Contacts of the helix formed by residues 341 - 352 (chain A) in PDB entry 5ID6
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 GLY 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A LYS 3.8 0.4 + - - -
340A ASN* 1.3 82.5 + - - +
342A PRO* 1.3 77.1 - - - +
343A ALA* 3.3 3.1 - - - -
344A ILE* 2.9 18.2 + - - +
345A SER* 3.9 2.4 + - - -
389A PHE* 6.1 0.6 - - - -
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Residues in contact with PRO 342 (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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341A GLY* 1.3 81.2 - - - +
343A ALA* 1.3 59.8 + - - +
344A ILE 2.8 7.6 + - - -
345A SER* 2.9 21.5 + - - +
346A THR* 3.1 14.4 + - - +
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Residues in contact with ALA 343 (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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338A VAL* 4.6 0.2 - - + -
339A LYS* 4.0 14.4 - - + +
341A GLY 3.2 0.8 + - - -
342A PRO* 1.3 79.2 - - - +
344A ILE* 1.3 58.1 + - - +
346A THR* 3.9 8.1 - - - -
347A ILE* 3.0 38.8 + - + +
472A ALA* 3.5 33.2 - - + -
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Residues in contact with ILE 344 (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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338A VAL* 3.8 19.1 - - + +
339A LYS 3.6 20.0 - - - +
340A ASN* 3.2 25.8 - - - +
341A GLY 2.9 13.2 + - - +
342A PRO 2.8 4.6 + - - -
343A ALA* 1.3 71.6 - - - +
345A SER* 1.3 65.5 + - - +
347A ILE* 5.0 0.9 - - + -
348A SER* 3.0 26.0 + - - -
358A ILE* 3.5 39.5 - - + +
359A ARG* 5.3 1.1 - - + +
389A PHE* 4.5 10.8 - - + -
395A PHE* 3.6 23.8 - - + -
400A LEU* 5.3 3.1 - - + -
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Residues in contact with SER 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A GLY 3.9 1.4 + - - -
342A PRO* 2.9 14.7 + - - +
344A ILE* 1.3 78.5 - - - +
346A THR* 1.3 63.2 + - - +
348A SER* 3.2 4.9 + - - -
349A LYS* 2.9 22.6 + - - +
355A TRP* 3.9 40.0 + - - +
356A ASN* 5.7 0.3 + - - -
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Residues in contact with THR 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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342A PRO* 3.1 13.5 + - - +
343A ALA* 4.2 6.5 - - - -
345A SER* 1.3 79.2 - - - +
347A ILE* 1.3 65.5 + - + +
349A LYS* 3.0 10.7 + - - +
350A ASP* 3.0 39.4 + - - +
355A TRP* 5.8 1.8 - - - +
469A TYR* 3.8 19.5 - - + -
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Residues in contact with ILE 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A VAL* 3.7 26.9 - - + -
343A ALA* 3.0 23.2 + - + +
344A ILE* 4.4 2.2 - - + +
346A THR* 1.3 78.4 - - + +
348A SER* 1.3 56.4 + - - +
350A ASP* 4.2 4.7 - - - -
351A ILE* 2.8 56.0 + - + +
358A ILE* 4.9 3.4 - - + -
400A LEU* 5.3 7.4 - - + -
414A LEU* 3.8 15.7 - - + -
469A TYR* 4.0 20.9 - - + +
472A ALA* 4.0 15.7 - - + -
473A PHE* 4.6 15.9 - - + -
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Residues in contact with SER 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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344A ILE 3.0 20.4 + - - -
345A SER 3.2 5.6 - - - -
346A THR 3.1 0.2 - - - -
347A ILE* 1.3 77.6 - - - +
349A LYS* 1.3 56.6 + - - +
352A PHE* 3.0 33.0 + - - -
353A GLY 3.3 2.8 + - - -
354A GLU 2.5 23.9 + - - +
355A TRP 2.9 15.3 + - - -
357A LEU* 3.6 16.8 + - - +
358A ILE* 3.7 23.0 + - - +
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Residues in contact with LYS 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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345A SER 2.9 11.6 + - - +
346A THR* 3.0 12.1 + - - +
348A SER* 1.3 76.5 - - - +
350A ASP* 1.3 70.2 + - - +
353A GLY* 3.2 41.4 + - - +
354A GLU* 3.2 12.0 + - - +
355A TRP* 3.9 29.4 - - + +
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Residues in contact with ASP 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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346A THR* 3.0 24.6 + - - +
347A ILE 3.9 2.7 - - - +
349A LYS* 1.3 87.1 - - - +
351A ILE* 1.3 57.8 + - + +
413A LYS* 2.6 33.6 + - - +
417A ILE* 3.5 24.4 - - + +
421A LYS* 5.3 0.9 + - - -
469A TYR* 3.0 35.2 + - - +
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Residues in contact with ILE 351 (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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347A ILE* 2.8 40.7 + - + +
350A ASP* 1.3 77.4 - - - +
352A PHE* 1.3 95.3 + - + +
358A ILE* 5.6 0.7 - - + -
400A LEU* 5.1 9.0 - - + -
408A LEU* 4.3 14.9 - - + +
410A VAL* 3.7 36.1 - - + +
413A LYS* 4.1 24.7 + - + +
414A LEU* 3.7 26.9 - - + -
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Residues in contact with PHE 352 (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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348A SER* 3.0 24.2 + - - +
351A ILE* 1.3 99.2 - - + +
353A GLY* 1.3 59.4 + - - +
354A GLU 3.7 0.9 - - - +
357A LEU* 3.5 37.5 - - + -
358A ILE* 3.5 32.1 - - + -
361A LYS* 6.3 0.2 - - + -
400A LEU* 4.0 18.8 - - + -
403A TYR* 4.5 11.0 - - + -
404A ALA* 4.1 23.3 - - + -
405A ASP* 5.4 5.2 - - - +
408A LEU* 4.5 20.7 - - + +
410A VAL* 4.2 7.0 - - + -
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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