Contacts of the strand formed by residues 148 - 153 (chain G) in PDB entry 6O81
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 PHE 148 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119G ILE* 3.7 15.3 - - + -
120G LYS 4.6 0.4 - - - -
122G GLY* 4.6 1.6 - - - -
123G ALA* 3.3 26.2 - - + +
125G ILE* 3.8 16.6 - - + -
138G LEU* 3.6 25.8 - - + -
141G ALA* 3.7 28.3 - - + -
142G VAL* 3.6 24.5 - - + -
146G LYS* 3.9 23.3 + - + -
147G ARG* 1.3 78.5 - - - +
149G SER* 1.3 59.9 + - - +
150G VAL* 3.8 21.1 + - + +
173G VAL* 5.4 5.1 - - + +
174G PRO* 3.3 25.3 - - - +
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Residues in contact with SER 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G ALA 2.9 10.6 + - - -
124G THR* 3.3 16.8 - - - +
125G ILE 2.9 25.6 + - - +
148G PHE* 1.3 73.2 - - - +
150G VAL* 1.3 63.6 + - - +
151G TYR* 4.4 12.2 + - - -
174G PRO* 3.8 16.0 + - - +
176G THR* 4.7 5.2 + - - +
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Residues in contact with VAL 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G ILE* 3.5 7.6 - - + +
127G THR* 3.8 27.6 - - + +
138G LEU* 4.3 5.8 - - + -
148G PHE* 3.8 29.6 - - + +
149G SER* 1.3 75.9 + - - +
151G TYR* 1.3 60.6 + - - +
152G VAL* 4.1 2.5 - - + +
168G LEU* 4.2 25.8 - - + -
173G VAL* 5.2 4.3 - - + -
174G PRO 3.0 15.8 + - - +
175G VAL* 3.6 13.9 - - + -
176G THR* 2.8 37.6 + - - -
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Residues in contact with TYR 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G THR* 3.6 33.4 - - + -
125G ILE 2.9 13.6 + - - +
126G LEU* 3.3 9.5 - - + +
127G THR 2.9 26.0 + - - -
149G SER* 4.4 9.8 + - - -
150G VAL* 1.3 74.5 - - - +
152G VAL* 1.3 60.1 + - - +
176G THR* 3.3 29.8 - - + +
178G VAL* 4.2 15.0 - - + -
186G ILE* 3.7 39.5 - - + -
189G LYS* 3.4 34.7 + - + +
190G ALA* 5.4 1.8 - - + -
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Residues in contact with VAL 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G THR* 3.4 9.2 - - + +
128G HIS 3.9 9.9 - - - +
150G VAL* 5.1 2.5 - - + -
151G TYR* 1.3 72.8 - - - +
153G THR* 1.3 70.5 + - - +
161G GLY* 3.4 22.2 - - - +
164G MET* 3.8 21.1 - - + -
165G ALA* 3.8 23.1 - - + -
168G LEU* 6.4 0.2 - - + -
175G VAL* 3.8 13.0 - - + -
176G THR 2.9 18.3 + - - +
177G VAL* 3.6 13.9 - - + +
178G VAL* 2.9 26.8 + - - +
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Residues in contact with THR 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G LEU* 4.3 4.5 - - - +
127G THR 2.9 18.4 + - - -
128G HIS* 4.1 28.2 - - + +
152G VAL* 1.3 72.9 - - - +
154G GLU* 1.3 65.4 + - - +
155G SER* 3.2 11.5 + - - +
161G GLY* 3.3 20.3 - - - -
178G VAL* 4.1 7.1 - - - +
179G LEU 4.9 0.9 - - - +
180G ASP* 3.3 31.0 - - - +
183G VAL* 4.0 12.1 - - + +
211G GLY* 6.0 0.2 - - - -
215G MET* 3.8 18.5 - - - +
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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