Contacts of the strand formed by residues 193 - 198 (chain A) in PDB entry 3IIY
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 ILE 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A TYR* 3.4 21.0 - - - +
149A THR* 4.3 2.5 - - + +
166A ALA* 3.8 22.9 - - + -
167A GLY* 3.0 14.7 + - - +
170A GLY* 3.5 33.7 - - - +
171A ILE 3.8 2.0 - - - +
172A ILE* 3.7 28.9 - - + -
188A GLY* 6.1 0.9 - - - +
191A ASN 4.0 2.7 - - - +
192A ALA* 1.3 74.8 - - - +
194A ASN* 1.3 61.9 + - - +
195A GLU 3.5 23.1 - - - +
196A LEU* 4.0 9.9 - - + -
208A SER* 4.2 9.2 - - - +
209A VAL 3.4 9.0 - - - +
210A SER* 4.8 5.8 - - - -
218A TRP* 6.5 0.2 - - + -
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Residues in contact with ASN 194 (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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148A TYR* 4.0 16.6 - - - -
149A THR* 3.8 6.5 - - - -
192A ALA* 4.6 4.9 - - - +
193A ILE* 1.3 77.0 - - - +
195A GLU* 1.3 56.1 + - - +
209A VAL* 2.8 10.8 + - + -
210A SER 4.1 0.2 - - - -
211A LYS 4.0 10.7 - - - +
238A GLU* 3.1 26.2 + - - +
239A VAL 2.7 29.7 + - - +
240A LEU* 3.6 24.1 - - - +
365A TYR* 2.5 35.5 + - + -
367A ARG* 2.8 8.0 + - - -
26B M3L 4.4 6.1 - - - -
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Residues in contact with GLU 195 (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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100A GLN* 5.6 1.7 + - - -
149A THR* 3.7 14.2 + - - +
193A ILE* 3.5 7.8 - - - +
194A ASN* 1.3 80.2 - - - +
196A LEU* 1.3 72.7 + - - +
197A LYS* 4.0 24.9 + - + -
207A LEU 4.1 0.4 - - - +
208A SER* 3.6 1.2 - - - -
209A VAL* 3.1 38.0 + - + +
240A LEU 3.6 10.8 - - - +
241A SER* 2.8 28.2 + - - -
242A ALA 3.8 10.4 + - - +
311A CYS* 5.6 0.7 - - - -
367A ARG* 3.5 27.6 + - - +
415A GLN* 4.5 10.2 + - - -
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Residues in contact with LEU 196 (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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100A GLN* 5.7 1.0 + - - -
149A THR* 3.4 22.6 + - + +
150A CYS* 4.5 2.3 - - - +
151A ALA* 4.0 17.6 - - + +
164A ALA* 3.8 34.8 - - + +
165A VAL* 3.9 8.1 - - - +
166A ALA* 3.9 19.5 - - + +
172A ILE* 4.1 17.7 - - + -
193A ILE* 4.0 7.0 - - + -
195A GLU* 1.3 76.3 - - - +
197A LYS* 1.3 77.6 + - - +
206A LEU* 4.1 12.8 - - + -
207A LEU 3.4 6.5 - - - +
208A SER* 3.5 29.6 - - - -
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Residues in contact with LYS 197 (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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100A GLN* 5.5 8.7 - - - +
151A ALA* 4.7 3.1 - - + -
195A GLU* 4.0 24.1 + - + -
196A LEU* 1.3 82.9 - - - +
198A PHE* 1.3 60.9 + - - +
206A LEU* 3.6 6.2 - - - +
207A LEU* 2.8 49.7 + - + +
242A ALA* 3.0 35.6 + - + +
243A ASP* 3.5 21.6 + - - +
244A TYR* 3.7 18.0 - - + -
312A VAL 4.4 5.3 + - - -
313A ARG* 5.0 8.3 - - - +
415A GLN* 6.4 0.2 - - - +
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Residues in contact with PHE 198 (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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104A HIS* 6.1 0.9 - - + -
151A ALA* 3.8 30.5 - - + +
152A TRP 3.4 22.0 - - - +
153A THR* 3.4 28.0 - - + +
164A ALA* 4.1 11.0 - - + -
174A ILE* 5.1 0.2 - - + -
197A LYS* 1.3 74.5 - - - +
199A HIS* 1.3 68.3 + - - +
200A PRO* 3.5 2.6 - - - +
203A PRO* 3.2 28.9 - - + -
205A LEU 3.5 13.0 - - - -
206A LEU* 3.7 37.9 - - + -
220A ILE* 3.9 16.4 - - + -
244A TYR* 3.4 11.0 - - - -
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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