Contacts of the strand formed by residues 148 - 153 (chain C) in PDB entry 6ACQ
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 LEU 148 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214B LYS 4.3 1.3 - - - +
215B ALA* 3.5 29.2 - - + +
218B LEU* 3.6 27.1 + - + +
219B GLY* 3.4 26.7 - - - -
139C PHE* 4.3 2.1 - - - -
140C PHE* 3.3 54.4 + - + +
146C MET* 3.3 6.7 - - + +
147C LYS* 1.3 81.7 - - - +
149C VAL* 1.3 66.5 + - - +
150C GLU* 4.7 1.3 - - + -
174C LYS* 5.0 0.5 - - - +
175C ASP 3.5 15.7 - - - +
177C VAL* 4.1 21.8 - - + -
187C VAL* 4.2 2.0 - - + -
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Residues in contact with VAL 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C MET* 4.3 15.5 - - + -
138C HIS 3.2 15.3 - - - +
139C PHE* 4.5 13.7 - - + -
147C LYS 4.0 0.2 - - - +
148C LEU* 1.3 80.6 - - - +
150C GLU* 1.3 67.6 + - - +
151C VAL* 3.9 21.3 - - + -
169C SER* 3.9 18.2 - - - +
174C LYS* 3.6 33.9 - - + -
175C ASP 3.3 6.3 + - - +
176C PRO* 3.4 2.4 - - + +
177C VAL* 3.2 25.5 + - - +
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Residues in contact with GLU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B ALA* 4.7 0.6 - - + +
136C GLY 3.5 1.2 - - - +
137C MET* 3.7 0.3 - - - -
138C HIS* 2.8 61.8 + - + +
140C PHE* 3.5 22.4 - - + -
148C LEU* 4.7 4.3 - - + -
149C VAL* 1.3 73.5 - - - +
151C VAL* 1.3 63.3 + - - +
152C ILE* 3.5 16.9 + - + +
177C VAL* 3.9 15.9 - - + -
179C VAL* 4.3 4.2 - - + +
184C GLY 5.0 0.2 - - - +
185C PHE* 3.5 15.8 - - - +
186C VAL* 3.0 34.7 + - - +
187C VAL* 3.2 14.3 + - + +
188C ASN* 5.3 0.7 + - - -
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Residues in contact with VAL 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C ILE* 3.5 22.9 - - + -
136C GLY 3.3 5.8 - - - +
137C MET* 5.1 0.2 - - + -
149C VAL* 3.9 17.9 - - + -
150C GLU* 1.3 74.1 - - - +
152C ILE* 1.3 59.7 + - - +
153C ARG* 3.6 2.3 + - - +
162C PHE* 3.4 35.2 - - + +
165C VAL* 4.0 19.7 - - + -
166C LYS* 5.1 2.5 - - - -
169C SER* 4.6 1.3 - - - +
176C PRO* 3.9 17.5 - - + -
177C VAL 2.9 17.2 + - - +
178C GLU* 3.8 1.0 - - - -
179C VAL* 2.9 26.7 + - - +
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Residues in contact with ILE 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C THR 5.5 0.7 - - - +
121C ILE* 4.0 14.7 - - + +
135C ILE* 3.4 4.8 - - - +
136C GLY* 2.7 50.0 + - - +
138C HIS* 4.6 2.9 - - + -
150C GLU* 3.6 30.3 - - + +
151C VAL* 1.3 72.0 - - - +
153C ARG* 1.3 62.5 + - - +
154C GLY 3.5 2.6 + - - -
179C VAL* 3.2 14.1 - - + +
180C ALA 4.6 0.2 - - - -
181C GLU* 3.9 22.7 - - + -
185C PHE* 3.5 56.5 - - + -
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Residues in contact with ARG 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C ILE* 4.8 1.6 - - + -
151C VAL 4.7 0.7 - - - +
152C ILE* 1.3 70.7 - - - +
154C GLY* 1.3 68.3 + - - +
157C THR* 3.4 39.5 + - + +
159C GLN* 3.2 44.5 + - - +
162C PHE* 4.1 26.8 - - + +
178C GLU* 2.9 38.3 + - + -
179C VAL 2.8 14.6 + - - +
180C ALA* 3.7 8.5 - - + +
181C GLU* 2.9 28.0 + - - +
262E LYS* 5.1 0.9 + - - -
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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