Contacts of the strand formed by residues 345 - 350 (chain A) in PDB entry 3IND
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 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A VAL* 4.6 2.5 - - + -
269A GLU 3.4 3.4 - - - +
270A ILE* 3.9 28.5 - - + -
296A LEU* 4.9 9.4 - - + -
306A ALA* 6.1 1.1 - - + -
310A ILE* 4.1 11.0 - - + -
343A PRO 4.6 0.7 - - - +
344A VAL* 1.3 79.2 - - - +
346A SER* 1.3 70.0 + - - +
347A LEU* 4.1 16.7 + - + +
360A ILE 3.5 1.6 - - - +
361A THR* 3.3 1.3 - - - -
362A ILE* 2.8 48.9 + - + +
367A TYR* 3.6 24.7 - - + -
386A ILE* 3.5 32.3 - - + -
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Residues in contact with SER 346 (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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268A VAL* 3.4 5.9 - - - +
269A GLU* 2.8 47.8 + - - +
272A GLY 6.0 0.2 + - - -
344A VAL* 4.7 4.0 - - - +
345A ILE* 1.3 72.2 - - - +
347A LEU* 1.3 63.3 + - - +
348A TYR* 3.8 20.4 + - - -
359A ARG* 4.2 10.5 + - - -
360A ILE 3.2 5.6 - - - -
361A THR* 2.7 31.2 + - - +
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Residues in contact with LEU 347 (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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265A ILE* 4.2 22.7 - - + -
267A ARG 3.9 0.7 - - - -
268A VAL* 3.6 35.7 - - + -
296A LEU* 4.4 13.0 - - + -
298A LEU* 5.3 8.5 - - + -
345A ILE* 4.1 12.3 + - + +
346A SER* 1.3 72.6 - - - +
348A TYR* 1.3 62.6 + - - +
349A LEU* 3.7 6.6 + - + +
359A ARG* 3.2 0.9 - - - -
360A ILE* 2.9 47.4 + - + +
362A ILE* 6.4 0.2 - - + -
393A THR* 5.3 0.4 - - + -
395A MET* 4.2 18.2 - - + -
399A ILE* 3.3 31.2 - - + -
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Residues in contact with TYR 348 (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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265A ILE* 3.3 8.1 - - - +
266A VAL* 2.8 33.6 + - + -
267A ARG* 2.7 51.7 + - + +
269A GLU* 2.9 42.7 + - + -
346A SER* 3.9 11.4 - - - -
347A LEU* 1.3 72.4 - - - +
349A LEU* 1.3 59.7 + - - +
357A SER* 3.9 15.5 - - - +
358A PHE 3.2 7.9 - - - +
359A ARG* 2.9 48.3 + - + -
436A PHE* 3.7 28.4 - + + -
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Residues in contact with LEU 349 (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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253A THR* 3.6 17.5 - - + +
263A VAL* 4.2 10.8 - - + -
264A ILE 3.4 6.5 - - - +
265A ILE* 3.6 28.9 - - + -
266A VAL* 4.3 0.4 - - - -
347A LEU* 4.3 7.9 - - + +
348A TYR* 1.3 75.6 - - - +
350A MET* 1.3 66.1 + - - +
357A SER* 3.2 5.8 - - - -
358A PHE* 2.7 53.1 + - + -
360A ILE* 4.3 10.3 - - + -
395A MET* 4.2 22.9 - - + -
416A PHE* 3.7 30.7 - - + -
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Residues in contact with MET 350 (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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252A TYR 3.9 0.2 - - - +
253A THR* 2.6 34.4 + - - +
254A PRO* 3.3 20.2 - - + +
264A ILE* 2.9 51.8 + - + +
266A VAL* 3.8 18.5 - - + +
349A LEU* 1.3 70.9 - - - +
351A GLY* 1.3 71.2 + - - +
354A THR* 4.5 16.6 - - - +
356A GLN 4.1 3.4 - - - +
357A SER* 4.5 0.2 - - - -
358A PHE* 4.1 0.3 - - - -
443A ASP 5.6 4.0 - - - +
444A CYS* 5.0 8.1 - - + +
445A GLY 5.6 0.9 - - - +
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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