Contacts of the strand formed by residues 355 - 360 (chain A) in PDB entry 3DC1
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 PHE 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A GLY 5.7 0.9 - - - -
201A ASN 5.1 0.4 - - - +
202A ASN* 3.3 34.5 - - + -
203A PRO 3.8 18.4 - - - +
205A GLY* 4.1 10.2 - - - +
233A TYR* 3.2 27.8 - + - -
350A PRO* 3.0 25.6 - - - +
352A ALA 4.8 0.6 + - - -
353A GLY* 3.7 1.4 - - - -
354A MET* 1.3 91.3 - - + +
356A LEU* 1.3 59.2 + - - +
399A ARG* 3.2 49.1 - - + -
400A ALA 3.5 8.3 - - - +
401A SER* 3.7 13.0 - - - -
402A PHE* 3.2 8.4 - - - -
427A GOL 5.2 0.4 - - - -
38B GLY 3.7 11.7 - - - -
39B GLY* 3.8 18.8 - - - -
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Residues in contact with LEU 356 (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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203A PRO 4.4 1.6 - - - -
333A ILE* 4.1 31.6 - - + +
334A LEU* 3.9 5.6 - - + -
337A ALA* 4.8 7.4 - - + -
347A TRP* 3.8 19.3 - - + -
348A HIS 3.4 25.6 - - - +
350A PRO* 3.6 19.1 - - + -
355A PHE* 1.3 74.3 - - - +
357A TRP* 1.3 63.0 + - - +
358A ILE* 3.5 29.8 + - + -
398A LEU 3.5 3.1 - - - +
399A ARG* 3.6 2.8 - - - +
400A ALA* 2.9 39.6 + - + +
402A PHE* 3.9 8.7 - - + -
414A PHE* 4.6 2.5 - - + -
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Residues in contact with TRP 357 (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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140A PRO* 3.6 16.1 - - + +
203A PRO* 3.4 46.4 - - + +
204A THR* 3.6 35.1 + - + +
206A ASN* 5.4 1.6 - - - -
346A GLU 4.2 0.2 - - - +
347A TRP* 3.4 20.6 - - - +
348A HIS* 4.4 7.3 + + - +
356A LEU* 1.3 75.4 - - - +
358A ILE* 1.3 60.5 + - - +
359A LYS 4.1 0.2 + - - -
384A GLY* 3.6 30.5 - - - -
387A PHE* 4.3 1.3 - + - -
388A TYR* 3.5 20.6 - + - -
397A TYR* 3.1 55.1 - + + -
398A LEU 3.4 21.1 - - - -
399A ARG* 4.0 9.2 - - + -
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Residues in contact with ILE 358 (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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337A ALA* 5.3 0.7 - - + -
341A LEU* 3.9 21.5 - - + -
345A ALA* 3.9 14.8 - - + -
346A GLU 3.8 4.3 - - - +
347A TRP* 4.1 8.5 - - + -
356A LEU* 3.5 35.7 - - + +
357A TRP* 1.3 78.7 - - - +
359A LYS* 1.3 63.7 + - - +
360A VAL* 3.8 9.4 + - + +
381A MET* 4.0 14.4 - - + -
396A PRO 3.9 0.2 - - - +
397A TYR* 3.4 4.1 - - - -
398A LEU* 2.9 43.8 + - + +
400A ALA* 4.3 4.3 - - + -
414A PHE* 3.7 29.4 - - + -
417A LEU* 5.5 1.1 - - + -
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Residues in contact with LYS 359 (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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345A ALA* 3.3 2.6 - - - -
346A GLU* 2.7 63.9 + - + +
357A TRP 4.1 0.4 + - - -
358A ILE* 1.3 70.3 - - - +
360A VAL* 1.3 68.4 + - - +
361A LYS* 3.6 3.2 + - + +
396A PRO* 3.9 21.9 - - + +
397A TYR* 3.3 52.6 + - + -
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Residues in contact with VAL 360 (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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344A LEU 3.8 8.5 - - - +
345A ALA* 4.1 2.9 - - + -
358A ILE* 4.2 12.1 - - + +
359A LYS* 1.3 76.5 - - - +
361A LYS* 1.3 62.3 + - - +
362A GLY 3.7 1.2 + - - -
363A ILE* 3.8 39.2 - - + +
366A VAL* 4.6 7.2 - - + -
369A LEU* 5.2 0.2 - - + -
396A PRO* 3.1 32.8 + - + +
398A LEU* 4.1 27.1 - - + -
417A LEU* 5.9 0.2 - - + -
421A ILE* 4.6 20.2 - - + -
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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
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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