Contacts of the strand formed by residues 331 - 336 (chain B) in PDB entry 3I8E
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 SER 331 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B THR 5.5 0.8 + - - -
15B VAL* 3.3 19.6 - - - +
323B PHE* 4.2 14.6 - - - -
324B VAL 3.4 9.9 - - - -
325B GLY* 3.2 7.8 - - - -
326B SER* 2.8 24.9 + - - +
329B GLY 3.5 4.2 + - - -
330B ASP* 1.3 80.3 - - - +
332B GLN* 1.3 57.3 + - - +
352B THR 3.7 0.2 - - - -
353B PHE* 2.8 43.2 + - - -
355B ASN* 4.6 3.5 - - - +
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Residues in contact with GLN 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLU 5.0 0.2 + - - -
308B THR* 3.4 20.2 - - - +
309B SER* 2.7 44.2 + - - +
323B PHE* 3.4 8.0 - - - -
324B VAL* 3.1 40.8 + - + +
330B ASP 4.5 0.4 - - - +
331B SER* 1.3 81.0 - - - +
333B LEU* 1.3 60.5 - - - +
334B VAL* 4.0 10.4 - - + +
349B ALA* 4.2 15.6 - - - +
351B GLU 3.1 15.5 - - - +
352B THR* 4.0 13.0 + - + +
353B PHE* 3.7 9.8 - - - -
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLY* 4.3 21.3 - - - -
49B LEU* 4.3 20.9 - - + +
317B LEU* 4.4 1.8 - - + -
321B VAL* 4.1 23.6 - - + -
322B VAL 3.6 1.3 - - - +
323B PHE* 3.7 33.9 - - + -
332B GLN* 1.3 73.5 - - - +
334B VAL* 1.3 65.9 + - - +
349B ALA* 4.0 0.5 - - - -
350B MET* 2.9 40.7 + - + -
351B GLU* 2.8 25.6 + - + +
353B PHE* 3.8 20.9 - - + -
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Residues in contact with VAL 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 4.7 2.9 - - + -
308B THR* 4.7 0.7 - - + -
320B GLY 3.1 2.4 - - - +
321B VAL* 3.3 2.8 - - - -
322B VAL* 2.6 59.1 + - + +
324B VAL* 4.0 14.4 - - + -
332B GLN* 4.0 24.5 - - - +
333B LEU* 1.3 80.6 - - - +
335B LYS* 1.3 66.7 + - - +
336B LEU* 4.6 4.0 - - + -
347B VAL* 3.7 35.0 - - + -
348B VAL 3.6 9.2 - - - +
349B ALA* 4.1 6.7 - - + -
350B MET* 3.9 4.5 - - - -
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Residues in contact with LYS 335 (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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319B ASN 3.4 18.8 + - - -
320B GLY* 3.2 17.3 - - - +
321B VAL* 4.9 4.2 - - + +
334B VAL* 1.3 74.1 - - - +
336B LEU* 1.3 68.6 + - - +
337B ASN* 3.0 31.0 + - - +
346B TYR 3.2 4.0 - - - +
347B VAL* 3.5 2.3 - - - -
348B VAL* 2.8 51.5 + - + +
350B MET* 3.7 24.4 - - + +
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Residues in contact with LEU 336 (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 VAL* 5.8 2.0 - - + -
272B LEU* 4.2 4.5 - - + -
280B LEU* 4.3 7.0 - - + -
282B MET* 4.0 26.7 - - + -
305B LEU* 3.8 27.1 - - + -
316B TYR* 5.0 8.7 - - + -
320B GLY* 2.6 28.0 + - - +
322B VAL* 3.9 26.2 - - + -
334B VAL* 4.6 2.2 - - + -
335B LYS* 1.3 74.7 - - - +
337B ASN* 1.3 67.3 + - - +
346B TYR 3.2 5.6 - - - +
347B VAL* 3.8 24.2 - - + -
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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
------------------------------------------------------------
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