 8.1 - - - +
147G ILE* 3.0 23.6 + - + +
150G ASP* 1.3 78.0 - - - +
152G SER* 1.3 55.8 + - - +
154G ILE* 2.7 32.1 + - + +
155G GLY 3.1 12.3 + - - +
158G VAL* 3.6 15.9 - - + -
169G PHE* 3.5 34.3 - - + -
170G SER* 4.2 2.0 - - - +
171G ALA* 4.3 12.5 - - + +
178G GLY 4.1 22.7 - - - +
180G ILE* 4.0 17.5 - - + -
209G LEU* 3.6 20.7 - - + +
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Residues in contact with SER 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F LYS* 5.0 1.4 + - - -
148G CYS 2.6 19.1 + - - -
149G ARG* 3.1 17.2 + - - -
150G ASP 3.0 0.2 + - - -
151G LEU* 1.3 77.4 - - - +
153G HIS* 1.3 64.3 + - - +
154G ILE 3.3 0.4 + - - -
155G GLY 3.7 15.3 + - - +
209G LEU* 3.7 9.8 - - - +
213G ASN* 2.7 24.5 + - - -
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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