Contacts of the strand formed by residues 215 - 219 (chain B) in PDB entry 1V1A
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 GLU 215 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ARG* 3.4 20.5 + - - +
188B ASP 3.3 10.3 + - - +
189B LEU* 3.3 19.4 - - + +
190B LEU 3.0 22.9 + - - -
213B ALA* 3.1 1.2 - - - +
214B PRO* 1.3 81.4 - - + +
216B VAL* 1.3 68.9 + - - +
217B VAL* 5.1 0.7 - - + -
228B PHE 3.2 3.6 - - - -
229B VAL* 3.7 29.1 - - + +
257B TYR* 2.6 34.5 + - + +
270B ARG* 3.0 26.0 + - - -
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Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LEU* 3.4 28.3 - - + +
192B LEU* 5.4 5.2 - - + -
208B LEU* 4.4 16.2 - - + -
211B LEU 4.2 9.6 - - - +
212B SER* 4.9 0.9 - - - -
213B ALA* 3.6 35.4 - - + +
215B GLU* 1.3 80.8 - - - +
217B VAL* 1.3 68.7 + - - +
218B LEU* 5.8 0.7 - - - -
227B ALA 3.5 0.2 - - - -
228B PHE* 2.7 61.6 + - + +
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 4.2 8.1 - - + -
190B LEU 2.9 9.6 + - - +
191B PHE* 3.5 14.0 - - + +
192B LEU* 3.0 27.3 + - - +
215B GLU* 5.1 0.7 - - + -
216B VAL* 1.3 79.8 - - - +
218B LEU* 1.3 62.7 - - - +
219B LYS* 3.8 0.9 + - - +
225B ALA* 4.5 0.7 - - + -
226B TRP 3.3 7.4 - - - +
227B ALA* 4.2 7.0 - - + -
253B PHE* 3.3 39.3 - - + -
257B TYR* 3.7 42.2 - - + +
271B LEU* 4.4 9.2 - - + -
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B LEU* 3.2 32.1 - - + +
193B SER 3.7 3.8 - - - +
194B GLU* 3.7 37.9 - - + +
197B ALA* 4.6 0.2 - - + -
204B VAL* 3.5 27.6 - - + -
208B LEU* 4.6 8.3 - - + -
216B VAL* 4.2 0.8 - - + -
217B VAL* 1.3 71.8 - - - +
219B LYS* 1.3 59.9 + - - +
220B ARG* 3.3 4.8 + - + +
225B ALA* 3.1 8.6 - - - +
226B TRP* 2.8 69.6 + - + +
228B PHE* 4.4 9.6 - - + -
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Residues in contact with LYS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B ASP* 2.9 34.7 + - - -
165B ASN* 5.0 1.4 + - - +
191B PHE* 4.2 7.7 - - - +
192B LEU 2.7 34.0 + - - +
193B SER* 3.3 10.1 - - - +
194B GLU* 2.9 25.5 + - - +
196B GLU* 5.9 0.4 - - - -
217B VAL 5.0 1.6 - - - +
218B LEU* 1.3 68.4 - - - +
220B ARG* 1.3 57.6 + - - +
221B GLY 3.4 4.5 + - - -
225B ALA* 4.0 1.3 - - - -
250B GLY* 3.4 18.6 + - - -
253B PHE* 3.3 41.3 - - + -
1303B ADP 3.5 46.0 + - - +
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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