Contacts of the strand formed by residues 326 - 330 (chain B) in PDB entry 3ISL
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 VAL 326 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B PRO* 4.0 12.3 - - + -
149B THR* 3.7 43.7 - - + +
152B GLY* 4.1 15.2 - - - +
322B LYS* 2.9 19.8 + - - +
323B MET* 3.0 24.4 + - + +
324B PRO 3.5 0.4 - - - -
325B VAL* 1.3 84.7 - - - +
327B THR* 1.3 64.8 + - - +
328B CYS* 4.3 10.5 + - - -
365B ARG* 4.3 15.3 - - + -
366B ILE 3.7 4.7 - - - +
368B THR* 5.5 0.2 - - - -
369B MET* 3.8 11.7 - - + -
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Residues in contact with THR 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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301B GLU* 4.5 7.3 + - - +
304B LEU* 3.7 33.6 - - + +
305B ALA* 5.5 5.5 - - + +
308B ILE* 5.0 3.1 - - + -
315B LEU* 3.6 34.5 - - + -
322B LYS* 3.0 20.9 + - - +
324B PRO 4.9 1.0 + - - -
326B VAL* 1.3 71.6 - - - +
328B CYS* 1.3 63.9 + - - +
329B VAL* 3.7 9.8 + - + +
365B ARG* 3.4 2.3 - - - -
366B ILE* 2.8 41.4 + - - +
368B THR* 5.1 2.8 + - - -
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Residues in contact with CYS 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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151B THR 3.9 9.0 - - - -
152B GLY* 3.8 30.5 - - - -
153B ARG* 4.3 3.1 - - - +
315B LEU* 3.3 9.6 - - - +
316B PHE* 2.8 53.5 + - + +
322B LYS* 5.2 1.8 - - - +
326B VAL* 4.3 3.1 - - - -
327B THR* 1.3 75.2 - - - +
329B VAL* 1.3 59.9 + - - +
363B ILE* 4.0 21.3 - - + -
364B TRP 3.5 4.7 - - - -
365B ARG* 4.0 10.3 - - - -
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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
----------------------------------------------------------
308B ILE* 4.0 15.9 - - + -
313B LEU* 3.8 36.3 - - + -
314B ARG 3.8 3.6 - - - +
315B LEU* 4.1 13.0 - - + -
327B THR* 4.2 12.3 - - + +
328B CYS* 1.3 74.3 - - - +
330B GLU* 1.3 70.8 + - - +
363B ILE* 3.1 3.9 - - - -
364B TRP* 2.8 52.2 + - + +
366B ILE* 4.1 25.6 - - + -
385B LEU* 5.1 1.3 - - + -
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Residues in contact with GLU 330 (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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313B LEU* 4.4 5.2 - - - +
314B ARG* 3.0 45.6 + - + +
315B LEU 3.9 10.9 - - - +
316B PHE* 3.9 28.2 - - + +
317B GLY 5.2 0.2 + - - -
328B CYS 3.8 0.8 + - - -
329B VAL* 1.3 76.3 - - - +
331B ILE* 1.3 66.7 + - - +
332B PRO* 3.4 10.6 - - + +
362B LYS 3.5 9.4 - - - +
363B ILE* 4.3 1.1 - - + -
364B TRP* 3.7 5.9 - - - -
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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