Contacts of the strand formed by residues 250 - 256 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161K ILE 3.4 5.0 - - - +
162K GLN* 3.6 0.2 - - - -
163K ILE* 2.9 45.3 + - + +
175K ILE* 5.4 1.3 - - + -
240K TYR* 3.6 24.3 + - + -
241K GLU* 3.0 40.0 + - + +
242K PRO 3.9 7.9 - - - +
243K PRO* 4.0 7.2 - - - +
248K GLU 4.3 0.2 + - - -
249K PHE* 1.3 70.6 - - - +
251K THR* 1.3 66.0 + - - +
252K ILE* 4.4 12.3 - - + +
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Residues in contact with THR 251 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160K PRO* 4.3 18.6 - - + -
161K ILE 3.6 9.4 - - - +
162K GLN* 4.0 19.2 + - - +
244K GLN* 4.8 13.5 + - - +
247K THR* 6.0 0.7 - - - +
249K PHE 3.6 7.3 + - - -
250K THR* 1.3 76.2 - - - +
252K ILE* 1.3 65.8 + - - +
253K LEU* 4.0 22.0 - - + +
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Residues in contact with ILE 252 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159K CYS 3.8 0.3 - - - +
160K PRO* 3.5 0.3 - - - +
161K ILE 2.9 33.1 + - - +
163K ILE* 4.3 14.1 - - + -
175K ILE* 3.4 37.7 - - + -
217K VAL* 4.3 11.0 - - + -
238K VAL* 4.1 17.9 - - + -
250K THR* 4.4 9.4 - - + +
251K THR* 1.3 76.8 - - - +
253K LEU* 1.3 69.8 + - - +
254K TYR* 3.5 47.5 + - + +
275K ILE* 6.1 0.2 - - + -
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Residues in contact with LEU 253 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158K THR* 3.2 25.4 - - + -
159K CYS 3.8 0.2 - - - -
160K PRO* 3.5 22.2 - - + -
217K VAL* 3.3 13.9 - - - +
218K GLU* 2.7 51.9 + - + +
219K GLY* 4.2 10.9 - - - +
251K THR* 4.0 19.3 - - + +
252K ILE* 1.3 79.0 - - - +
254K TYR* 1.3 58.2 + - - +
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Residues in contact with TYR 254 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158K THR* 3.6 0.7 - - - -
159K CYS* 2.6 47.7 + - + +
161K ILE* 3.7 32.5 - - + -
163K ILE* 6.1 0.4 - - + -
175K ILE* 4.0 20.1 + - - +
176K ARG 4.9 0.2 - - - -
177K ALA* 3.4 31.7 - - + +
215K ILE* 4.9 8.3 - - + -
216K ARG 3.3 13.7 - - - -
217K VAL* 4.3 7.4 - - + -
236K VAL* 4.4 12.1 + - + -
238K VAL* 5.4 3.5 - - + +
252K ILE* 3.5 39.9 - - + +
253K LEU* 1.3 76.5 - - - +
255K ASN* 1.3 67.0 + - - +
256K PHE* 4.1 19.7 - + + -
273K ILE* 6.4 0.4 - - + -
275K ILE* 4.3 11.3 - - + +
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Residues in contact with ASN 255 (chain K).
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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156K ALA 3.0 23.1 + - - +
157K LYS 3.7 2.2 - - - -
158K THR* 3.5 27.1 + - - +
214K LEU 3.4 0.7 - - - +
215K ILE* 3.1 6.1 - - - -
216K ARG* 2.7 40.6 + - + +
217K VAL 4.4 0.5 - - - -
218K GLU* 3.1 37.9 + - - +
254K TYR* 1.3 74.4 - - - +
256K PHE* 1.3 65.9 + - - +
257K MET* 3.9 17.9 - - - -
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Residues in contact with PHE 256 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151K LEU* 4.3 11.0 - - + -
153K CYS* 2.9 34.3 - - - -
154K GLN 4.9 1.1 + - - +
155K ILE 2.3 30.9 + - - +
156K ALA 5.0 0.2 + - - -
157K LYS 4.9 3.0 + - - -
159K CYS* 3.6 24.2 - - + -
161K ILE* 5.4 2.9 - - + -
214K LEU* 3.3 8.3 - - + +
215K ILE* 3.2 41.1 - - + -
254K TYR* 4.1 19.3 - + + -
255K ASN* 1.3 74.4 - - - +
257K MET* 1.3 60.4 + - - +
258K CYS 3.5 2.5 + - - -
273K ILE* 4.1 27.4 - - + -
290K PHE* 5.4 0.2 - + - -
294K ILE* 3.3 32.2 - - + +
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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