Contacts of the strand formed by residues 219 - 225 (chain A) in PDB entry 1I9R
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 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A PHE* 3.9 0.9 - - - +
178A CYS* 3.6 3.2 - - - -
179A SER* 2.7 25.7 + - - +
213A SER* 3.4 10.9 + - - -
215A ALA* 3.0 25.2 + - - +
218A CYS* 1.3 73.0 - - - +
220A GLN* 1.3 69.1 + - - +
221A GLN* 3.8 5.5 + - - +
188B PRO* 6.5 0.4 - - - -
211B THR* 3.6 6.5 - - - -
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Residues in contact with GLN 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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176A THR* 3.9 2.7 + - - +
177A PHE 3.0 8.7 - - - +
178A CYS* 3.6 13.7 - - - +
218A CYS 4.3 0.2 + - - -
219A GLY* 1.3 72.8 - - - -
221A GLN* 1.3 62.7 + - - +
248A SER* 3.3 29.0 + - - +
253A PHE* 3.0 45.0 - - - -
188B PRO* 3.9 25.6 - - + +
190B ILE* 5.0 1.9 - - - +
209B ALA* 3.2 20.4 - - + +
210B ASN* 3.6 0.3 - - - -
211B THR* 2.7 30.7 + - - +
57H ASP* 4.4 9.7 + - - +
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Residues in contact with GLN 221 (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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176A THR* 3.0 2.0 - - - -
177A PHE* 2.8 56.4 + - + +
179A SER* 5.5 0.2 + - - -
210A ASN* 3.0 42.1 + - - +
211A THR 3.6 20.8 + - - +
212A HIS 4.3 1.2 - - - +
213A SER* 4.3 11.3 - - - +
219A GLY 4.4 4.2 + - - +
220A GLN* 1.3 82.5 - - - +
222A SER* 1.3 60.9 + - - +
209B ALA 3.0 9.9 + - - -
210B ASN* 4.3 14.6 + - - +
211B THR* 4.3 6.7 - - - +
221B GLN* 4.7 4.4 - - - +
221C GLN* 4.7 5.4 - - - +
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Residues in contact with SER 222 (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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174A GLN* 4.1 5.4 + - - -
175A VAL 3.3 4.0 - - - -
176A THR* 2.9 24.5 - - - +
177A PHE* 5.3 0.2 - - - -
210A ASN* 4.2 12.5 + - - +
221A GLN* 1.3 74.6 - - - +
223A ILE* 1.3 68.2 + - - +
208B ALA* 3.2 25.4 - - - -
209B ALA 3.1 19.5 + - - -
210B ASN* 3.6 12.7 + - - +
223B ILE* 5.2 1.8 - - - -
224B HIS 6.0 1.6 - - - -
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Residues in contact with ILE 223 (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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173A ALA 4.8 0.9 - - - +
174A GLN* 3.3 7.3 - - - +
175A VAL* 2.5 58.3 + - + +
177A PHE* 4.2 7.4 - - + -
189A PHE* 4.1 25.6 - - + +
191A ALA* 4.2 9.9 - - + -
208A ALA* 3.6 43.1 - - + +
209A ALA 4.0 0.7 - - - +
210A ASN* 3.6 20.4 - - - +
222A SER* 1.3 79.5 - - - +
224A HIS* 1.3 64.1 + - - +
225A LEU* 4.2 9.2 - - + -
222C SER* 5.2 2.2 - - - -
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Residues in contact with HIS 224 (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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170A TYR* 4.6 0.8 + - - -
172A TYR* 4.5 16.3 - + + +
173A ALA 3.6 3.6 - - - -
174A GLN* 3.3 19.8 - - + +
208A ALA* 4.8 1.7 - - - +
223A ILE* 1.3 77.8 - - - +
225A LEU* 1.3 71.8 + - - +
170B TYR* 4.0 9.1 + - - -
224B HIS* 3.0 38.1 + + + +
226B GLY* 3.1 34.8 - - - -
174C GLN* 3.5 9.2 - - - +
222C SER* 6.0 0.9 - - - -
224C HIS* 3.1 54.7 + + + +
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Residues in contact with LEU 225 (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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171A ILE 3.3 0.9 - - - +
172A TYR* 2.8 25.2 - - - -
173A ALA* 3.1 32.6 + - + +
175A VAL* 6.5 0.2 - - + -
191A ALA* 4.3 5.8 - - + +
192A SER* 4.9 2.5 - - - +
193A LEU* 3.8 32.8 - - + +
206A LEU* 3.8 18.3 - - + +
207A ARG* 3.7 7.6 - - - -
208A ALA* 3.2 46.0 - - + +
223A ILE* 4.2 7.0 - - + -
224A HIS* 1.3 76.4 - - - +
226A GLY* 1.3 61.4 + - - +
239A VAL* 5.7 2.2 - - + -
174C GLN* 3.5 10.8 - - - +
224C HIS* 3.7 4.9 - - - -
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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