Contacts of the strand formed by residues 212 - 217 (chain A) in PDB entry 1SOT
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 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A VAL* 4.8 1.1 - - + -
85A MSE 3.9 28.3 - - + -
141A ILE* 4.0 16.8 - - + -
142A PRO 2.8 19.1 + - - +
143A ILE* 3.9 11.6 - - + +
144A ASN 5.3 3.1 + - - -
204A ALA* 3.7 21.3 - - + -
205A LEU 3.6 9.0 - - - +
206A VAL* 4.1 2.9 - - + +
210A GLY 3.7 1.0 + - - -
211A GLU* 1.3 72.2 - - - +
213A MSE 1.3 59.3 - - - +
214A GLY 3.2 28.5 - - - +
215A ILE* 4.3 16.8 - - + -
238A PHE* 3.2 39.0 - - + -
241A ALA* 5.9 1.3 - - + -
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Residues in contact with MSE 213 (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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147A ARG* 4.6 10.8 - - + -
148A VAL 5.3 0.2 - - - +
149A PRO* 3.9 32.6 - - + +
153A ASP* 3.6 31.2 - - + +
155A VAL* 3.9 17.9 - - + -
173A ILE* 4.3 6.7 - - + -
190A LEU* 3.9 9.6 - - + +
205A LEU* 2.7 22.2 + - + +
207A ASN* 3.3 55.2 - - + +
211A GLU* 3.3 1.5 + - - +
212A LEU* 1.3 76.8 - - - +
214A GLY* 1.3 55.2 + - - +
237A PRO* 3.8 5.4 - - - +
238A PHE* 2.9 28.5 + - - -
239A GLN* 4.7 0.3 + - - -
44C PRO* 5.0 2.0 - - + -
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Residues in contact with GLY 214 (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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190A LEU* 5.0 0.7 - - - -
204A ALA* 3.9 0.5 - - - -
205A LEU* 3.0 33.2 + - - +
212A LEU* 3.2 14.0 - - - +
213A MSE 1.3 80.6 - - - +
215A ILE* 1.3 63.5 + - - -
216A ASN 4.0 0.2 - - - -
235A ALA* 4.3 5.2 - - - -
236A ILE 3.1 15.3 - - - -
237A PRO* 4.5 0.2 - - - -
238A PHE* 3.7 7.6 - - - -
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Residues in contact with ILE 215 (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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83A VAL* 4.0 29.6 - - + -
92A ILE* 4.0 26.5 - - + -
93A THR 4.8 0.9 - - - +
94A ASN* 4.5 1.3 - - - +
127A LEU* 3.8 23.8 - - + -
202A GLY* 4.1 13.7 - - - +
203A GLY 3.6 6.7 - - - +
212A LEU* 4.3 15.0 - - + -
214A GLY* 1.3 76.8 - - - +
216A ASN* 1.3 73.1 + - - +
235A ALA* 3.1 3.8 - - - -
236A ILE* 3.0 31.6 + - + +
241A ALA* 3.8 25.8 - - + -
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Residues in contact with ASN 216 (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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94A ASN* 3.4 7.1 + - - +
157A ALA* 4.0 8.1 - - - +
158A ILE 4.1 2.4 + - - +
196A ILE* 3.6 33.2 - - + +
200A ASN* 3.5 20.1 - - - +
201A SER* 4.5 0.4 - - - -
202A GLY* 2.8 26.9 + - - -
203A GLY* 3.0 16.9 + - - +
204A ALA 3.2 16.2 + - - +
205A LEU* 3.3 37.6 - - - +
215A ILE* 1.3 73.0 - - - +
217A THR* 1.3 57.6 + - - +
234A PHE 3.7 5.4 - - - -
235A ALA* 3.9 3.0 - - - +
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Residues in contact with THR 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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94A ASN* 3.6 12.1 + - - +
126A ASP* 3.1 21.7 + - - +
189A PHE* 4.4 12.3 - - + -
196A ILE* 4.3 5.6 - - - +
201A SER* 3.9 0.9 - - - -
216A ASN* 1.3 76.5 - - - +
218A LEU* 1.3 57.3 + - - +
219A SER* 2.8 12.5 + - - -
220A PHE* 3.9 14.8 - - + -
234A PHE* 3.0 38.9 + - + +
235A ALA* 3.9 2.9 - - - +
236A ILE* 3.5 25.1 - - + -
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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