Contacts of the strand formed by residues 323 - 329 (chain B) in PDB entry 3V4P
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 ILE 323 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B ALA* 4.0 3.6 - - + +
250B ALA* 4.0 28.0 - - + -
253B GLN* 5.2 0.9 - - - +
258B TRP* 3.7 37.0 - - + +
263B ARG* 3.8 19.3 - - + +
265B LEU* 3.7 34.1 - - + +
318B LEU* 3.3 29.4 + - + +
321B ALA* 3.1 19.5 - - + +
322B ASN* 1.3 81.0 - - - +
324B GLN* 1.3 64.0 + - - +
325B PRO* 3.6 11.0 - - - +
345B PRO 5.8 0.2 - - - +
441B LEU* 5.2 4.0 - - - +
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Residues in contact with GLN 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B SER* 3.3 20.2 + - - -
263B ARG 2.9 20.1 + - - +
264B LEU* 3.5 16.9 - - + +
265B LEU 2.9 25.8 + - - -
322B ASN 4.5 1.6 - - - +
323B ILE* 1.3 78.4 - - - +
325B PRO* 1.3 64.7 - - - +
326B ILE* 3.7 0.9 + - - -
346B LYS* 3.3 35.1 + - + +
367B TYR* 5.5 2.6 - - - -
370B LEU* 3.3 30.6 + - + +
371B SER* 5.1 1.8 - - - +
441B LEU* 5.4 2.7 - - + -
442B GLY* 3.1 33.1 - - - +
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Residues in contact with PRO 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ILE* 6.5 0.4 - - + -
265B LEU* 3.8 11.9 - - + +
267B PHE* 6.4 0.2 - - + -
318B LEU* 3.7 29.8 - - + -
323B ILE 3.6 7.4 - - - +
324B GLN* 1.3 81.6 - - - +
326B ILE* 1.3 61.6 + - - +
327B PHE* 3.6 29.1 - - + -
344B ILE* 3.8 20.4 - - + -
345B PRO 4.8 0.9 - - - +
346B LYS 3.6 13.0 - - - +
347B SER* 3.2 8.3 - - - -
348B ALA 3.0 24.3 + - - +
370B LEU* 5.1 0.2 - - - +
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Residues in contact with ILE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B LEU* 3.9 32.5 - - + -
265B LEU 2.9 13.9 + - - +
266B VAL* 3.6 15.4 - - + +
267B PHE* 2.9 28.4 + - - +
324B GLN 4.2 5.6 - - - +
325B PRO* 1.3 75.7 - - - +
327B PHE* 1.3 64.9 + - - +
328B ALA* 3.5 7.5 + - + +
348B ALA* 3.4 9.4 - - + +
350B GLY 5.8 2.0 - - - +
362B LEU* 5.3 4.5 - - + +
363B ILE* 4.4 23.3 - - + +
366B ALA* 3.7 30.1 - - + -
367B TYR 5.0 1.8 - - - +
370B LEU* 4.2 16.8 - - + -
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Residues in contact with PHE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B PHE* 6.0 0.7 - + - -
246B ILE* 4.5 14.1 - - + -
267B PHE* 3.6 28.7 - + + +
318B LEU* 5.5 2.0 - - + -
325B PRO* 3.6 31.6 - - + -
326B ILE* 1.3 72.7 - - - +
328B ALA* 1.3 60.5 + - - +
329B VAL* 3.5 3.0 + - - +
337B TYR* 3.6 31.6 - + + -
340B LEU* 4.0 25.8 - - + -
341B SER* 4.6 5.4 - - - -
344B ILE* 4.4 12.3 - - + -
347B SER* 4.4 9.6 - - - -
348B ALA 2.8 13.5 + - - -
349B VAL* 3.5 31.6 - - + +
350B GLY 3.1 28.2 + - - +
362B LEU* 5.6 0.2 - - - -
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Residues in contact with ALA 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B VAL* 4.8 10.5 - - + -
267B PHE 2.9 11.7 + - - +
268B THR* 3.0 37.1 + - - -
269B SER 3.0 3.5 + - - +
326B ILE* 3.5 6.2 + - + +
327B PHE* 1.3 69.5 - - - +
329B VAL* 1.3 61.6 + - - +
350B GLY 3.8 5.4 - - - -
352B LEU* 3.8 12.2 - - + +
359B VAL* 5.2 5.6 - - + -
362B LEU* 3.7 23.3 - - + -
363B ILE* 6.2 1.3 - - + -
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Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PHE 4.7 2.5 - - - +
269B SER* 3.1 18.4 - - - +
270B ASP* 5.5 0.2 - - - -
327B PHE 3.5 3.1 + - - +
328B ALA* 1.3 82.9 - - - +
330B THR* 1.3 68.2 + - - +
332B ALA 4.8 2.0 - - - +
333B ALA* 5.0 1.8 - - + -
334B LEU* 3.5 37.9 - - + +
337B TYR* 3.5 48.0 - - + -
350B GLY 3.4 3.8 + - - +
351B GLU* 3.4 3.6 - - - -
352B LEU* 2.6 33.4 + - - -
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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