Contacts of the strand formed by residues 250 - 256 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162L GLN* 3.7 0.7 - - - -
163L ILE* 2.7 50.3 + - + +
175L ILE* 5.1 4.3 - - + -
240L TYR* 3.9 11.9 + - + -
241L GLU* 2.6 43.5 + - + +
243L PRO* 3.1 22.9 - - + +
249L PHE* 1.3 74.0 - - - +
251L THR* 1.3 67.4 + - - +
252L ILE* 4.8 9.4 - - + -
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Residues in contact with THR 251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184I ALA* 4.7 20.4 - - + -
132L GLN* 4.7 4.5 + - - -
160L PRO* 4.5 9.4 - - - +
161L ILE 3.3 16.7 + - - -
162L GLN* 4.6 7.0 - - - +
249L PHE* 4.6 6.7 - - - +
250L THR* 1.3 81.6 - - - +
252L ILE* 1.3 68.5 + - - +
253L LEU* 4.3 7.1 + - + +
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Residues in contact with ILE 252 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159L CYS 3.5 3.1 - - - +
160L PRO* 3.5 0.2 - - - +
161L ILE* 2.7 43.7 + - + +
163L ILE* 4.0 11.9 - - + -
175L ILE* 3.9 23.8 - - + -
217L VAL* 4.1 13.2 - - + -
238L VAL* 3.8 29.4 - - + -
250L THR* 4.8 8.3 - - + -
251L THR* 1.3 79.4 + - - +
253L LEU* 1.3 70.0 + - - +
254L TYR* 3.5 44.3 + - + +
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Residues in contact with LEU 253 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184I ALA* 4.0 17.0 - - + +
185I GLU* 3.6 42.6 - - + +
158L THR* 3.9 24.0 - - + -
159L CYS 3.4 1.8 - - - -
160L PRO* 4.0 19.5 - - + -
217L VAL* 3.4 11.1 - - - +
218L GLU* 2.9 55.7 + - + +
219L GLY* 5.2 0.4 - - - +
251L THR* 4.6 9.0 - - - +
252L ILE* 1.3 78.5 - - - +
254L TYR* 1.3 62.1 + - - +
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Residues in contact with TYR 254 (chain L).
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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157L LYS 2.9 3.5 - - - +
158L THR* 3.7 0.3 - - - -
159L CYS* 2.6 39.1 + - + +
161L ILE* 3.2 36.6 - - + -
175L ILE* 4.2 11.1 + - - +
176L ARG 4.9 0.2 - - - -
177L ALA* 3.4 33.0 + - + +
215L ILE* 3.9 14.8 - - + -
216L ARG 3.4 14.6 - - - -
217L VAL* 3.9 15.0 - - + -
236L VAL* 4.4 1.4 + - + -
238L VAL* 5.6 0.7 - - - +
252L ILE* 3.5 38.9 - - + +
253L LEU* 1.3 76.5 - - - +
255L ASN* 1.3 67.4 + - - +
256L PHE* 4.2 22.2 - + + -
273L ILE* 6.3 1.1 - - + -
275L ILE* 4.4 9.9 - - + +
290L PHE* 6.2 0.4 - + - -
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Residues in contact with ASN 255 (chain L).
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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156L ALA* 4.2 5.0 - - - -
157L LYS* 3.4 21.7 + - - +
207L GLN* 5.5 1.7 - - - +
214L LEU 3.6 1.0 - - - +
215L ILE* 3.5 4.7 - - - +
216L ARG* 3.0 42.2 + - + +
218L GLU* 3.2 48.9 + - - +
254L TYR* 1.3 84.8 + - - +
256L PHE* 1.3 64.7 + - - +
257L MET* 3.6 26.5 - - + +
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Residues in contact with PHE 256 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151L LEU* 4.0 19.3 - - + -
153L CYS* 4.1 20.2 - - + -
154L GLN 4.8 3.0 + - - +
155L ILE* 3.4 5.5 - - - -
156L ALA 2.8 27.5 + - - +
157L LYS 4.8 1.2 + - - +
159L CYS* 4.1 14.8 - - + -
161L ILE* 6.1 0.7 - - + -
214L LEU* 3.5 16.8 - - + +
215L ILE* 4.0 29.4 - - + -
254L TYR* 4.2 20.9 - + + -
255L ASN* 1.3 71.4 - - - +
257L MET* 1.3 56.6 + - - +
258L CYS 3.2 10.4 + - - +
271L ILE* 5.5 0.4 - - + -
273L ILE* 3.6 40.4 - - + -
290L PHE* 5.3 2.5 - + - -
294L ILE* 3.3 31.9 - - + -
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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