Contacts of the strand formed by residues 213 - 219 (chain A) in PDB entry 4IJ3
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 VAL 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A GLU* 3.7 6.9 - - - +
187A TYR* 3.4 26.5 - - + +
189A ALA* 4.3 12.8 - - + +
207A LEU* 4.4 28.3 - - + +
210A HIS* 3.5 14.9 + - + +
211A LYS 3.4 0.7 - - - -
212A GLY* 1.3 80.5 - - - +
214A ALA* 1.3 76.7 + - - +
215A VAL* 4.4 4.6 + - + +
263A LEU* 4.8 4.0 - - + +
266A LEU* 4.1 14.6 - - + -
269A LEU* 3.4 23.6 - - + -
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Residues in contact with ALA 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A PHE* 3.4 38.1 - - + -
185A GLU* 3.7 12.5 - - + +
187A TYR 3.0 4.8 + - - +
188A LEU* 3.5 5.0 - - + +
189A ALA 2.8 26.5 + - - -
213A VAL* 1.3 78.6 - - - +
215A VAL* 1.3 61.5 + - - +
216A ARG* 5.5 2.9 - - + -
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Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A PRO* 5.6 2.1 - - - +
167A PRO* 4.4 6.8 - - - +
189A ALA* 3.5 9.9 - - + +
191A ILE* 3.8 30.1 - - + -
200A GLY 4.3 2.2 - - - +
203A VAL* 4.3 2.0 - - + +
204A ALA* 3.7 44.3 - - + +
207A LEU* 4.2 20.9 - - + -
213A VAL* 4.7 4.5 - - + +
214A ALA* 1.3 78.8 - - - +
216A ARG* 1.3 75.2 + - - +
263A LEU* 4.2 17.7 - - + -
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Residues in contact with ARG 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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167A PRO* 3.8 32.3 + - - +
169A GLU* 3.3 35.8 + - - +
170A PRO 3.7 2.8 + - - -
171A ALA* 3.6 33.1 - - + +
175A GLU* 3.2 35.0 + - - +
176A ILE* 5.7 0.4 - - + -
179A PHE* 5.3 8.7 - - + -
188A LEU* 3.9 22.4 - - + +
189A ALA 2.9 9.7 + - - +
190A LEU* 3.4 12.0 - - + +
191A ILE* 3.1 23.5 + - - +
200A GLY* 6.4 0.2 - - - -
214A ALA* 4.2 2.2 - - + -
215A VAL* 1.3 87.6 - - - +
217A ARG* 1.3 59.9 + - - +
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Residues in contact with ARG 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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155A GLU* 4.3 2.4 + - - -
168A LEU* 3.0 29.4 + - - +
169A GLU* 3.8 3.5 + - - +
170A PRO* 3.5 37.0 - - + +
171A ALA* 2.8 27.7 + - - +
191A ILE* 3.4 10.8 - - - +
193A GLU* 2.9 34.9 + - + +
195A GLY* 5.1 5.9 - - - -
196A GLY 5.2 0.8 - - - +
197A SER 4.1 2.2 + - - -
200A GLY* 4.8 10.3 - - - -
201A ARG* 3.6 45.2 - - - +
216A ARG* 1.3 75.4 - - - +
218A VAL* 1.3 64.4 + - - +
219A LEU* 3.7 19.6 - - - +
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Residues in contact with VAL 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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171A ALA* 4.6 8.1 - - + +
176A ILE* 3.9 24.9 - - + -
190A LEU* 4.5 9.0 - - + -
191A ILE 3.0 6.8 + - - +
192A PHE* 3.2 41.5 - - + +
193A GLU* 3.0 25.6 + - - -
216A ARG 4.5 6.1 - - - +
217A ARG* 1.3 80.7 - - - +
219A LEU* 1.3 71.9 + - - +
222A GLU* 4.1 7.9 - - + -
225A VAL* 3.5 22.4 - - + -
226A VAL* 4.9 0.9 - - + -
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Residues in contact with LEU 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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170A PRO* 3.8 28.1 - - + +
193A GLU* 3.3 6.3 - - - +
194A LYS 4.3 1.3 - - - +
195A GLY* 4.1 25.6 - - - +
217A ARG* 3.7 28.0 - - - +
218A VAL* 1.3 80.9 - - - +
220A ASN* 1.3 65.4 + - - +
221A THR* 2.9 23.2 + - - +
222A GLU* 3.0 28.2 + - + +
226A VAL* 3.9 3.2 - - - +
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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