Contacts of the strand formed by residues 214 - 219 (chain B) in PDB entry 1V2E
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 THR 214 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B LEU* 3.2 34.5 - - + +
190B SER* 4.3 6.1 - - - -
206B LEU* 4.1 16.5 - - + +
207B ARG* 4.1 22.9 + - - +
210B ALA* 3.1 19.9 + - - +
211B PRO* 4.3 4.1 + - - +
212B GLU 3.9 0.2 - - - -
213B ARG* 1.3 78.9 - - - +
215B PHE* 1.3 71.3 + - - +
216B THR* 4.1 11.3 + - - +
235B VAL 3.9 2.3 - - - +
236B GLY* 3.8 4.3 - - - -
237B PRO* 3.4 18.2 - - - +
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Residues in contact with PHE 215 (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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3A LEU* 5.2 0.9 - - + -
94B LEU* 4.3 21.8 - - + -
98B LEU* 3.8 33.7 - - + -
187B PHE* 3.7 24.7 - + - -
188B LEU 2.7 16.3 + - - +
189B ILE* 3.7 5.2 - - + +
190B SER 2.9 26.7 + - - +
213B ARG 4.3 3.6 - - - -
214B THR* 1.3 73.6 - - - +
216B THR* 1.3 62.5 + - - +
217B VAL* 3.9 0.5 + - - +
234B ILE* 4.3 6.1 - - + -
235B VAL 3.8 1.6 - - - -
236B GLY* 4.0 13.0 - - - -
237B PRO* 4.1 11.9 - - + -
240B PHE* 3.6 36.6 - + + -
241B MET* 4.4 4.9 - - - -
244B LEU* 4.0 27.6 - - + -
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Residues in contact with THR 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PHE* 4.5 11.0 - - + -
190B SER* 3.5 3.1 - - - -
192B GLU* 3.5 38.5 + - + +
195B ASP* 6.0 0.2 - - - +
205B ARG* 4.0 11.4 - - - +
207B ARG* 3.9 28.8 - - - +
214B THR* 4.1 4.9 + - - +
215B PHE* 1.3 74.6 - - - +
217B VAL* 1.3 66.9 + - - +
218B GLY 4.3 0.2 + - - -
233B TRP* 3.6 1.3 - - - +
234B ILE* 3.3 5.4 - - - -
235B VAL* 2.7 51.5 + - - +
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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
----------------------------------------------------------
87B ALA* 3.7 22.4 - - + +
90B ALA* 3.5 35.0 - - + -
91B LEU* 4.6 9.4 - - + -
94B LEU* 3.5 28.0 - - + -
189B ILE* 5.1 0.2 - - + -
190B SER 2.8 16.3 + - - +
191B ASP* 4.2 12.3 - - - -
192B GLU* 2.8 34.1 + - - +
193B VAL* 3.5 3.3 + - + -
215B PHE 4.8 0.7 - - - +
216B THR* 1.3 81.1 - - - +
218B GLY* 1.3 60.6 + - - +
233B TRP* 3.3 4.9 - - - +
234B ILE* 4.2 2.9 - - + -
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Residues in contact with GLY 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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74B PHE* 6.0 0.2 - - - -
87B ALA* 3.7 8.0 - - - +
192B GLU 4.5 2.5 - - - -
193B VAL* 3.7 12.1 - - - -
195B ASP* 5.2 2.7 - - - -
217B VAL* 1.3 76.2 - - - +
219B SER* 1.3 62.7 + - - -
232B GLY* 3.5 2.6 - - - -
233B TRP* 3.0 52.5 + - - +
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Residues in contact with SER 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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87B ALA* 4.0 0.4 - - - -
193B VAL* 3.4 26.5 + - - +
218B GLY* 1.3 75.1 - - - -
220B ALA* 1.3 63.7 + - - +
221B GLY* 3.0 14.7 + - - -
222B LYS* 3.2 12.0 + - - +
223B ARG* 3.1 24.3 + - - +
231B VAL 4.0 4.2 + - - -
233B TRP* 3.7 10.4 - - - -
1510B PLP 2.7 31.4 + - - -
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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