Contacts of the strand formed by residues 323 - 327 (chain A) in PDB entry 3VI4
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 ARG 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A GLU* 2.9 28.5 + - - -
306A ALA 2.9 32.2 + - - +
309A LEU* 3.5 31.0 - - + +
311A ASP* 4.3 12.5 + - - +
322A GLY* 1.3 75.0 - - - +
324A VAL* 1.3 67.6 + - - +
325A TYR* 3.3 37.3 - - + +
341A THR* 4.1 15.3 + - - +
342A LEU 3.0 15.0 - - - +
343A THR* 3.0 31.5 + - - +
351A PHE* 4.1 1.1 - - - -
352A GLY* 4.3 0.8 - - - +
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Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LEU* 5.0 5.4 - - + -
304A VAL 3.2 14.4 - - - +
305A GLY* 4.1 0.7 - - - -
323A ARG* 1.3 78.6 - - - +
325A TYR* 1.3 69.9 + - - +
326A VAL* 4.2 6.7 + - + +
340A LEU 4.2 0.2 - - - +
341A THR* 3.3 3.6 - - - -
342A LEU* 2.7 45.2 + - + +
351A PHE* 3.7 23.1 - - + -
352A GLY* 3.7 21.8 - - - -
355A LEU* 3.8 23.1 - - + -
369A VAL* 6.5 0.2 - - + -
371A ILE* 4.0 18.8 - - + -
394A LEU* 6.0 0.7 - - + -
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Residues in contact with TYR 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLU* 2.8 47.5 + - + +
283A SER* 4.9 0.3 + - - -
285A PHE* 3.4 36.5 - + + -
303A LEU* 3.4 3.6 - - - -
304A VAL* 2.9 45.3 + - + +
306A ALA* 3.8 8.0 - - + +
309A LEU* 3.3 15.8 - - - +
323A ARG* 3.3 28.7 - - + -
324A VAL* 1.3 75.6 - - - +
326A VAL* 1.3 62.6 + - - +
327A TYR* 3.5 25.3 - - + -
338A PRO* 4.2 10.5 - - + -
340A LEU 3.6 5.4 - - - +
341A THR* 3.6 21.1 - - + -
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Residues in contact with VAL 326 (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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294A VAL* 4.6 18.8 - - + -
301A ASP* 5.0 1.1 - - + -
302A LEU 3.3 3.8 - - - +
303A LEU* 3.5 27.6 - - + -
324A VAL* 5.0 7.4 - - + +
325A TYR* 1.3 74.4 - - - +
327A TYR* 1.3 70.4 + - - +
328A LEU* 4.6 10.1 - - + +
338A PRO* 3.4 2.8 - - - +
339A THR* 2.9 27.0 + - - -
340A LEU* 3.0 33.9 + - + +
342A LEU* 5.1 1.1 - - + -
394A LEU* 3.7 25.8 - - + +
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Residues in contact with TYR 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A PHE* 3.3 31.3 - + + +
277A SER 4.1 7.6 + - - -
285A PHE* 3.4 21.1 - - - -
301A ASP* 3.6 2.4 - - - +
302A LEU* 2.7 56.6 + - + +
304A VAL* 4.4 11.4 - - + -
325A TYR* 3.5 32.0 - - + +
326A VAL* 1.3 74.8 - - - +
328A LEU* 1.3 64.4 + - - +
329A GLN 3.5 1.9 + - - -
334A ILE* 4.1 13.5 - - + +
335A GLU* 3.3 14.4 - - - +
336A PRO 3.2 21.3 + - - -
337A THR 5.4 0.2 - - - -
338A PRO* 3.6 27.6 - - + +
339A THR* 4.5 2.2 - - - +
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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
------------------------------------------------------------
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