Contacts of the strand formed by residues 250 - 256 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162C GLN* 3.3 0.9 - - - -
163C ILE* 2.6 52.8 + - + +
164C LYS* 5.8 0.3 - - - -
175C ILE* 6.1 0.2 - - + -
240C TYR* 3.6 10.5 - - + -
241C GLU* 2.7 46.0 + - + +
243C PRO* 3.3 20.4 - - + +
249C PHE* 1.3 71.4 - - - +
251C THR* 1.3 64.4 + - - +
252C ILE* 3.6 21.9 + - + -
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Residues in contact with THR 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C PRO* 4.2 20.4 - - + -
161C ILE 3.5 11.9 - - - +
162C GLN* 3.5 20.6 - - + +
244C GLN* 5.8 0.5 + - - -
249C PHE* 4.0 5.0 + - - -
250C THR* 1.3 76.5 - - - +
252C ILE* 1.3 64.6 + - - +
253C LEU* 3.6 12.9 + - + +
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Residues in contact with ILE 252 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161C ILE* 3.0 31.8 + - + +
163C ILE* 4.1 22.7 - - + -
175C ILE* 4.1 21.3 - - + -
217C VAL* 4.5 10.8 - - + -
220C ASN* 5.9 2.0 - - - +
238C VAL* 3.5 31.2 - - + -
239C PRO 5.5 1.6 - - - +
241C GLU* 6.2 0.9 - - + +
250C THR* 3.6 14.5 + - + -
251C THR* 1.3 71.0 - - - +
253C LEU* 1.3 61.5 + - - +
254C TYR* 3.2 41.0 + - + +
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Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158C THR* 4.5 9.4 - - - +
159C CYS 3.2 10.3 - - - +
160C PRO* 3.9 14.8 - - + -
217C VAL* 4.0 4.0 - - + +
218C GLU* 2.9 77.5 + - + +
219C GLY* 5.0 4.5 - - - +
220C ASN* 6.2 0.4 - - + -
251C THR* 4.3 12.3 - - + +
252C ILE* 1.3 74.9 - - - +
254C TYR* 1.3 62.4 + - - +
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Residues in contact with TYR 254 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159C CYS* 2.5 38.4 + - + +
161C ILE* 3.3 43.5 - - + -
175C ILE* 3.6 25.5 + - + +
177C ALA* 3.4 29.7 - - + +
215C ILE* 3.8 12.1 - - + -
216C ARG 3.6 14.4 - - - -
217C VAL* 3.6 24.0 - - + +
236C VAL* 4.2 1.8 - - + -
238C VAL* 5.1 0.7 - - - +
252C ILE* 3.2 25.7 - - + +
253C LEU* 1.3 72.7 - - - +
255C ASN* 1.3 75.5 + - - +
256C PHE* 4.4 19.1 - + + -
273C ILE* 6.4 1.1 - - + -
275C ILE* 3.9 6.1 - - + +
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Residues in contact with ASN 255 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156C ALA* 4.4 9.0 + - - +
157C LYS 3.2 21.1 + - - +
158C THR* 3.4 12.1 - - - +
215C ILE* 3.3 10.0 - - - +
216C ARG* 2.9 39.8 + - + +
218C GLU* 3.5 30.0 + - - +
254C TYR* 1.3 92.3 + - - +
256C PHE* 1.3 70.5 + - - +
257C MET* 3.9 17.0 - - - +
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Residues in contact with PHE 256 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151C LEU* 4.1 14.4 - - + -
153C CYS* 3.8 22.2 - - + -
154C GLN 4.7 2.0 + - - +
155C ILE* 3.8 0.5 - - - -
156C ALA* 2.6 36.5 + - - +
157C LYS 4.8 1.4 + - - -
159C CYS* 3.8 29.2 - - + -
161C ILE* 6.5 0.2 - - + -
214C LEU* 3.5 11.0 - - + -
215C ILE* 4.0 19.1 - - + -
254C TYR* 4.4 13.7 - + + -
255C ASN* 1.3 81.6 - - - +
257C MET* 1.3 61.0 + - - +
258C CYS 3.6 2.0 + - - +
271C ILE* 5.4 0.9 - - + -
273C ILE* 3.5 38.8 - - + -
290C PHE* 5.8 0.9 - + - -
294C ILE* 3.5 34.1 - - + -
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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