Contacts of the strand formed by residues 157 - 162 (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 ALA 157 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155G GLY* 5.0 0.2 - - - -
156G ASP* 1.3 85.2 + - - +
158G VAL* 1.3 60.0 + - - +
159G VAL* 5.6 1.1 - - - +
170G SER 3.9 0.3 - - - +
171G ALA* 3.3 25.8 - - - +
172G SER 4.9 0.7 + - - -
206G THR* 3.9 16.4 - - + -
207G PHE 3.2 13.7 - - - +
208G ALA* 4.6 0.4 - - - -
209G LEU* 3.9 3.1 - - - +
254G LYS* 3.6 26.2 - - - +
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Residues in contact with VAL 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G LEU* 3.6 26.2 - - + -
157G ALA* 1.3 75.5 - - - +
159G VAL* 1.3 67.4 + - - +
160G ILE* 3.7 6.5 + - + +
169G PHE* 3.7 15.9 - - + -
170G SER 3.4 14.1 - - - +
205G LEU 3.6 1.4 - - - +
206G THR* 3.5 1.8 - - - -
207G PHE* 2.7 38.2 + - + +
209G LEU* 3.6 17.7 - - + +
212G LEU* 3.4 33.4 - - + -
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Residues in contact with VAL 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G ALA 5.6 1.1 - - - +
158G VAL* 1.3 73.2 - - - +
160G ILE* 1.3 61.2 + - - +
161G SER* 3.7 9.3 + - - +
168G LYS* 3.1 7.3 - - - +
169G PHE* 3.3 0.9 - - - -
170G SER* 2.9 46.8 + - - +
171G ALA* 5.9 0.7 - - - -
204G GLN* 3.9 31.4 - - + +
205G LEU 3.4 7.2 - - - +
206G THR* 4.0 20.4 - - + +
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Residues in contact with ILE 160 (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* 6.0 1.6 - - + -
158G VAL* 4.4 12.1 - - + +
159G VAL* 1.3 72.1 - - - +
161G SER* 1.3 60.2 + - - +
162G CYS 3.9 0.3 + - - -
167G VAL* 3.9 9.9 - - + -
168G LYS 3.3 3.1 - - - -
169G PHE* 3.7 37.0 - - + -
203G VAL 3.7 1.7 - - - +
204G GLN* 3.5 3.3 + - - -
205G LEU 2.8 31.4 + - - +
207G PHE* 3.5 34.3 - - + -
212G LEU* 5.0 3.8 - - + -
227G LEU* 5.4 4.7 - - + -
229G MET* 3.3 39.0 - - + +
235G LEU* 4.2 14.4 - - + -
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Residues in contact with SER 161 (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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159G VAL* 3.7 7.4 + - - +
160G ILE* 1.3 70.7 - - - +
162G CYS* 1.3 60.0 + - - +
163G ALA* 4.1 1.0 + - - +
166G GLY 4.2 0.7 - - - +
167G VAL* 3.4 2.7 - - - -
168G LYS* 2.6 64.6 + - - +
203G VAL 3.5 5.8 - - - -
204G GLN* 3.1 30.2 + - - +
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Residues in contact with CYS 162 (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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135G CYS* 3.3 38.6 - - - -
137G VAL* 4.2 7.4 - - - -
160G ILE 3.9 0.6 + - - -
161G SER* 1.3 74.2 - - - +
163G ALA* 1.3 62.9 + - - +
166G GLY 3.9 2.2 - - - -
167G VAL* 4.3 7.0 - - + +
197G ILE* 4.0 24.2 - - - -
199G MET* 4.7 0.2 - - - -
202G PRO* 3.2 7.8 - - - +
203G VAL* 2.9 37.1 + - + +
229G MET* 3.7 22.9 - - + -
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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