Contacts of the strand formed by residues 216 - 220 (chain A) in PDB entry 3STJ
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 GLY 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A GLN* 3.2 8.3 - - - +
178A THR* 2.8 48.4 + - - +
180A ALA 5.3 1.3 + - - -
182A ILE* 4.3 12.3 - - - -
204A ALA 3.7 5.8 - - - -
205A ILE* 4.1 9.6 - - - -
215A ILE* 1.3 73.7 - - - +
217A PHE* 1.3 63.5 + - - -
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Residues in contact with PHE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ARG* 4.4 5.8 - - + -
167A LEU* 3.7 29.6 - - + -
169A LEU* 4.2 10.8 - - + -
175A PHE* 3.7 31.4 - - + -
176A ILE 3.2 4.5 - - - -
177A GLN* 3.5 30.5 - - + -
178A THR* 5.6 0.2 - - - -
182A ILE* 4.9 2.3 - - - +
202A ASN* 3.8 4.3 - - - +
203A THR 2.9 28.8 + - - -
204A ALA* 2.7 34.1 + - + +
205A ILE* 4.2 1.6 - - - -
206A LEU* 3.8 28.9 - - + -
215A ILE* 3.7 27.4 - - + -
216A GLY* 1.3 78.2 - - - -
218A ALA* 1.3 54.4 + - - +
150C LEU* 4.3 7.4 - - + -
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Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A PHE* 3.4 8.7 - - - -
176A ILE* 2.9 34.7 + - + +
178A THR* 5.6 1.1 - - + -
191A LEU* 3.9 21.1 - - + -
200A GLY* 4.2 2.9 - - - -
201A ILE 3.3 19.3 - - - +
202A ASN* 3.7 20.6 - - - +
203A THR 4.2 0.2 - - - +
217A PHE* 1.3 74.8 - - - +
219A ILE* 1.3 62.0 + - - +
220A PRO 3.4 0.9 - - - -
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Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ASN* 3.6 15.9 - - - +
111A SER 3.2 27.6 - - - +
112A ASP 3.7 5.4 - - - +
113A ILE* 3.5 29.8 - - + -
172A LEU 6.1 0.4 - - - +
175A PHE* 3.8 16.6 - - + -
200A GLY* 3.0 1.6 - - - -
201A ILE* 2.8 41.6 + - + +
203A THR* 3.2 23.9 + - + +
218A ALA* 1.3 69.7 - - - +
220A PRO* 1.3 81.9 - - + +
223A MET* 4.0 20.0 - - + -
224A ALA* 4.2 1.6 - - + +
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Residues in contact with PRO 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A SER* 3.4 21.8 - - - +
174A ASN* 3.2 43.7 - - - +
176A ILE* 3.7 13.2 - - + +
199A ILE 3.6 6.5 - - - +
218A ALA 3.4 6.0 - - - +
219A ILE* 1.3 89.9 - - + +
221A SER* 1.3 60.5 + - - +
222A ASN* 3.3 1.1 - - + +
223A MET* 3.2 20.7 + - + +
224A ALA* 2.9 24.3 + - - +
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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