Contacts of the strand formed by residues 250 - 256 (chain D) in PDB entry 3VD1
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 250 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A PHE* 6.2 3.4 - - + -
161D ILE 3.7 0.3 - - - +
162D GLN 3.5 0.2 - - - -
163D ILE* 2.5 68.7 + - - +
164D LYS* 4.5 2.4 - - - -
165D VAL* 5.0 0.9 - - - +
240D TYR* 4.1 15.4 + - + -
241D GLU* 2.7 38.8 - - + +
242D PRO 4.4 1.3 - - - -
243D PRO* 3.7 19.3 - - + +
249D PHE* 1.3 74.0 - - - +
251D THR* 1.3 59.0 + - - +
252D ILE* 4.3 7.9 - - + -
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Residues in contact with THR 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PHE* 3.9 26.2 - - - -
115A ILE* 4.2 20.5 + - - +
132D GLN* 5.7 2.9 - - - +
160D PRO* 5.6 5.6 - - + -
161D ILE 3.3 12.1 - - - +
162D GLN* 4.3 18.8 - - + +
249D PHE* 3.8 13.6 + - + +
250D THR* 1.3 78.3 - - - +
252D ILE* 1.3 64.5 + - - +
253D LEU* 5.5 4.7 - - - -
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Residues in contact with ILE 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PHE* 5.7 6.1 - - + -
159D CYS 3.6 2.4 - - - +
160D PRO* 3.7 0.3 - - - +
161D ILE* 3.0 33.8 + - + +
163D ILE* 3.8 28.7 - - + -
175D ILE* 5.1 13.2 - - + -
217D VAL* 4.3 13.9 - - + -
238D VAL* 4.6 17.7 - - + -
250D THR* 4.0 13.2 - - + +
251D THR* 1.3 80.8 - - - +
253D LEU* 1.3 65.3 + - - +
254D TYR* 3.1 48.2 + - + +
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Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ILE* 3.6 27.1 - - + +
184A ALA* 5.2 3.1 - - + -
187A VAL* 3.5 31.0 - - + -
188A THR* 3.6 20.2 - - + -
158D THR* 4.0 16.8 - - + -
159D CYS 3.6 2.2 - - - -
160D PRO* 3.7 29.4 - - + -
217D VAL* 3.5 3.6 - - - +
218D GLU* 2.9 49.2 + - + +
219D GLY* 5.4 0.2 - - - -
251D THR* 5.5 3.1 - - - -
252D ILE* 1.3 75.7 - - - +
254D TYR* 1.3 61.2 + - - +
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Residues in contact with TYR 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LYS 3.5 0.9 - - - +
159D CYS* 3.0 31.9 + - + +
161D ILE* 4.0 32.3 - - + -
163D ILE* 6.1 0.6 - - + +
175D ILE* 4.0 22.9 + - - +
177D ALA* 3.7 29.3 + - + +
215D ILE* 3.6 12.3 - - + -
216D ARG 3.1 15.7 - - - +
217D VAL* 3.3 24.4 - - + +
236D VAL* 3.8 2.8 + - + -
238D VAL* 5.4 2.4 - - - +
252D ILE* 3.1 32.2 - - + +
253D LEU* 1.3 72.5 - - - +
255D ASN* 1.3 73.9 + - - +
256D PHE* 3.6 24.0 - + + -
273D ILE* 6.4 0.7 - - + -
275D ILE* 4.6 13.2 - - + +
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Residues in contact with ASN 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D ALA 4.2 10.2 + - - +
157D LYS 3.6 15.5 + - - +
158D THR* 3.8 1.0 - - - +
214D LEU 3.4 2.4 - - - +
215D ILE* 3.5 3.1 - - - +
216D ARG* 2.6 61.6 + - + +
218D GLU* 2.8 41.6 + - - +
254D TYR* 1.3 94.7 + - - +
256D PHE* 1.3 66.9 + - - +
257D MET* 3.8 12.9 - - - +
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Residues in contact with PHE 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D LEU* 4.8 13.5 - - + -
153D CYS* 3.8 18.6 - - - -
155D ILE* 3.4 6.8 - - - +
156D ALA 2.8 29.0 + - - +
157D LYS 4.8 1.6 + - - -
159D CYS* 4.1 15.5 - - + -
161D ILE* 5.7 1.3 - - + -
214D LEU* 3.5 12.6 - - + -
215D ILE* 4.1 17.0 - - + -
254D TYR* 3.6 30.5 - + + -
255D ASN* 1.3 77.9 - - - +
257D MET* 1.3 60.6 + - - +
258D CYS 3.4 3.2 + - - +
273D ILE* 3.3 45.1 - - + -
290D PHE* 5.5 1.3 - + - -
292D GLY* 6.0 1.3 - - - -
294D ILE* 3.3 37.2 - - + -
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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