Contacts of the strand formed by residues 214 - 219 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A LEU* 3.3 26.0 - - + +
190A SER* 4.6 4.5 - - - -
206A LEU* 3.7 15.6 + - + -
207A ARG* 3.8 27.7 + - - +
210A ALA 2.7 24.3 + - - -
211A PRO 3.3 5.4 + - - +
212A GLU 3.7 0.2 - - - -
213A ARG* 1.3 76.6 - - - +
215A PHE* 1.3 68.8 + - - +
216A THR* 3.9 18.8 + - - +
235A VAL 3.8 1.4 - - - +
236A GLY* 3.5 6.6 - - - -
237A PRO* 3.3 20.8 - - - +
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Residues in contact with PHE 215 (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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94A LEU* 4.1 21.3 - - + -
98A LEU* 4.1 25.1 - - + -
187A PHE* 3.7 30.7 - + - -
188A LEU 2.7 18.7 + - - +
189A ILE* 3.5 2.8 - - - +
190A SER* 2.7 33.1 + - - +
213A ARG 4.5 1.3 - - - -
214A THR* 1.3 74.1 - - - +
216A THR* 1.3 58.4 + - - +
217A VAL* 3.9 1.5 + - - +
234A ILE* 3.8 19.3 - - + -
235A VAL 3.8 1.1 - - - -
236A GLY* 4.3 10.1 - - - -
237A PRO* 4.3 5.2 - - + -
240A PHE* 3.8 30.1 - + + -
241A MET* 3.9 14.1 - - - -
244A LEU* 3.6 24.2 - - + -
3B LEU* 4.9 0.7 - - + -
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Residues in contact with THR 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PHE* 4.1 23.1 - - + -
190A SER* 3.6 3.8 - - - -
192A GLU* 2.9 33.7 + - + +
195A ASP* 5.9 0.2 - - - +
205A ARG* 4.2 1.8 - - - +
207A ARG* 3.6 24.7 + - - +
214A THR* 3.9 12.5 - - - +
215A PHE* 1.3 73.4 - - - +
217A VAL* 1.3 68.0 + - - +
218A GLY 4.1 0.2 + - - -
233A TRP* 3.7 1.9 - - - +
234A ILE* 3.6 3.3 - - - -
235A VAL* 2.9 44.8 + - - +
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA* 3.7 30.5 - - + +
90A ALA* 4.0 23.8 - - + -
91A LEU* 4.2 15.7 - - + -
94A LEU* 3.8 29.2 - - + -
189A ILE* 5.0 0.4 - - + -
190A SER 2.7 18.1 + - - +
191A ASP* 4.2 7.4 - - - +
192A GLU* 2.9 34.7 + - - +
193A VAL* 3.4 4.7 + - + -
215A PHE 4.8 1.1 - - - +
216A THR* 1.3 78.4 - - - +
218A GLY* 1.3 61.3 + - - +
233A TRP* 3.5 5.8 - - - +
234A ILE* 4.9 4.0 - - + -
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Residues in contact with GLY 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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74A PHE* 6.0 0.2 - - - -
87A ALA* 3.8 6.4 - - - +
192A GLU 4.6 2.2 - - - -
193A VAL* 4.0 11.9 - - - -
195A ASP* 5.4 2.7 - - - -
216A THR* 5.9 0.4 - - - -
217A VAL* 1.3 75.7 - - - +
219A SER* 1.3 60.7 + - - -
232A GLY* 3.4 2.9 - - - -
233A TRP* 3.0 56.4 + - - +
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Residues in contact with SER 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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87A ALA* 3.9 0.9 - - - -
193A VAL* 3.6 29.6 + - - +
218A GLY* 1.3 75.4 - - - -
220A ALA* 1.3 64.4 + - - +
221A GLY* 3.5 10.6 + - - -
222A LYS* 3.4 12.7 + - - +
223A ARG* 3.1 26.0 + - - +
231A VAL 4.1 3.9 + - - -
232A GLY* 4.2 0.7 - - - -
233A TRP* 3.9 7.3 - - - -
510A PLP 2.4 32.3 + - - -
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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