Contacts of the strand formed by residues 152 - 157 (chain F) in PDB entry 6CP3
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 LYS 152 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C LYS* 4.6 8.9 - - - +
148F ALA* 4.8 1.1 + - - +
151F GLY* 1.3 78.3 - - - +
153F ILE* 1.3 65.8 + - - +
154F GLY 4.3 0.2 - - - -
293F GLN* 2.8 55.9 + - - +
294F GLU* 4.1 8.7 + - - +
296F ILE* 3.1 27.4 + - + +
297F THR* 5.4 1.1 - - - +
304F VAL 5.3 0.4 - - - +
306F SER* 3.3 25.1 - - - +
308F GLN* 4.2 2.2 - - - +
328F HIS 3.4 20.7 + - - +
329F LEU* 3.8 13.9 - - + -
330F ASP* 3.2 29.0 + - - +
331F ALA* 3.3 8.5 + - - +
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Residues in contact with ILE 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F LEU* 5.3 4.5 - - + -
147F TYR* 3.6 70.4 - - + +
148F ALA 4.3 8.5 - - - +
152F LYS* 1.3 81.2 - - - +
154F GLY* 1.3 64.6 + - - +
155F LEU* 4.9 1.3 - - + -
305F THR* 4.2 19.1 - - + -
306F SER 3.0 12.3 + - - +
307F VAL* 3.8 29.7 - - + +
308F GLN* 2.8 30.9 + - - +
329F LEU* 4.4 2.5 - - - -
331F ALA* 3.7 5.8 - - + +
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Residues in contact with GLY 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F LYS 4.3 0.4 - - - -
153F ILE* 1.3 73.8 - - - +
155F LEU* 1.3 68.5 + - - +
156F PHE* 3.7 4.9 - - - -
308F GLN 3.5 5.8 - - - -
310F VAL* 5.3 0.7 - - - -
329F LEU* 3.7 27.4 - - - +
331F ALA 3.1 11.1 + - - +
332F THR* 3.6 2.4 - - - -
333F THR* 3.1 26.2 + - - -
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Residues in contact with LEU 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F TYR* 3.6 24.2 - - + +
153F ILE* 4.9 2.0 - - + -
154F GLY* 1.3 80.6 - - - +
156F PHE* 1.3 66.2 + - - +
157F GLY* 3.3 3.3 + - - -
163F LYS* 4.3 12.4 - - + +
166F PHE* 3.6 31.9 - - + -
167F ILE* 3.7 30.1 - - + -
307F VAL* 4.2 15.7 - - + -
308F GLN 3.1 11.8 + - - +
309F ALA* 3.8 5.8 - - + -
310F VAL* 3.0 21.7 + - - +
333F THR* 3.7 15.5 - - + -
335F LEU* 5.1 11.2 - - + -
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Residues in contact with PHE 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F GLY* 4.6 3.6 - - - -
155F LEU* 1.3 71.0 - - - +
157F GLY* 1.3 57.4 + - - +
310F VAL* 3.6 27.8 - - + -
312F VAL* 4.6 8.1 - - + -
317F LEU* 5.0 5.6 - - + -
322F PRO* 3.4 33.7 - - + -
325F THR* 4.1 2.0 - - - -
326F PHE* 3.4 56.3 - + + -
329F LEU* 3.7 31.0 - - + -
332F THR* 3.8 15.7 - - + -
333F THR 3.1 13.0 + - - +
334F VAL* 4.6 8.5 - - + +
335F LEU* 2.8 29.4 + - - +
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Residues in contact with GLY 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F LEU 3.3 1.4 + - - -
156F PHE* 1.3 75.7 - - - +
158F GLY* 1.3 67.6 + - - +
161F VAL* 4.5 0.2 - - - -
163F LYS* 3.4 24.0 - - - +
310F VAL 3.0 9.1 + - - -
311F TYR* 3.7 0.9 - - - -
312F VAL* 3.4 25.3 + - - +
335F LEU* 3.8 15.0 - - - -
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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