Contacts of the strand formed by residues 361 - 367 (chain A) in PDB entry 2VDY
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 PHE 361 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PHE* 4.0 14.4 - + - -
243A PHE* 4.1 12.8 - + - -
244A ILE 3.3 13.5 - - - +
245A LEU* 4.4 3.6 - - + -
246A PRO* 4.2 0.9 - - - -
251A MET* 3.6 5.9 - - - +
279A ILE* 5.7 0.9 - - + -
280A PRO* 4.1 18.8 - - + -
282A VAL* 4.2 14.4 - - + -
331A LEU* 5.2 1.8 - - + -
357A PHE* 3.5 31.4 - + + -
359A GLN 3.2 15.3 - - - +
360A PRO* 1.3 73.7 - - - +
362A ILE* 1.3 74.9 + - - +
363A ILE* 3.5 25.8 - - + -
378A ARG* 3.6 3.6 - - - -
379A VAL* 2.9 59.9 + - + +
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Residues in contact with ILE 362 (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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29A TYR* 3.8 16.2 - - + +
242A PHE 3.6 0.9 - - - +
243A PHE* 3.5 4.9 - - - -
244A ILE* 2.8 54.1 + - + -
246A PRO* 4.5 4.0 - - + -
251A MET* 3.8 19.5 - - + -
254A VAL* 3.8 27.8 - - + -
255A ILE* 3.8 23.6 - - + +
258A LEU* 4.5 14.1 - - + -
361A PHE* 1.3 78.4 - - - +
363A ILE* 1.3 67.8 + - - +
364A MET* 4.1 16.6 - - + -
376A LEU* 5.9 0.4 - - + -
377A ALA 3.4 9.4 - - - +
378A ARG* 5.0 0.4 - - + -
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Residues in contact with ILE 363 (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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42A PHE* 5.7 0.9 - - + -
241A VAL* 3.7 24.5 - - + -
242A PHE 3.4 2.9 - - - +
243A PHE* 4.1 8.3 - - + -
329A LEU* 3.8 23.8 - - + -
331A LEU* 4.2 17.3 - - + -
361A PHE* 3.5 32.5 - - + -
362A ILE* 1.3 73.2 - - - +
364A MET* 1.3 67.5 + - - +
365A ILE* 4.0 17.3 - - + -
375A PHE 4.5 0.7 - - - +
376A LEU* 3.4 4.9 - - - +
377A ALA* 2.8 47.2 + - + +
379A VAL* 3.7 17.0 - - + -
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Residues in contact with MET 364 (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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26A PHE* 4.0 25.8 - - - -
241A VAL* 3.3 2.4 - - - -
242A PHE* 2.8 69.0 + - + +
244A ILE* 4.2 2.2 - - + -
258A LEU* 4.2 17.0 - - - -
263A ILE* 3.8 17.3 - - + -
266A TRP* 3.7 28.0 - - + -
362A ILE* 4.1 12.3 - - + -
363A ILE* 1.3 77.2 - - - +
365A ILE* 1.3 63.6 + - - +
366A PHE* 3.8 15.7 + - + -
375A PHE 3.6 4.3 - - - -
376A LEU* 3.7 12.3 - - + -
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Residues in contact with ILE 365 (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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42A PHE* 4.9 1.3 - - + -
181A PHE* 4.4 8.7 - - + -
235A TYR* 4.1 25.4 - - + +
239A GLY* 5.8 0.2 - - - -
240A THR 3.4 9.4 - - - +
241A VAL* 3.9 17.9 - - + -
329A LEU* 4.8 9.6 - - + -
331A LEU* 6.1 0.7 - - + -
336A THR* 4.4 15.3 - - + -
338A ALA* 5.0 1.3 - - + -
363A ILE* 4.0 13.0 - - + -
364A MET* 1.3 74.3 - - - +
366A PHE* 1.3 67.3 + - - +
373A SER* 3.8 2.1 + - - -
374A LEU* 2.8 41.3 + - + -
375A PHE* 2.8 46.1 + - + +
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Residues in contact with PHE 366 (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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22A VAL* 3.8 19.5 - - + -
26A PHE* 4.0 14.4 - + - -
239A GLY* 3.5 3.8 - - - -
240A THR* 2.8 43.5 + - + +
242A PHE* 4.1 20.4 - + - -
263A ILE* 4.3 8.7 - - + -
364A MET* 3.8 33.0 - - + -
365A ILE* 1.3 77.4 - - - +
367A ASP* 1.3 58.8 + - - +
368A HIS 4.0 0.2 - - - -
371A TRP 3.8 2.2 - - - -
372A SER 3.5 18.2 - - - -
373A SER* 3.6 26.5 - - - -
374A LEU* 4.2 8.6 - - - +
1384A HCY 3.7 42.4 - - + -
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Residues in contact with ASP 367 (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 PHE* 3.7 16.4 - - + -
103A MET* 6.2 1.3 - - - -
238A ASN* 3.4 21.5 - - - +
239A GLY* 4.7 0.9 - - - -
366A PHE* 1.3 77.0 - - - +
368A HIS* 1.3 58.9 + - - +
369A PHE* 3.1 16.5 + - - +
370A THR* 2.7 38.7 + - - +
371A TRP* 2.9 32.2 + - - -
372A SER 3.1 12.1 + - - +
374A LEU* 4.3 15.3 - - + -
1384A HCY 5.0 0.5 - - - +
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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