Contacts of the helix formed by residues 345 - 353 (chain A) in PDB entry 3H44
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 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A HIS* 3.3 37.3 + - - -
341A GLU* 3.6 5.5 - - - -
342A GLY 2.9 23.3 + - - -
343A PRO 3.1 2.0 + - - -
344A GLY* 1.3 79.9 - - - +
346A LEU* 1.3 65.9 + - - +
347A LEU 3.5 2.6 + - - -
348A SER* 2.9 30.4 + - - -
349A GLU 3.5 2.9 + - - -
397A TYR* 4.4 7.9 - - - -
522A PHE* 4.0 2.9 - - - -
523A LYS 4.8 0.9 - - - -
525A PRO* 6.6 0.2 - - - -
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Residues in contact with LEU 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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337A LEU 5.6 0.2 + - - -
338A ILE* 4.2 32.5 + - + +
340A HIS 4.7 0.2 + - - -
345A SER* 1.3 73.0 - - - +
347A LEU* 1.3 63.2 + - - +
349A GLU 3.3 2.1 + - - -
350A LEU* 3.2 39.8 + - + +
359A LEU* 3.9 15.3 - - + -
375A ILE* 4.5 1.3 - - + -
393A HIS* 4.1 13.7 - - + +
394A MET* 3.8 31.6 - - + +
397A TYR* 3.7 29.8 - - + -
398A ILE* 6.5 0.2 - - + -
522A PHE* 3.6 28.6 - - + -
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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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340A HIS 4.1 8.4 + - - +
341A GLU* 3.5 40.8 - - + +
345A SER* 3.3 8.3 + - - +
346A LEU* 1.3 77.5 - - - +
348A SER* 1.3 63.5 + - - +
350A LEU* 4.4 3.4 - - - -
351A LYS* 2.8 42.8 + - + +
356A VAL* 3.7 25.4 - - + -
357A ASN 3.9 19.1 - - - +
358A THR* 4.1 4.5 - - - +
359A LEU* 3.6 33.7 - - + +
605A ASN* 4.8 3.8 - - - +
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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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341A GLU 4.2 1.5 + - - -
342A GLY 3.3 13.7 + - - -
343A PRO* 4.4 0.2 - - - +
344A GLY 4.5 5.6 - - - -
345A SER* 2.9 25.3 + - - -
347A LEU* 1.3 75.9 - - - +
349A GLU* 1.3 56.9 + - - -
351A LYS* 3.6 5.0 - - - +
352A SER* 2.9 33.6 + - - -
606A GLU* 2.5 33.6 + - - +
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Residues in contact with GLU 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 3.5 1.8 + - - -
346A LEU 3.3 3.0 + - - -
348A SER* 1.3 79.4 - - - +
350A LEU* 1.3 63.1 + - + +
351A LYS 3.2 0.2 + - - -
352A SER* 3.2 11.4 + - - -
353A LYS* 2.9 54.2 + - + +
393A HIS* 4.4 22.6 - - + +
519A ASN* 4.9 1.5 + - - +
521A LYS* 3.5 53.8 + - + +
522A PHE* 3.6 26.5 - - + -
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Residues in contact with LEU 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 LEU* 3.2 40.5 + - + +
347A LEU 3.8 4.7 - - - +
349A GLU* 1.3 76.0 - - + +
351A LYS* 1.3 58.4 + - - +
353A LYS* 3.8 2.9 + - - -
354A GLY 3.5 1.0 + - - -
355A TRP* 2.9 38.4 + - + +
356A VAL* 3.2 30.8 + - + -
359A LEU* 4.2 15.3 - - + -
377A VAL* 4.5 3.1 - - + -
390A ILE* 3.8 49.6 - - + +
393A HIS* 4.3 12.3 - - + -
394A MET* 5.0 3.1 - - + -
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Residues in contact with LYS 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 LEU* 2.8 28.9 + - + +
348A SER* 3.6 4.9 - - - +
350A LEU* 1.3 76.3 - - - +
352A SER* 1.3 54.7 + - - +
354A GLY* 2.5 28.4 + - - -
356A VAL 3.4 16.2 - - - +
357A ASN 4.0 22.0 + - - +
602A ASP* 3.2 42.0 + - - +
605A ASN* 3.9 22.6 + - - +
606A GLU* 5.4 4.1 - - - +
658A ARG* 3.9 25.3 + - - +
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Residues in contact with SER 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* 2.9 18.8 + - - -
349A GLU* 3.6 17.8 + - - -
351A LYS* 1.3 71.1 - - - +
353A LYS* 1.3 60.3 + - - +
354A GLY* 3.0 5.8 + - - -
521A LYS* 6.3 0.2 - - - -
657A LYS* 5.4 2.8 + - - -
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Residues in contact with LYS 353 (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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349A GLU* 2.9 39.5 + - + +
350A LEU 4.2 1.1 - - - +
351A LYS 3.2 0.2 - - - -
352A SER* 1.3 76.6 - - - +
354A GLY* 1.3 65.0 + - - +
355A TRP* 3.2 55.5 + - + -
382A GLU* 4.8 3.1 - - - +
393A HIS* 4.0 21.3 + - + +
657A LYS* 4.6 6.8 + - - -
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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